A list of papers citing NAMD is included below.

How to Cite NAMD

The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:

"NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

Any published work which utilizes NAMD shall include the following reference:

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid.
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475
abstract, DOI

Electronic documents shall include a direct link to the official NAMD page:

http://www.ks.uiuc.edu/Research/namd/

Proper citation is essential to continued NIH funding for NAMD development, as it is a primary way in which we demonstrate the value of our software to the scientific community. Thank you for your attention to these details.

Papers About NAMD

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid.
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475
DOI

B. Acun, D. J. Hardy, L. V. Kale, K. Li, J. C. Phillips, and J. E. Stone.
Scalable Molecular Dynamics with NAMD on the Summit System.
IBM Journal of Research and Development, 2018.
journal, DOI

James C. Phillips.
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore.
In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18). ACM, New York, NY, USA, Article 55, 6 pages. 2018.
DOI

Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd B Rocha, João V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, & Zaida Luthey-Schulten.
NAMD goes quantum: an integrative suite for hybrid simulations.
Nature Methods, volume 15, pages 351-354, 2018.
DOI

Bilge Acun, Ronak Buch, Laxmikant Kale, and James C. Phillips.
NAMD: Scalable Molecular Dynamics Based on the Charm++ Parallel Runtime System.
Exascale Scientific Applications: Scalability and Performance Portability, Tjerk P. Straatsma, Katerina B. Antypas, and Timothy J. Williams, editors, CRC Press, 2017.
abstract

Brian K. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C. Phillips, Klaus Schulten, and Benoît Roux.
Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
J. Chem. Theory Comput., 2017.
abstract

Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten.
QwikMD-integrative molecular dynamics toolkit for novices and experts.
Scientific Reports, 6:26536, 2016.
abstract

John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms.
International Workshop on OpenPOWER for HPC (IWOPH'16), 2016. In Press.
abstract

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten.
Multilevel Summation Method for Electrostatic Force Evaluation.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot.
Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V. Kale.
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014.
abstract, conference, journal, benchmark inputs: directory, 2.5K .tar.gz,

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Petascale Tcl with NAMD, VMD, and Swift/T.
In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014.
abstract, journal

Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux.
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Computer Physics Communications, 185:908-916, 2014.
abstract, journal

Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V. Kale, and James C. Phillips.
Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6.
In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012.
abstract, conference, journal

David E. Tanner, James C. Phillips, and Klaus Schulten.
GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations.
Journal of Chemical Theory and Computation, 8:2521-2530, 2012.
abstract, journal

David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten.
Parallel generalized Born implicit solvent calculations with NAMD.
Journal of Chemical Theory and Computation, 7:3635-3642, 2011.
abstract, journal

Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale, James C. Phillips, and Chris Harrison.
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime.
In Proceedings of the 2011 ACM/IEEE Conference on Supercomputing (SC11), 2011.
abstract, conference, journal

Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Jr., Klaus Schulten, and Benoit Roux.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD.
J. Phys. Chem. Lett., Vol. 2, pp. 87-92, 2011.
abstract, journal

Abhinav Bhatele, Laxmikant V. Kale and Sameer Kumar.
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications.
In Proceedings of 23rd ACM International Conference on Supercomputing (ICS), 2009.
abstract

James C. Phillips, John E. Stone, and Klaus Schulten.
Adapting a message-driven parallel application to GPU-accelerated clusters.
In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), 2008.
abstract, conference

Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale.
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms.
In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008.
abstract

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten.
Accelerating molecular modeling applications with graphics processors.
Journal of Computational Chemistry, 28:2618-2640, 2007.
abstract, journal

Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele.
Biomolecular modeling in the era of petascale computing.
In Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008.
abstract

Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale.
Scalable Molecular Dynamics with NAMD on Blue Gene/L.
IBM Journal of Research and Development, Volume 52, No. 1/2, 2007.
abstract

K.Y. Sanbonmatsu and C.-S. Tung.
High performance computing in biology: Multimillion atom simulations of nanoscale systems.
Journal of Structural Biology, 157:470-480, 2007.
journal

Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten.
Managing biomolecular simulations in a grid environment with NAMD-G.
Proceedings of the 2006 TeraGrid Conference, 2006. In Press.
abstract

Sameer Kumar, Chao Huang, Gheorghe Almasi, and Laxmikant V. Kale.
Achieving Strong Scaling with NAMD on Blue Gene/L.
Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006, 2006.
abstract

Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
Biomolecular modeling using parallel supercomputers.
In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.
abstract

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal

Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood.
On the performance of molecular dynamics applications on current high-end systems.
Phil. Trans. R. Soc. A, 363:1987-1998, 2005.
journal

James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kal�.
NAMD: Biomolecular Simulation on Thousands of Processors.
Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002. Technical Paper 277.
abstract, pdf

Robert K. Brunner, James C. Phillips, Laxmikant V. Kal�.
Scalable Molecular Dynamics for Large Biomolecular Systems.
Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Technical Paper 271.
abstract, pdf

R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao, J. Phillips, and K. Schulten.
Speech/Gesture Interface to a Visual Computing Environment.
IEEE Computer Graphics and Applications, March/April 2000, 29-37.
abstract,

Laxmikant Kal�, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten.
NAMD2: Greater scalability for parallel molecular dynamics.
Journal of Computational Physics, 151:283-312, 1999.
abstract

Robert Brunner, Laxmikant Kal�, and James Phillips.
Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code.
In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.

James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kal�, Robert D. Skeel, and Klaus Schulten.
Avoiding algorithmic obfuscation in a message-driven parallel MD code.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag.
abstract

L. V. Kal�, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki.
NAMD: A Case Study in Multilingual Parallel Programming.
In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert D. Skeel, and Klaus Schulten.
NAMD-A parallel, object-oriented molecular dynamics program.
International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
Computational Physics Communications, 91:111-134, 1995.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995.
abstract

Papers Citing NAMD

The "full text" links lead to Google Scholar searches for the article. We do not provide copies of these articles ourselves. Articles by TCBG members are available in the TCBG Publications Database.

7066 citations found April 29, 2016.

Shen, Meng; Keten, Sinan; Lueptow, Richard M.
Rejection mechanisms for contaminants in polyamide reverse osmosis membranes
JOURNAL OF MEMBRANE SCIENCE, 509:36-47, JUL 1 2016
abstract, full text, DOI:10.1016/j.memsci.2016.02.043

Chiang, Ying-Chih; Wang, Yi
Virtual Substitution Scan Via Single-Step Free Energy Perturbation
BIOPOLYMERS, 105:324-336, JUN 2016
abstract, full text, DOI:10.1002/bip.22820

Shen, Meng; Keten, Sinan; Lueptow, Richard M.
Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations
JOURNAL OF MEMBRANE SCIENCE, 506:95-108, MAY 15 2016
abstract, full text, DOI:10.1016/j.memsci.2016.01.051

Eifler, Jay; Podgornik, Rudi; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Ching, Wai-Yim
Charge distribution and hydrogen bonding of a collagen (2)-chain in vacuum, hydrated, neutral, and charged structural models
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 116:681-691, MAY 5 2016
abstract, full text, DOI:10.1002/qua.25089

Roussou, Roza-Eleftheria; Karatasos, Kostas
Graphene/poly(ethylene glycol) nanocomposites as studied by molecular dynamics simulations
MATERIALS & DESIGN, 97:163-174, MAY 5 2016
abstract, full text, DOI:10.1016/j.matdes.2016.02.078

Salmas, Ramin Ekhteiari; Senturk, Murat; Yurtsever, Mine; Durdagi, Serdar
Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening and in vitro analysis
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 31:425-433, MAY 3 2016
abstract, full text, DOI:10.3109/14756366.2015.1036049

Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
COMPUTER PHYSICS COMMUNICATIONS, 202:337-350, MAY 2016
abstract, full text, DOI:10.1016/j.cpc.2016.01.014

Kopaczynska, M.; Schulz, A.; Fraczkowska, K.; Kraszewski, S.; Podbielska, H.; Fuhrhop, J. H.
Selective condensation of DNA by aminoglycoside antibiotics
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 45:287-299, MAY 2016
abstract, full text, DOI:10.1007/s00249-015-1095-9

Du, Hongbo; Qian, Xianghong
The Hydration Properties of Carboxybetaine Zwitterion Brushes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:877-885, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24234

Osman, Roman; Mezei, Mihaly; Engel, Stanislav
The Role of Protein "Stability Patches" in Molecular Recognition: A Case Study of the Human Growth Hormone-Receptor Complex
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:913-919, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24276

Arthur, Evan J.; Brooks, Charles L., I.I.I.
Parallelization and Improvements of the Generalized Born Model with a Simple sWitching Function for Modern Graphics Processors
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:927-939, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24280

Kucuk, Sami Emre; Sezer, Deniz
Multiscale computational modeling of C-13 DNP in liquids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:9353-9357, APR 14 2016
abstract, full text, DOI:10.1039/c6cp01028h

Yang, Jing; Bonomi, Massimiliano; Calero, Carles; Marti, Jordi
Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:9036-9041, APR 7 2016
abstract, full text, DOI:10.1039/c5cp05527j

Salveson, Patrick J.; Spencer, Ryan K.; Nowick, James S.
X-ray Crystallographic Structure of Oligomers Formed by a Toxic beta-Hairpin Derived from alpha-Synuclein: Trimers and Higher-Order Oligomers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:4458-4467, APR 6 2016
abstract, full text, DOI:10.1021/jacs.5b13261

Zhou, Wenjin; Rossetto, Allison M.; Pang, Xiaodong; Zhou, Linxiang
Computational full electron structure study of biological activity in Cyclophilin A
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:870-876, APR 2 2016
abstract, full text, DOI:10.1080/07391102.2015.1057527

Zhao, Yuan; Chen, Nanhao; Wang, Chaojie; Cao, Zexing
A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the alpha/beta-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release
ACS CATALYSIS, 6:2145-2157, APR 2016
abstract, full text, DOI:10.1021/acscatal.5b02855

Mendoza, Fernanda; Gomez, Hansel; Lluch, Jose M.; Masgrau, Laura
alpha 1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration
ACS CATALYSIS, 6:2577-2589, APR 2016
abstract, full text, DOI:10.1021/acscatal.5b02945

Brown, Patricia M. G. E.; Aurousseau, Mark R. P.; Musgaard, Maria; Biggin, Philip C.; Bowie, Derek
Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism
JOURNAL OF PHYSIOLOGY-LONDON, 594:1821-1840, APR 1 2016
abstract, full text, DOI:10.1113/JP271690

Jang, Hyunbum; Banerjee, Avik; Chavan, Tanmay S.; Lu, Shaoyong; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth
The higher level of complexity of K-Ras4B activation at the membrane
FASEB JOURNAL, 30:1643-1655, APR 2016
abstract, full text, DOI:10.1096/fj.15-279091

Hui, Wen-Qi; Cheng, Qi; Liu, Tian-Yu; Ouyang, Qin
Homology modeling, docking, and molecular dynamics simulation of the receptor GALR2 and its interactions with galanin and a positive allosteric modulator
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 90, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2944-x

Ilizaliturri-Flores, Ian; Correa-Basurto, Jose; Bello, Martiniano; Rosas-Trigueros, Jorge L.; Zamora-Lopez, Beatriz; Benitez-Cardoza, Claudia G.; Zamorano-Carrillo, Absalom
Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 98, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2940-1

Hilbert, Manuel; Noga, Akira; Frey, Daniel; Hamel, Virginie; Guichard, Paul; Kraatz, Sebastian H. W.; Pfreundschuh, Moritz; Hosner, Sarah; Flueckiger, Isabelle; Jaussi, Rolf; Wieser, Mara M.; Thieltges, Katherine M.; Deupi, Xavier; Mueller, Daniel J.; Kammerer, Richard A.; Goenczy, Pierre; Hirono, Masafumi; Steinmetz, Michel O.
SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture
NATURE CELL BIOLOGY, 18:393-+, APR 2016
abstract, full text, DOI:10.1038/ncb3329

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew
General trends of dihedral conformational transitions in a globular protein
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:501-514, APR 2016
abstract, full text, DOI:10.1002/prot.24996

Shim, Joong-Youn; Khurana, Leepakshi; Kendall, Debra A.
Computational analysis of the CB1 carboxyl-terminus in the receptor-G protein complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:532-543, APR 2016
abstract, full text, DOI:10.1002/prot.24999

Liberato, Marcelo V.; Silveira, Rodrigo L.; Prates, Erica T.; de Araujo, Evandro A.; Pellegrini, Vanessa O. A.; Camilo, Cesar M.; Kadowaki, Marco A.; Neto, Mario de O.; Popov, Alexander; Skaf, Munir S.; Polikarpov, Igor
Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism
SCIENTIFIC REPORTS, 6 Art. No. 23473, APR 1 2016
abstract, full text, DOI:10.1038/srep23473

Wang, Qi; Heizer, Esley; Rosa, Bruce A.; Wildman, Scott A.; Janetka, James W.; Mitreva, Makedonka
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting
INFECTION GENETICS AND EVOLUTION, 39:201-211, APR 2016
abstract, full text, DOI:10.1016/j.meegid.2016.01.025

Chandramouli, Balasubramanian; Di Maio, Danilo; Mancini, Giordano; Brancato, Giuseppe
Introducing an artificial photo-switch into a biological pore: A model study of an engineered alpha-hemolysin
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:689-697, APR 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.12.030

Kyriakou, Panagiota K.; Ekblad, Bie; Kristiansen, Per Eugen; Kaznessis, Yiannis N.
Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:824-835, APR 2016
abstract, full text, DOI:10.1016/j.bbamem.2016.01.005

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Molecular dynamics simulations of trihalomethanes removal from water using boron nitride nanosheets
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 82, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2939-7

He, Jianfeng; Wang, Jiabin; Hu, Jun; Sun, Jielin; Czajkowsky, Daniel Mark; Shao, Zhifeng
Single molecule atomic force microscopy of aerolysin pore complexes reveals unexpected star-shaped topography
JOURNAL OF MOLECULAR RECOGNITION, 29:174-181, APR 2016
abstract, full text, DOI:10.1002/jmr.2517

Kaplan, Elise; Guichou, Jean-Francois; Chaloin, Laurent; Kunzelmann, Simone; Leban, Nadia; Serpersu, Engin H.; Lionne, Corinne
Aminoglycoside binding and catalysis specificity of aminoglycoside 2 ''-phosphotransferase IVa: A thermodynamic, structural and kinetic study
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1860:802-813, APR 2016
abstract, full text, DOI:10.1016/j.bbagen.2016.01.016

Devineni, Subba Rao; Golla, Madhava; Chamarthi, Naga Raju; Meriga, Balaji; Saddala, Madhu Sudhana; Asupathri, Usha Rani
2-Amino-2,3-dihydro-1H-2 lambda(5)-[1,3,2]diazaphospholo[4,5-b]pyridin-2-one-based urea and thiourea derivatives: synthesis, molecular docking study and evaluation of anti-inflammatory and antimicrobial activities
MEDICINAL CHEMISTRY RESEARCH, 25:751-768, APR 2016
abstract, full text, DOI:10.1007/s00044-016-1518-x

Caruso, Icaro Putinhon; Barbosa Filho, Jose Maria; de Araujo, Alexandre Suman; de Souza, Fatima Pereira; Fossey, Marcelo Andres; Cornelio, Marinonio Lopes
An integrated approach with experimental and computational tools outlining the cooperative binding between 2-phenylchromone and human serum albumin
FOOD CHEMISTRY, 196:935-942, APR 1 2016
abstract, full text, DOI:10.1016/j.foodchem.2015.10.027

Carballo-Pacheco, Martin; Strodel, Birgit
Advances in the Simulation of Protein Aggregation at the Atomistic Scale
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2991-2999, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.6b00059

Punihaole, David; Workman, Riley J.; Hong, Zhenmin; Madura, Jeffry D.; Asher, Sanford A.
Polyglutamine Fibrils: New Insights into Antiparallel beta-Sheet Conformational Preference and Side Chain Structure
JOURNAL OF PHYSICAL CHEMISTRY B, 120:3012-3026, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11380

Saurabh, Suman; Glaser, Matthew A.; Lansac, Yves; Maiti, Prabal K.
Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces
JOURNAL OF PHYSICAL CHEMISTRY B, 120:3048-3060, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11863

Kannan, Srinivasaraghavan; Lane, David P.; Verma, Chandra S.
Long range recognition and selection in IDPs: the interactions of the C-terminus of p53
SCIENTIFIC REPORTS, 6 Art. No. 23750, MAR 31 2016
abstract, full text, DOI:10.1038/srep23750

Vukovic, Lela; Chipot, Christophe; Makino, Debora L.; Conti, Elena; Schulten, Klaus
Molecular Mechanism of Processive 3 ' to 5 ' RNA Translocation in the Active Subunit of the RNA Exosome Complex
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:4069-4078, MAR 30 2016
abstract, full text, TCBG publications, DOI:10.1021/jacs.5b12065

Mukhi, Nitika; Dhindwal, Sonali; Uppal, Sheetal; Kapoor, Abhijeet; Arya, Richa; Kumar, Pravindra; Kaur, Jagreet; Kundu, Suman
Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin
BIOCHEMISTRY, 55:1724-1740, MAR 29 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01013

Patel, Dharmeshkumar; Mahdavi, Somayeh; Kuyucak, Serdar
Computational Study of Binding of mu-Conotoxin GIIIA to Bacterial Sodium Channels Na(V)Ab and NaVRh
BIOCHEMISTRY, 55:1929-1938, MAR 29 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01324

Motlagh, Hesam N.; Toptygin, Dmitri; Kaiser, Christian M.; Hilser, Vincent J.
Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates
BIOPHYSICAL JOURNAL, 110:1280-1290, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.042

Nishima, Wataru; Mizukami, Wataru; Tanaka, Yoshiki; Ishitani, Ryuichiro; Nureki, Osamu; Sugita, Yuji
Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter
BIOPHYSICAL JOURNAL, 110:1346-1354, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.027

Khan, Hanif M.; He, Tao; Fuglebakk, Edvin; Grauffel, Cedric; Yang, Boqian; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie
A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding
BIOPHYSICAL JOURNAL, 110:1367-1378, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.02.020

Shams, Hengameh; Golji, Javad; Garakani, Kiavash; Mofrad, Mohammad R. K.
Dynamic Regulation of alpha-Actinin's Calponin Homology Domains on F-Actin
BIOPHYSICAL JOURNAL, 110:1444-1455, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.02.024

Wulf, Sarah F.; Ropars, Virginie; Fujita-Becker, Setsuko; Oster, Marco; Hofhaus, Goetz; Trabuco, Leonardo G.; Pylypenko, Olena; Sweeney, H. Lee; Houdusse, Anne M.; Schroeder, Rasmus R.
Force-producing ADP state of myosin bound to actin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113:E1844-E1852, MAR 29 2016
abstract, full text, DOI:10.1073/pnas.1516598113

Luan, Binquan; Zhou, Ruhong
Wettability and friction of water on a MoS2 nanosheet
APPLIED PHYSICS LETTERS, 108 Art. No. 131601, MAR 28 2016
abstract, full text, DOI:10.1063/1.4944840

Reese, Anna; List, Nanna Holmgaard; Kongsted, Jacob; Solov'yov, Ilia A.
How Far Does a Receptor Influence Vibrational Properties of an Odorant?
PLOS ONE, 11 Art. No. e0152345, MAR 25 2016
abstract, full text, DOI:10.1371/journal.pone.0152345

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
How Does the Solvent Modulate Shuttling in a Pillararene/Imidazolium [2]Rotaxane? Insights from Free Energy Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 120:6287-6293, MAR 24 2016
abstract, full text, DOI:10.1021/acs.jpcc.6b00852

Chopra, Nikita; Wales, Thomas E.; Joseph, Raji E.; Boyken, Scott E.; Engen, John R.; Jernigan, Robert L.; Andreotti, Amy H.
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases
PLOS ONE, 11 Art. No. e1004826, MAR 24 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004826

Fuentealba, Matias; Munoz, Rodrigo; Maturana, Pablo; Krapp, Adriana; Cabrera, Ricardo
Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies
PLOS ONE, 11 Art. No. e0152403, MAR 24 2016
abstract, full text, DOI:10.1371/journal.pone.0152403

Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.
Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 114112, MAR 21 2016
abstract, full text, TCBG publications, DOI:10.1063/1.4943868

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:7780-7788, MAR 21 2016
abstract, full text, DOI:10.1039/c5cp07562a

Deng, Qingming; Pan, Jun; Yin, Xiaohui; Wang, Xiaofeng; Zhao, Lina; Kang, Seung-gu; Jimenez-Cruz, Camilo A.; Zhou, Ruhong; Li, Jingyuan
Toward high permeability, selectivity and controllability of water desalination with FePc nanopores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:8140-8147, MAR 21 2016
abstract, full text, DOI:10.1039/c6cp00322b

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Weigele, Peter R.; Wanunu, Meni
Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA
NUCLEIC ACIDS RESEARCH, 44:2085-2092, MAR 18 2016
abstract, full text, DOI:10.1093/nar/gkv1199

Speltz, Thomas E.; Fanning, Sean W.; Mayne, Christopher G.; Fowler, Colin; Tajkhorshid, Emad; Greene, Geoffrey L.; Moore, Terry W.
Stapled Peptides with -Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 55:4252-4255, MAR 18 2016
abstract, full text, DOI:10.1002/anie.201510557

Rossi, Pia; Sterlini, Bruno; Castroflorio, Enrico; Marte, Antonella; Onofri, Franco; Valtorta, Flavia; Maragliano, Luca; Corradi, Anna; Benfenati, Fabio
A Novel Topology of Proline-rich Transmembrane Protein 2 (PRRT2): HINTS FOR AN INTRACELLULAR FUNCTION AT THE SYNAPSE
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:6111-6123, MAR 18 2016
abstract, full text, DOI:10.1074/jbc.M115.683888

Gan, Quan; Dai, Jian; Zhou, Huan-Xiang; Wollmuth, Lonnie P.
The Transmembrane Domain Mediates Tetramerization of -Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:6595-6606, MAR 18 2016
abstract, full text, DOI:10.1074/jbc.M115.686246

Zhang, Yunfeng; Ling, Zhenmin; Du, Guocheng; Chen, Jian; Kang, Zhen
Improved Production of Active Streptomyces griseus Trypsin with a Novel Auto-Catalyzed Strategy
SCIENTIFIC REPORTS, 6 Art. No. 23158, MAR 17 2016
abstract, full text, DOI:10.1038/srep23158

Katava, Marina; Kalimeri, Maria; Stirnemann, Guillaume; Sterpone, Fabio
Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2721-2730, MAR 17 2016
abstract, full text, DOI:10.1021/acs.jpcb.6b00306

Hosseinzadeh, Parisa; Mirts, Evan N.; Pfister, Thomas D.; Gao, Yi-Gui; Mayne, Christopher; Robinson, Howard; Tajkhorshid, Emad; Lu, Yi
Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions
BIOCHEMISTRY, 55:1494-1502, MAR 15 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01299

Angarica, Vladimir Espinosa; Orozco, Modesto; Sancho, Javier
Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia
HUMAN MOLECULAR GENETICS, 25:1233-1246, MAR 15 2016
abstract, full text, DOI:10.1093/hmg/ddw004

Jones, Peter M.; George, Anthony M.
Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding
SCIENTIFIC REPORTS, 6 Art. No. 23174, MAR 15 2016
abstract, full text, DOI:10.1038/srep23174

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Separation of copper and mercury as heavy metals from aqueous solution using functionalized boron nitride nanosheets: A theoretical study
JOURNAL OF MOLECULAR STRUCTURE, 1108:144-149, MAR 15 2016
abstract, full text, DOI:10.1016/j.molstruc.2015.11.058

Baul, Upayan; Kanth, J. Maruthi Pradeep; Anishetty, Ramesh; Vemparala, Satyavani
Effect of simple solutes on the long range dipolar correlations in liquid water
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 104502, MAR 14 2016
abstract, full text, DOI:10.1063/1.4943097

Luan, Binquan; Huynh, Tien; Zhou, Ruhong
Potential Interference of Protein-Protein Interactions by Graphyne
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2124-2131, MAR 10 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11449

Zuo, Zhicheng; Weng, Jingwei; Wang, Wenning
Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2145-2154, MAR 10 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11942

Jiang, Tao; Han, Wei; Maduke, Merritt; Tajkhorshid, Emad
Molecular Basis for Differential Anion Binding and Proton Coupling in the CI-/H+ Exchanger CIC-ec1
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:3066-3075, MAR 9 2016
abstract, full text, DOI:10.1021/jacs.5b12062

Prakash, Priyanka; Zhou, Yong; Liang, Hong; Hancock, John F.; Gorfe, Alemayehu A.
Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis
BIOPHYSICAL JOURNAL, 110:1125-1138, MAR 8 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.019

Ben Halima, Saoussen; Mishra, Sabyashachi; Raja, K. Muruga Poopathi; Willem, Michael; Baici, Antonio; Simons, Kai; Bruestle, Oliver; Koch, Philipp; Haass, Christian; Caflisch, Amedeo; Rajendran, Lawrence
Specific Inhibition of beta-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein
CELL REPORTS, 14:2127-2141, MAR 8 2016
abstract, full text, DOI:10.1016/j.celrep.2016.01.076

Borthwick, Lee A.; Kerbiriou, Mathieu; Taylor, Christopher J.; Cozza, Giorgio; Lascu, Ioan; Postel, Edith H.; Cassidy, Diane; Trouve, Pascal; Mehta, Anil; Robson, Louise; Muimo, Richmond
Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A
PLOS ONE, 11 Art. No. e0149097, MAR 7 2016
abstract, full text, DOI:10.1371/journal.pone.0149097

Vergadou, Niki; Androulaki, Eleni; Hill, Joerg-Ruediger; Economou, Ioannis G.
Molecular simulations of imidazolium-based tricyanomethanide ionic liquids using an optimized classical force field
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:6850-6860, MAR 7 2016
abstract, full text, DOI:10.1039/c5cp05892a

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui
Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:614-622, MAR 5 2016
abstract, full text, DOI:10.1002/jcc.24227

Takahashi, Tsukasa; Ngo, Bao C. Vo; Xiao, Leyang; Arya, Gaurav; Heller, Michael J.
Molecular mechanical properties of short-sequence peptide enzyme mimics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:463-474, MAR 3 2016
abstract, full text, DOI:10.1080/07391102.2015.1039586

Skelton, A. A.; Khedkar, V. M.; Fried, J. R.
All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:529-539, MAR 3 2016
abstract, full text, DOI:10.1080/07391102.2015.1044473

Mogami, George; Suzuki, Makoto; Matubayasi, Nobuyuki
Spatial-Decomposition Analysis of Energetics of Ionic Hydration
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1813-1821, MAR 3 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b09481

Zvereva, Elena E.; Katsyuba, Sergey A.; Dyson, Paul J.; Aleksandrov, Alexey V.
Solvation of Palladium Clusters in an Ionic Liquid: A QM/MM Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY C, 120:4596-4604, MAR 3 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b11229

Pietra, Francesco
On the Permeation by Dioxygen of the Cofactor-Independent Unusual Oxygenase RhCC, in Complex with Substrate 4-Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 13:331-335, MAR 2016
abstract, full text, DOI:10.1002/cbdv.201500211

Setiadi, Jeffry; Kuyucak, Serdar
Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A
MEMBRANES, 6, MAR 2016
abstract, full text, DOI:10.3390/membranes6010020

Kidmose, Rune T.; Andersen, Gregers R.
Interacting with the Human Insulin Receptor
STRUCTURE, 24:351-352, MAR 1 2016
abstract, full text, DOI:10.1016/j.str.2016.02.003

Croll, Tristan I.; Smith, Brian J.; Margetts, Mai B.; Whittaker, Jonathan; Weiss, Michael A.; Ward, Colin W.; Lawrence, Michael C.
Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain
STRUCTURE, 24:469-476, MAR 1 2016
abstract, full text, DOI:10.1016/j.str.2015.12.014

Lucius, Melissa; Falatach, Rebecca; McGlone, Cameron; Makaroff, Katherine; Danielson, Alex; Williams, Cameron; Nix, Jay C.; Konkolewicz, Dominik; Page, Richard C.; Berberich, Jason A.
Investigating the Impact of Polymer Functional Groups on the Stability and Activity of Lysozyme-Polymer Conjugates
BIOMACROMOLECULES, 17:1123-1134, MAR 2016
abstract, full text, DOI:10.1021/acs.biomac.5b01743

Li Qing; Yang Deng-Feng; Wang Jian-Hua; Wu Qi; Liu Qing-Zhi
Biomimetic Modification and Desalination Behavior of (15,15) Carbon Nanotubes with a Diameter Larger than 2 nm
ACTA PHYSICO-CHIMICA SINICA, 32:691-700, MAR 2016
abstract, full text, DOI:10.3866/PKU.WHXB201512182

Elmore, Donald E.
Why should biochemistry students be introduced to molecular dynamics simulationsand how can we introduce them?
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:118-123, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20943

Lundquist, Karl; Herndon, Conner; Harty, Tyson H.; Gumbart, James C.
Accelerating the use of molecular modeling in the high school classroom with VMD Lite
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:124-129, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20940

Spitznagel, Benjamin; Pritchett, Paige R.; Messina, Troy C.; Goadrich, Mark; Rodriguez, Juan
An undergraduate laboratory activity on molecular dynamics simulations
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:130-139, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20939

Roy, Durba; Lakshminarayanan, Madhavkrishnan
Scrambling of disulfide bond scaffolds in neurotoxin AuIB: A molecular dynamics simulation study
BIOPOLYMERS, 106:196-209, MAR 2016
abstract, full text, DOI:10.1002/bip.22799

Fu, Xuegang; Zhang, Gang; Liu, Ran; Wei, Jing; Zhang-Negrerie, Daisy; Jian, Xiaodong; Gao, Qingzhi
Mechanistic Study of Human Glucose Transport Mediated by GLUT1
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:517-526, MAR 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00597

Kapoor, Karan; McGill, Nicole; Peterson, Cynthia B.; Meyers, Harold V.; Blackburn, Michael N.; Baudry, Jerome
Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:535-547, MAR 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00596

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang
Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography
NATURE COMMUNICATIONS, 7 Art. No. 11083, MAR 2016
abstract, full text, DOI:10.1038/ncomms11083

Laghaei, Rozita; Yu, Alan S. L.; Coalson, Rob D.
Water and ion permeability of a claudin model: A computational study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:305-315, MAR 2016
abstract, full text, DOI:10.1002/prot.24969

Bairagya, Hridoy R.; Bansal, Manju
New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:360-373, MAR 2016
abstract, full text, DOI:10.1002/prot.24983

Qi, Yifei; Jo, Sunhwan; Im, Wonpil
Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies
GLYCOBIOLOGY, 26:251-260, MAR 2016
abstract, full text, DOI:10.1093/glycob/cwv101

Niinivehmas, Sanna P.; Manivannan, Elangovan; Rauhamaki, Sanna; Huuskonen, Juhani; Pentikainen, Olli T.
Identification of estrogen receptor alpha ligands with virtual screening techniques
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 64:30-39, MAR 2016
abstract, full text, DOI:10.1016/j.jmgm.2015.12.006

Barzegar, Abolfazl; Mansouri, Alireza; Azamat, Jafar
Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 64:75-84, MAR 2016
abstract, full text, DOI:10.1016/j.jmgm.2016.01.003

Arango-Lievano, Margarita; Sensoy, Ozge; Borie, Amelie; Corbani, Maithe; Guillon, Gilles; Sokoloff, Pierre; Weinstein, Harel; Jeanneteau, Freddy
A GIPC1-Palmitate Switch Modulates Dopamine Drd3 Receptor Trafficking and Signaling
MOLECULAR AND CELLULAR BIOLOGY, 36:1019-1031, MAR 2016
abstract, full text, DOI:10.1128/MCB.00916-15

Bai, Hua; Xue, Renhao; Bao, Huan; Zhang, Leili; Yethiraj, Arun; Cui, Qiang; Chapman, Edwin R.
Different states of synaptotagmin regulate evoked versus spontaneous release
NATURE COMMUNICATIONS, 7 Art. No. 10971, MAR 2016
abstract, full text, DOI:10.1038/ncomms10971

Liu, Xin; Zhang, Chen-Song; Lu, Chang; Lin, Sheng-Cai; Wu, Jia-Wei; Wang, Zhi-Xin
A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation
NATURE COMMUNICATIONS, 7 Art. No. 10879, MAR 2016
abstract, full text, DOI:10.1038/ncomms10879

Kinde, Monica N.; Bu, Weiming; Chen, Qiang; Xu, Yan; Eckenhoff, Roderic G.; Tang, Pei
Common Anesthetic-binding Site for Inhibition of Pentameric Ligand-gated Ion Channels
ANESTHESIOLOGY, 124:664-673, MAR 2016
abstract, full text, DOI:10.1097/ALN.0000000000001005

Mahinthichaichan, Paween; Gennis, Robert B.; Tajkhorshid, Emad
All the O-2 Consumed by Thermus thermophilus Cytochrome ba(3) Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer
BIOCHEMISTRY, 55:1265-1278, MAR 1 2016
abstract, full text

Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun
Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site
NATURE COMMUNICATIONS, 7 Art. No. 10714, MAR 2016
abstract, full text, TCBG publications, DOI:10.1038/ncomms10714

Sauer, Maximilian M.; Jakob, Roman P.; Eras, Jonathan; Baday, Sefer; Eris, Deniz; Navarra, Giulio; Berneche, Simon; Ernst, Beat; Maier, Timm; Glockshuber, Rudi
Catch-bond mechanism of the bacterial adhesin FimH
NATURE COMMUNICATIONS, 7 Art. No. 10738, MAR 2016
abstract, full text, DOI:10.1038/ncomms10738

Berti, Claudio; Furini, Simone; Gillespie, Dirk
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:925-929, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01044

Pachov, Dimitar V.; Fonseca, Rasmus; Arnol, Damien; Bernauer, Julie; van den Bedem, Henry
Coupled Motions in beta(2)AR:G alpha s Conformational Ensembles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:946-956, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00995

Ngo, Van A.; Kim, Ilsoo; Allen, Toby W.; Noskov, Sergei Y.
Estimation of Potentials of Mean Force from Nonequilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1000-1010, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01050

Pan, Albert C.; Weinreich, Thomas M.; Piana, Stefano; Shaw, David E.
Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1360-1367, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00913

Muecksch, Christian; Urbassek, Herbert M.
Accelerating Steered Molecular Dynamics: Toward Smaller Velocities in Forced Unfolding Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1380-1384, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01024

Whiteley, C. G.; Shing, C.-.Y.; Kuo, C.-.C.; Lee, Duu-Jong
Docking of HIV protease to silver nanoparticles
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 60:83-91, MAR 2016
abstract, full text, DOI:10.1016/j.jtice.2015.10.029

Luan, Binquan
Radial dependence of DNA translocation velocity in a solid-state nanopore
MICROCHIMICA ACTA, 183:995-1002, MAR 2016
abstract, full text, DOI:10.1007/s00604-015-1589-2

Baltzis, Athanasios S.; Glykos, Nicholas M.
Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data
PROTEIN SCIENCE, 25:587-596, MAR 2016
abstract, full text, DOI:10.1002/pro.2850

Aitha, Mahesh; Moller, Abraham J.; Sahu, Indra D.; Horitani, Masaki; Tierney, David L.; Crowder, Michael W.
Investigating the position of the hairpin loop in New Delhi metallo-beta-lactamase, NDM-1, during catalysis and inhibitor binding
JOURNAL OF INORGANIC BIOCHEMISTRY, 156:35-39, MAR 2016
abstract, full text, DOI:10.1016/j.jinorgbio.2015.10.011

Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
COMPUTER PHYSICS COMMUNICATIONS, 200:57-65, MAR 2016
abstract, full text, DOI:10.1016/j.cpc.2015.10.024

Noroozi, Javad; Ghotbi, Cyrus; Sardroodi, Jaber Jahanbin; Karirni-Sabet, Javad; Robert, Marc A.
Solvation free energy and solubility of acetaminophen and ibuprofen in supercritical carbon dioxide: Impact of the solvent model
JOURNAL OF SUPERCRITICAL FLUIDS, 109:166-176, MAR 2016
abstract, full text, DOI:10.1016/j.supflu.2015.11.009

Jana, Asis K.; Tiwari, Mrityunjay K.; Vanka, Kumar; Sengupta, Neelanjana
Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:5910-5924, FEB 28 2016
abstract, full text, DOI:10.1039/c5cp04675k

Sorensen, Anders B.; Madsen, Jesper J.; Svensson, L. Anders; Pedersen, Anette A.; Ostergaard, Henrik; Overgaard, Michael T.; Olsen, Ole H.; Gandhi, Prafull S.
Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:4671-4683, FEB 26 2016
abstract, full text, DOI:10.1074/jbc.M115.698613

Jana, Suvamay; Hamre, Anne Grethe; Wildberger, Patricia; Holen, Matilde Mengkrog; Eijsink, Vincent G. H.; Beckham, Gregg T.; Sorlie, Morten; Payne, Christina M.
Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1236-1249, FEB 25 2016
abstract, full text, DOI:10.1021/acs.jpcb.8b12610

Prudovsky, Igor; Kacer, Doreen; Davis, Julie; Shah, Varun; Jayanthi, Srinivas; Huber, Isabelle; Dakshinamurthy, Rajalingam; Ganter, Owen; Soldi, Raffaella; Neivandt, David; Guvench, Olgun; Kumar, Thallapuranam Krishnaswamy Suresh
Folding of Fibroblast Growth Factor 1 Is Critical for Its Nonclassical Release
BIOCHEMISTRY, 55:1159-1167, FEB 23 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01341

Zhang, Liqun; Borthakur, Susmita; Buck, Matthias
Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations
BIOPHYSICAL JOURNAL, 110:877-886, FEB 23 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.036

Patel, Dhilon S.; Re, Suyong; Wu, Emilia L.; Qi, Yifei; Klebba, Phillip E.; Widmalm, Goeran; Yeom, Min Sun; Sugita, Yuji; Im, Wonpil
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability
BIOPHYSICAL JOURNAL, 110:930-938, FEB 23 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.002

Fuglestad, Brian; Gupta, Kushol; Wand, A. Joshua; Sharp, Kim A.
Characterization of Cetyltrimethylammonium Bromide/Hexanol Reverse Micelles by Experimentally Benchmarked Molecular Dynamics Simulations
LANGMUIR, 32:1674-1684, FEB 23 2016
abstract, full text, DOI:10.1021/acs.langmuir.5b03981

Niu, Yuzhen; Li, Shuyan; Pan, Dabo; Liu, Huanxiang; Yao, Xiaojun
Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:5622-5629, FEB 21 2016
abstract, full text, DOI:10.1039/c5cp06257h

Bai, Qifeng; Yao, Xiaojun
Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis
SCIENTIFIC REPORTS, 6 Art. No. 21763, FEB 18 2016
abstract, full text, DOI:10.1038/srep21763

Mulholland, Sam; Turpin, Eleanor R.; Bonev, Boyan B.; Hirst, Jonathan D.
Docking and molecular dynamics simulations of the ternary complex nisin(2):lipid II
SCIENTIFIC REPORTS, 6 Art. No. 21185, FEB 18 2016
abstract, full text, DOI:10.1038/srep21185

Cai, Kaicong; Du, Fenfen; Zheng, Xuan; Liu, Jia; Zheng, Renhui; Zhao, Juan; Wang, Jianping
General Applicable Frequency Map for the Amide-I Mode in beta-Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1069-1079, FEB 18 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11643

Lang, Eric J. M.; Heyes, Logan C.; Jameson, Geoffrey B.; Parker, Emily J.
Calculated pK(a) Variations Expose Dynamic Allosteric Communication Networks
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:2036-2045, FEB 17 2016
abstract, full text, DOI:10.1021/jacs.5b13134

LeVine, Michael V.; Khelashvili, George; Shi, Lei; Quick, Matthias; Javitch, Jonathan A.; Weinstein, Harel
Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles
BIOCHEMISTRY, 55:850-859, FEB 16 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01268

Miner, Kyle D.; Kurtz, Donald M., Jr.
Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP
BIOCHEMISTRY, 55:970-979, FEB 16 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01227

Liu, Huihui; Gao, Yan-Song; Chen, Xiang-Jun; Chen, Zhe; Zhou, Hai-Meng; Yan, Yong-Bin; Gong, Haipeng
A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase
SCIENTIFIC REPORTS, 6 Art. No. 21191, FEB 16 2016
abstract, full text, DOI:10.1038/srep21191

Ataseyer-Arslan, Belkis; Yilancioglu, Kaan; Kalkan, Zeynep; Timucin, Ahmet Can; Gur, Hazal; Isik, Fatma Busra; Deniz, Emre; Erman, Batu; Cetiner, Selim
Screening of new antileukemic agents from essential oils of algae extracts and computational modeling of their interactions with intracellular signaling nodes
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 83:120-131, FEB 15 2016
abstract, full text, DOI:10.1016/j.ejps.2015.12.001

Roeland Boer, D.; Angel Ruiz-Maso, Jose; Rueda, Manuel; Petoukhov, Maxim V.; Machon, Cristina; Svergun, Dmitri I.; Orozco, Modesto; del Solar, Gloria; Coll, Miquel
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158
SCIENTIFIC REPORTS, 6 Art. No. 20915, FEB 15 2016
abstract, full text, DOI:10.1038/srep20915

Hofmann, Sascha; Voitchovsky, Kislon; Spijker, Peter; Schmidt, Moritz; Stumpf, Thorsten
Visualising the molecular alteration of the calcite (104) - water interface by sodium nitrate
SCIENTIFIC REPORTS, 6 Art. No. 21576, FEB 15 2016
abstract, full text, DOI:10.1038/srep21576

Lavecchia, Martin J.; Puig de la Bellacasa, Raimon; Borrell, Jose I.; Cavasotto, Claudio N.
Investigating molecular dynamics-guided lead optimization of EGFR inhibitors
BIOORGANIC & MEDICINAL CHEMISTRY, 24:768-778, FEB 15 2016
abstract, full text, DOI:10.1016/j.bmc.2015.12.046

Stachiewicz, Anna; Molski, Andrzej
Diffusive dynamics of DNA unzipping in a nanopore
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:467-476, FEB 15 2016
abstract, full text, DOI:10.1002/jcc.24236

Azamat, Jafar; Balaei, Ali; Gerami, Mehdi
A theoretical study of nanostructure membranes for separating Li+ and Mg2+ from Cl-
COMPUTATIONAL MATERIALS SCIENCE, 113:66-74, FEB 15 2016
abstract, full text, DOI:10.1016/j.commatsci.2015.11.029

Elber, Ron
Perspective: Computer simulations of long time dynamics
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 060901, FEB 14 2016
abstract, full text, DOI:10.1063/1.4940794

Sasselli, I. Ramos; Ulijn, R. V.; Tuttle, T.
CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:4659-4667, FEB 14 2016
abstract, full text, DOI:10.1039/c5cp06770g

Lee, Myeongsang; Kwon, Junpyo; Na, Sungsoo
Mechanical behavior comparison of spider and silkworm silks using molecular dynamics at atomic scale
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:4814-4821, FEB 14 2016
abstract, full text, DOI:10.1039/c5cp06809f

Thomas, Michael; Corry, Ben
A computational assessment of the permeability and salt rejection of carbon nanotube membranes and their application to water desalination
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 374 Art. No. 20150020, FEB 13 2016
abstract, full text, DOI:10.1098/rsta.2015.0020

Ren, Jinqi; Huo, Lin; Wang, Wenjuan; Zhang, Yong; Li, Wei; Lou, Jizhong; Xu, Tao; Feng, Wei
Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:3581-3594, FEB 12 2016
abstract, full text, DOI:10.1074/jbc.M115.689091

Allison, Jane R.; Lechner, Marcus; Hoeppner, Marc P.; Poole, Anthony M.
Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics
PLOS ONE, 11 Art. No. e0147619, FEB 12 2016
abstract, full text, DOI:10.1371/journal.pone.0147619

Farhi, Asaf; Singh, Bipin
Calculation of molecular free energies in classical potentials
NEW JOURNAL OF PHYSICS, 18 Art. No. 023039, FEB 11 2016
abstract, full text, DOI:10.1088/1367-2630/18/2/023039

Jin, Tiantian; Yu, Haibo; Huang, Xu-Feng
Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B
SCIENTIFIC REPORTS, 6 Art. No. 20766, FEB 11 2016
abstract, full text, DOI:10.1038/srep20766

Martinez-Montiel, Nancy; Morales-Lara, Laura; Hernandez-Perez, Julio M.; Martinez-Contreras, Rebeca D.
In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis
PLOS ONE, 11 Art. No. e0148191, FEB 10 2016
abstract, full text, DOI:10.1371/journal.pone.0148191

Boyer, Patrick D.; Ganesh, Sairaam; Qin, Zhao; Holt, Brian D.; Buehler, Markus J.; Islam, Mohammad F.; Dahl, Kris Noel
Delivering Single-Walled Carbon Nanotubes to the Nucleus Using Engineered Nuclear Protein Domains
ACS APPLIED MATERIALS & INTERFACES, 8:3524-3534, FEB 10 2016
abstract, full text, DOI:10.1021/acsami.5b12602

Bae, Chanhyung; Anselmi, Claudio; Kalia, Jeet; Jara-Oseguera, Andres; Schwieters, Charles D.; Krepkiy, Dmitriy; Lee, Chul Won; Kim, Eun-Hee; Kim, Jae Il; Faraldo-Gomez, Jose D.; Swartz, Kenton J.
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin
ELIFE, 5 Art. No. e11273, FEB 10 2016
abstract, full text, DOI:10.7554/elife.11273.001

Kang, Myungshim; Zhang, Pengcheng; Cui, Honggang; Loverde, Sharon M.
pi-pi Stacking Mediated Chirality in Functional Supramolecular Filaments
MACROMOLECULES, 49:994-1001, FEB 9 2016
abstract, full text, DOI:10.1021/acs.macromol.5b02148

Petridis, Loukas; Smith, Jeremy C.
Conformations of Low-Molecular-Weight Lignin Polymers in Water
CHEMSUSCHEM, 9:289-295, FEB 8 2016
abstract, full text, DOI:10.1002/cssc.201501350

Silveira, Rodrigo L.; Skaf, Munir S.
Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3510-3521, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp06674c

Vogel, Alexander; Scheidt, Holger A.; Baek, Dong Jae; Bittman, Robert; Huster, Daniel
Structure and dynamics of the aliphatic cholesterol side chain in membranes as studied by H-2 NMR spectroscopy and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3730-3738, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp05084g

Ham, Sujin; Lee, Ji-Eun; Song, Suhwan; Peng, Xiaobin; Hori, Takaaki; Aratani, Naoki; Osuka, Atsuhiro; Sim, Eunji; Kim, Dongho
Direct observation of structural properties and fluorescent trapping sites in macrocyclic porphyrin arrays at the single-molecule level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3871-3877, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp06859b

Bajaj, Harsha; Scorciapino, Mariano A.; Moynie, Lucile; Page, Malcolm G. P.; Naismith, James H.; Ceccarelli, Matteo; Winterhalter, Mathias
Molecular Basis of Filtering Carbapenems by Porins from beta-Lactam-resistant Clinical Strains of Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:2837-2847, FEB 5 2016
abstract, full text, DOI:10.1074/jbc.M115.690156

Kuenze, Georg; Koehling, Sebastian; Vogel, Alexander; Rademann, Joerg; Huster, Daniel
Identification of the Glycosaminoglycan Binding Site of Interleukin-10 by NMR Spectroscopy
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:3100-3113, FEB 5 2016
abstract, full text, DOI:10.1074/jbc.M115.681759

Druart, Karen; Palmai, Zoltan; Omarjee, Eyaz; Simonson, Thomas
Protein:Ligand Binding Free Energies: A Stringent Test for Computational Protein Design
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:404-415, FEB 5 2016
abstract, full text, DOI:10.1002/jcc.24230

Chakrabarti, Mayukh; Jang, Hyunbum; Nussinov, Ruth
Comparison of the Conformations of KRAS Isoforms, K-Ras4A and K-Ras4B, Points to Similarities and Significant Differences
JOURNAL OF PHYSICAL CHEMISTRY B, 120:667-679, FEB 4 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11110

Lee, Myeongsang; Na, Sungsoo
End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105-115) Amyloid Protofibrils
CHEMPHYSCHEM, 17:425-432, FEB 3 2016
abstract, full text, DOI:10.1002/cphc.201500945

Kasuya, Go; Fujiwara, Yuichiro; Takemoto, Mizuki; Dohmae, Naoshi; Nakada-Nakura, Yoshiko; Ishitani, Ryuichiro; Hattori, Motoyuki; Nureki, Osamu
Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels
CELL REPORTS, 14:932-944, FEB 2 2016
abstract, full text, DOI:10.1016/j.celrep.2015.12.087

Guo, Tao; Li, Haiyan; Wu, Li; Guo, Zhen; Yin, Xianzhen; Wang, Caifen; Sun, Lixin; Shao, Qun; Gu, Jingkai; York, Peter; Zhang, Jiwen
Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations
JOURNAL OF PHYSICAL CHEMISTRY A, 120:981-991, FEB 2 2016
abstract, full text, DOI:10.1021/acs.jpca.5b11816

Luo, Yun; Rossi, Angelo R.; Harris, Andrew L.
Computational Studies of Molecular Permeation through Connexin26 Channels
BIOPHYSICAL JOURNAL, 110:584-599, FEB 2 2016
abstract, full text, DOI:10.1016/j.bpj.2015.11.3528

Halim, Danny; Hofstra, Robert M. W.; Signorile, Luca; Verdijk, Rob M.; van der Werf, Christine S.; Sribudiani, Yunia; Brouwer, Rutger W. W.; van IJcken, Wilfred F. J.; Dahl, Niklas; Verheij, Joke B. G. M.; Baumann, Clarisse; Kerner, John; van Bever, Yolande; Galjart, Niels; Wijnen, Rene M. H.; Tibboel, Dick; Burns, Alan J.; Muller, Franoise; Brooks, Alice S.; Alves, Maria M.
ACTG2 variants impair actin polymerization in sporadic Megacystis Microcolon Intestinal Hypoperistalsis Syndrome
HUMAN MOLECULAR GENETICS, 25:571-583, FEB 1 2016
abstract, full text, DOI:10.1093/hmg/ddv497

Simonson, Thomas; Ye-Lehmann, Shixin; Palmai, Zoltan; Amara, Najette; Wydau-Dematteis, Sandra; Bigan, Erwan; Druart, Karen; Moch, Clara; Plateau, Pierre
Redesigning the stereospecificity of tyrosyl-tRNA synthetase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:240-253, FEB 2016
abstract, full text, DOI:10.1002/prot.24972

Louros, Nikolaos N.; Baltoumas, Fotis A.; Hamodrakas, Stavros J.; Iconomidou, Vassiliki A.
A beta-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 30:153-164, FEB 2016
abstract, full text, DOI:10.1007/s10822-015-9892-x

Datta, Siddhartha A. K.; Clark, Patrick K.; Fan, Lixin; Ma, Buyong; Harvin, Demetria P.; Sowder, Raymond C., I.I.; Nussinov, Ruth; Wang, Yun-Xing; Rein, Alan
Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly
JOURNAL OF VIROLOGY, 90:1773-1787, FEB 2016
abstract, full text, DOI:10.1128/JVI.02061-15

Zhang, Dejiu; Yan, Kaige; Liu, Guangqiao; Song, Guangtao; Luo, Jiejian; Shi, Yi; Cheng, Erchao; Wu, Shan; Jiang, Taijiao; Lou, Jizhong; Gao, Ning; Qin, Yan
EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 23:125-+, FEB 2016
abstract, full text, DOI:10.1038/nsmb.3160

Hollingsworth, Scott A.; Holden, Jeffrey K.; Li, Huiying; Poulos, Thomas L.
Elucidating nitric oxide synthase domain interactions by molecular dynamics
PROTEIN SCIENCE, 25:374-382, FEB 2016
abstract, full text, DOI:10.1002/pro.2824

Harpole, Kyle W.; O'Brien, Evan S.; Clark, Matthew A.; McKnight, C. James; Vugmeyster, Liliya; Wand, A. Joshua
The unusual internal motion of the villin headpiece subdomain
PROTEIN SCIENCE, 25:423-432, FEB 2016
abstract, full text, DOI:10.1002/pro.2831

Yu, Lili; Rodriguez, Roberto A.; Chen, L. Laurie; Chen, Liao Y.; Perry, George; McHardy, Stanton F.; Yeh, Chih-Ko
1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins
PROTEIN SCIENCE, 25:433-441, FEB 2016
abstract, full text, DOI:10.1002/pro.2832

Cui, Dachao; Ren, Weitong; Li, Wenfei; Wang, Wei
Molecular simulations of substrate release and coupled conformational motions in adenylate kinase
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 15 Art. No. 1650004, FEB 2016
abstract, full text, DOI:10.1142/S0219633616500048

Aoun, Bachir; Russo, Daniela
Nano-confinement of biomolecules: Hydrophilic confinement promotes structural order and enhances mobility of water molecules
NANO RESEARCH, 9:273-281, FEB 2016
abstract, full text, DOI:10.1007/s12274-015-0907-7

Ngo, Thuy T. M.; Yoo, Jejoong; Dai, Qing; Zhang, Qiucen; He, Chuan; Aksimentiev, Aleksei; Ha, Taekjip
Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability
NATURE COMMUNICATIONS, 7 Art. No. 10813, FEB 2016
abstract, full text, DOI:10.1038/ncomms10813

Suzuki, Nozomu; Wang, Yichun; Elvati, Paolo; Qu, Zhi-Bei; Kim, Kyoungwon; Jiang, Shuang; Baumeister, Elizabeth; Lee, Jaewook; Yeom, Bongjun; Bahng, Joong Hwan; Lee, Jaebeom; Violi, Angela; Kotov, Nicholas A.
Chiral Graphene Quantum Dots
ACS NANO, 10:1744-1755, FEB 2016
abstract, full text, DOI:10.1021/acsnano.5b06369

DeBenedictis, Elizabeth P.; Hamed, Elham; Keten, Sinan
Mechanical Reinforcement of Proteins with Polymer Conjugation
ACS NANO, 10:2259-2267, FEB 2016
abstract, full text, DOI:10.1021/acsnano.5b06917

Cui Da-Chao; Ren Wei-Tong; Li Wen-Fei; Wang Wei
Metadynamics Simulations of Mg2+ Transfer in the Late Stage of the Adenylate Kinase Catalytic Cycle
ACTA PHYSICO-CHIMICA SINICA, 32:429-435, FEB 2016
abstract, full text, DOI:10.3866/PKU.WHXB201511201

Thomas, Trayder; Fang, Yu; Yuriev, Elizabeth; Chalmers, David K.
Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D-2 and D-3 Receptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:308-321, FEB 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00457

Giesa, Tristan; Perry, Carole C.; Buehler, Markus J.
Secondary Structure Transition and Critical Stress for a Model of Spider Silk Assembly
BIOMACROMOLECULES, 17:427-436, FEB 2016
abstract, full text, DOI:10.1021/acs.biomac.5b01246

Sun, Huiyong; Chen, Pengcheng; Li, Dan; Li, Youyong; Hou, Tingjun
Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:851-860, FEB 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00973

Capponi, Sara; Freites, J. Alfredo; Tobias, Douglas J.; White, Stephen H.
Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:354-362, FEB 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.11.024

Milenkovic, Stefan; Bondar, Ana-Nicoleta
Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:374-385, FEB 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.11.010

Quan, Xiaoping; Chen, Xiuqiang; Sun, Deliang; Xu, Bo; Zhao, Linlin; Shi, Xiaoqian; Liu, Hongsheng; Gao, Bing; Lu, Xiuli
The mechanism of the effect of U18666a on blocking the activity of 3 beta-hydroxysterol Delta-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 46, FEB 2016
abstract, full text, DOI:10.1007/s00894-016-2907-2

Li, Minghui; Kales, Stephen C.; Ma, Ke; Shoemaker, Benjamin A.; Crespo-Barreto, Juan; Cangelosi, Andrew L.; Lipkowitz, Stanley; Panchenko, Anna R.
Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation
CANCER RESEARCH, 76:561-571, FEB 1 2016
abstract, full text, DOI:10.1158/0008-5472.CAN-14-3812

Cuevas-Hernandez, Roberto I.; Correa-Basurto, Jos; Flores-Sandoval, Cesar A.; Padilla-Martinez, Itzia I.; Nogueda-Torres, Benjamin; de Lourdes Villa-Tanaca, Maria; Tamay-Cach, Feliciano; Nolasco-Fidencio, Juan J.; Trujillo-Ferrara, Jose G.
Fluorine-containing benzothiazole as a novel trypanocidal agent: design, in silico study, synthesis and activity evaluation
MEDICINAL CHEMISTRY RESEARCH, 25:211-224, FEB 2016
abstract, full text, DOI:10.1007/s00044-015-1475-9

Xie, Xiao-Xiao; Li, Jun-Wei; Xiao, Shao-Ying; Liu, Yu-Zhi; Liu, Hui; Geng, Jin-Peng; Zhang, Su-Hua; Yu, Hui; Zhan, Yong; An, Hai-Long
The Structural Stability of Alpha-Helix Determined by the Preference of Amino Acids
CHINESE PHYSICS LETTERS, 33 Art. No. 028701, FEB 2016
abstract, full text, DOI:10.1088/0256-307X/33/2/028701

Das, Amit; Ghosh, Mahua; Chakrabarti, J.
Time dependent correlation between dihedral angles as probe for long range communication in proteins
CHEMICAL PHYSICS LETTERS, 645:200-204, FEB 2016
abstract, full text, DOI:10.1016/j.cplett.2015.12.060

Li, Qing; Yang, Dengfeng; Shi, Jinsheng; Xu, Xiang; Yan, Shihai; Liu, Qingzhi
Biomimetic modification of large diameter carbon nanotubes and the desalination behavior of its reverse osmosis membrane
DESALINATION, 379:164-171, FEB 1 2016
abstract, full text, DOI:10.1016/j.desal.2015.11.008

Ray, Angana; Panigrahi, Swati; Bhattacharyya, Dhananjay
A Comparison of Four Different Conformations Adopted by Human Telomeric G-Quadruplex Using Computer Simulations
BIOPOLYMERS, 105:83-99, FEB 2016
abstract, full text, DOI:10.1002/bip.22751

Aliaga, Carolina; Bravo-Moraga, Felipe; Gonzalez-Nilo, Danilo; Marquez, Sebastian; Luehr, Susan; Mena, Geraldine; Caroli Rezende, Marcos
Location of TEMPO derivatives in micelles: subtle effect of the probe orientation
FOOD CHEMISTRY, 192:395-401, FEB 1 2016
abstract, full text, DOI:10.1016/j.foodchem.2015.07.036

Sikorra, Stefan; Litschko, Christa; Mueller, Carina; Thiel, Nadine; Galli, Thierry; Eichner, Timo; Binz, Thomas
Identification and Characterization of Botulinum Neurotoxin A Substrate Binding Pockets and Their Re-Engineering for Human SNAP-23
JOURNAL OF MOLECULAR BIOLOGY, 428:372-384, JAN 29 2016
abstract, full text, DOI:10.1016/j.jmb.2015.10.024

Ricci, Clarisse G.; Silveira, Rodrigo L.; Rivalta, Ivan; Batista, Victor S.; Skaf, Munir S.
Allosteric Pathways in the PPAR gamma-RXR alpha nuclear receptor complex
SCIENTIFIC REPORTS, 6 Art. No. 19940, JAN 29 2016
abstract, full text, DOI:10.1038/srep19940

Baram, Michal; Atsmon-Raz, Yoav; Ma, Buyong; Nussinov, Ruth; Miller, Yifat
Amylin-A beta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:2330-2338, JAN 28 2016
abstract, full text, DOI:10.1039/c5cp03338a

Kohler, Jonatan; Schonbeck, Christian; Westh, Peter; Holm, Rene
Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified gamma-Cyclodextrins with Bile Salts
JOURNAL OF PHYSICAL CHEMISTRY B, 120:396-405, JAN 28 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b10536

Kitjaruwankul, Sunan; Wapeesittipan, Pattama; Boonamnaj, Panisak; Sompompisut, Pornthep
Inner and Outer Coordination Shells of Mg2+ in CorA Selectivity Filter from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 120:406-417, JAN 28 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b10925

Brock, Joseph S.; Hamberg, Mats; Balagunaseelan, Navisraj; Goodman, Michael; Morgenstern, Ralf; Strandback, Emilia; Samuelsson, Bengt; Rinaldo-Matthis, Agnes; Haeggstrom, Jesper Z.
A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E-2 synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113:972-977, JAN 26 2016
abstract, full text, DOI:10.1073/pnas.1522891113

Habermacher, Chloe; Martz, Adeline; Calimet, Nicolas; Lemoine, Damien; Peverini, Laurie; Specht, Alexandre; Cecchini, Marco; Grutter, Thomas
Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel
ELIFE, 5 Art. No. e11050, JAN 25 2016
abstract, full text, DOI:10.7554/eLife.11050

Khantwal, Chandra M.; Abraham, Sherwin J.; Han, Wei; Jiang, Tao; Chavan, Tanmay S.; Cheng, Ricky C.; Elvington, Shelley M.; Liu, Corey W.; Mathews, Irimpan I.; Steins, Richard A.; Mchaourab, Hassane S.; Tajkhorshid, Emad; Maduke, Merritt
Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter
ELIFE, 5 Art. No. e11189, JAN 22 2016
abstract, full text, DOI:10.7554/eLife.11189

Sellers, Michael S.; Hurley, Margaret M.
XPairIt Docking Protocol for peptide docking and analysis
MOLECULAR SIMULATION, 42:149-161, JAN 22 2016
abstract, full text, DOI:10.1080/08927022.2015.1025267

Dutta, Debodyuti; Mishra, Sabyashachi
Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1671-1680, JAN 21 2016
abstract, full text, DOI:10.1039/c5cp06024a

Verde, Ana Vila; Santer, Mark; Lipowsky, Reinhard
Solvent-shared pairs of densely charged ions induce intense but short-range supra-additive slowdown of water rotation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1918-1930, JAN 21 2016
abstract, full text, DOI:10.1039/c5cp05726d

Roth, M. W.; Firlej, L.; Kuchta, B.; Connolly, M. J.; Maldonado, E.; Wexler, C.
Simulation and Characterization of Tetracosane on Graphite: Molecular Dynamics Beyond the Monolayer
JOURNAL OF PHYSICAL CHEMISTRY C, 120:984-994, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09677

Kritikos, Georgios; Vergadou, Niki; Economou, Ioannis G.
Molecular Dynamics Simulation of Highly Confined Glassy Ionic Liquids
JOURNAL OF PHYSICAL CHEMISTRY C, 120:1013-1024, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09947

Dolores Elola, M.; Rodriguez, Javier
Excess Sorption of Supercritical CO2 within Cylindrical Silica Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 120:1262-1269, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09000

Pan, Qunxing; Wang, Hui; Ouyang, Wei; Wang, Xiaoli; Bi, Zhenwei; Xia, Xingxia; Wang, Yongshan; He, Kongwang
Immunogenicity of adenovirus-derived porcine parvovirus-like particles displaying B and T cell epitopes of foot-and-mouth disease
VACCINE, 34:578-585, JAN 20 2016
abstract, full text, DOI:10.1016/j.vaccine.2015.11.003

Majumdar, Sarmistha; Maiti, Satyabrata; Dastidar, Shubhra Ghosh
Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity
BIOCHEMISTRY, 55:335-347, JAN 19 2016
abstract, full text, DOI:10.1021/acs.biochem.5b00853

Bowerman, Samuel; Wereszczynski, Jeff
Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 110:327-337, JAN 19 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.015

Shaytan, Alexey K.; Armeev, Grigoriy A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions
JOURNAL OF MOLECULAR BIOLOGY, 428:221-237, JAN 16 2016
abstract, full text, DOI:10.1016/j.jmb.2015.12.004

Zhang, Qi-Lin; Yang, Rong-Yao
Fast transport of water molecules across carbon nanotubes induced by static electric fields
CHEMICAL PHYSICS LETTERS, 644:201-204, JAN 16 2016
abstract, full text, DOI:10.1016/j.cplett.2015.11.061

Hanson, M. Gartz; Aiken, Jayne; Sietsema, Daniel V.; Sept, David; Bates, Emily A.; Niswander, Lee; Moore, Jeffrey K.
Novel alpha-tubulin mutation disrupts neural development and tubulin proteostasis
DEVELOPMENTAL BIOLOGY, 409:406-419, JAN 15 2016
abstract, full text, DOI:10.1016/j.ydbio.2015.11.022

Musille, Paul M.; Kossmann, Bradley R.; Kohn, Jeffrey A.; Ivanov, Ivaylo; Ortlund, Eric A.
Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:1411-1426, JAN 15 2016
abstract, full text

Tavoulari, Sotiria; Margheritis, Eleonora; Nagarajan, Anu; DeWitt, David C.; Zhang, Yuan-Wei; Rosado, Edwin; Ravera, Silvia; Rhoades, Elizabeth; Forrest, Lucy R.; Rudnick, Gary
Two Na+ Sites Control Conformational Change in a Neurotransmitter Transporter Homolog
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:1456-1471, JAN 15 2016
abstract, full text

Ingolfsson, Helgi I.; Arnarez, Clement; Periole, Xavier; Marrink, Siewert J.
Computational 'microscopy' of cellular membranes
JOURNAL OF CELL SCIENCE, 129:257-268, JAN 15 2016
abstract, full text, DOI:10.1242/jcs.176040

Zygmunt, William; Potoff, Jeffrey J.
The effect of fluorination on the physical properties and the free energies of hydration of 1-alcohols
FLUID PHASE EQUILIBRIA, 407:314-321, JAN 15 2016
abstract, full text, DOI:10.1016/j.fluid.2015.07.005

Zanuy, David; Poater, Jordi; Sola, Miquel; Hamley, Ian W.; Aleman, Carlos
Fmoc-RGDS based fibrils: atomistic details of their hierarchical assembly
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1265-1278, JAN 14 2016
abstract, full text, DOI:10.1039/c5cp04269k

Irudayanathan, Flaviyan Jerome; Trasatti, John P.; Karande, Pankaj; Nangia, Shikha
Molecular Architecture of the Blood Brain Barrier Tight Junction Proteins-A Synergistic Computational and In Vitro Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 120:77-88, JAN 14 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b09977

Poblete, Horacio; Agarwal, Anirudh; Thomas, Suma S.; Bohne, Cornelia; Ravichandran, Ranjithkumar; Phospase, Jaywant; Comer, Jeffrey; Alarcon, Emilio I.
New Insights into Peptide-Silver Nanoparticle Interaction: Deciphering the Role of Cysteine and Lysine in the Peptide Sequence
LANGMUIR, 32:265-273, JAN 12 2016
abstract, full text, DOI:10.1021/acs.langmuir.5b03601

Zielinska, Joanna; Wieczor, Milosz; Baczek, Tomasz; Gruszecki, Marcin; Czub, Jacek
Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
SCIENTIFIC REPORTS, 6 Art. No. 19109, JAN 8 2016
abstract, full text, DOI:10.1038/srep19109

Krzeminska, A.; Swiderek, K. P.; Paneth, P.
Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:310-317, JAN 7 2016
abstract, full text, DOI:10.1039/c5cp06050h

Au, Loretta; Green, David F.
Direct Calculation of Protein Fitness Landscapes through Computational Protein Design
BIOPHYSICAL JOURNAL, 110:75-84, JAN 5 2016
abstract, full text, DOI:10.1016/j.bpj.2015.11.029

Juvonen, Risto O.; Kuusisto, Mira; Fohrgrup, Carolin; Pitkanen, Mari H.; Nevalainen, Tapio J.; Auriola, Seppo; Raunio, Hannu; Pasanen, Markku; Pentikainen, Olli T.
Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes
XENOBIOTICA, 46:14-24, JAN 2 2016
abstract, full text, DOI:10.3109/00498254.2015.1048327

Haq, Imran; Irving, James A.; Saleh, Aarash D.; Dron, Louis; Regan-Mochrie, Gemma L.; Motamedi-Shad, Neda; Hurst, John R.; Gooptu, Bibek; Lomas, David A.
Deficiency Mutations of Alpha-1 Antitrypsin Effects on Folding, Function, and Polymerization
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, 54:71-80, JAN 2016
abstract, full text, DOI:10.1165/rcmb.2015-0154OC

Ljubetic, A.; Drobnak, I.; Gradisar, H.; Jerala, R.
Designing the structure and folding pathway of modular topological bionanostructures
CHEMICAL COMMUNICATIONS, 52:5220-5229, 2016
abstract, full text, DOI:10.1039/c6cc00421k

Nevidimov, A. V.; Razumov, V. F.
Computer Simulation of Ligand Shells of Colloidal Cadmium Selenide Quantum Dots
COLLOID JOURNAL, 78:83-89, JAN 2016
abstract, full text, DOI:10.1134/S1061933X16010129

Karandur, D.; Pettitt, B. M.
The contribution of electrostatic interactions to the collapse of oligoglycine in water
CONDENSED MATTER PHYSICS, 19 Art. No. 23802, 2016
abstract, full text, DOI:10.5488/CMP.19.23802

Brasili, Davide; Watly, Joanna; Simonovsky, Eyal; Guerrini, Remo; Barbosa, Nuno A.; Wieczorek, Robert; Remelli, Maurizio; Kozlowski, Henryk; Miller, Yifat
The unusual metal ion binding ability of histidyl tags and their mutated derivatives
DALTON TRANSACTIONS, 45:5629-5639, 2016
abstract, full text, DOI:10.1039/c5dt04747a

Verma, Saroj; Pandey, Shashi; Agarwal, Pooja; Verma, Pravesh; Deshpande, Shreekant; Saxena, Jitendra Kumar; Srivastava, Kumkum; Chauhan, Prem M. S.; Prabhakar, Yenamandra S.
N-(7-Chloroquinolinyl-4-aminoalkyl)arylsulfonamides as antimalarial agents: rationale for the activity with reference to inhibition of hemozoin formation
RSC ADVANCES, 6:25584-25593, 2016
abstract, full text, DOI:10.1039/c6ra00846a

Chatterjee, Prathit; Sengupta, Neelanjana
Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study
MOLECULAR BIOSYSTEMS, 12:1139-1150, 2016
abstract, full text, DOI:10.1039/c6mb00017g

Yang, Chao; Zhang, Shilei; Bai, Zhengya; Hou, Shasha; Wu, Di; Huang, Jian; Zhou, Peng
A two-step binding mechanism for the self-binding peptide recognition of target domains
MOLECULAR BIOSYSTEMS, 12:1201-1213, 2016
abstract, full text, DOI:10.1039/c5mb00800j

Han, Dan; Su, Min; Tan, Jianjun; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin
Structure-activity relationship and binding mode studies for a series of diketo-acids as HIV integrase inhibitors by 3D-QSAR, molecular docking and molecular dynamics simulations
RSC ADVANCES, 6:27594-27606, 2016
abstract, full text, DOI:10.1039/c6ra00713a

Garrido-Acosta, Osvaldo; Meza-Toledo, Sergio E.; Anguiano-Robledo, Liliana; Soriano-Ursua, Marvin A.; Correa-Basurto, Jose; Davood, Asghar; Chamorro-Cevallos, German
Anticonvulsant and Toxicological Evaluation of Parafluorinated/Chlorinated Derivatives of 3-Hydroxy-3-ethyl-3-phenylpropionamide
BIOMED RESEARCH INTERNATIONAL, Art. No. 3978010, 2016
abstract, full text, DOI:10.1155/2016/3978010

Yu, Alvin; Wied, Tyler; Belcher, John; Lau, Albert Y.
Computing Conformational Free Energies of iGluR Ligand-Binding Domains
IONOTROPIC GLUTAMATE RECEPTOR TECHNOLOGIES, 119-132, 2016
abstract, full text, DOI:10.1007/978-1-4939-2812-5_9

Xu, Lei; Li, Dan; Tao, Li; Yang, Yanling; Li, Youyong; Hou, Tingjun
Binding mechanisms of 1,4-dihydropyridine derivatives to L-type calcium channel Ca(v)1.2: a molecular modeling study
MOLECULAR BIOSYSTEMS, 12:379-390, 2016
abstract, full text, DOI:10.1039/c5mb00781j

Sikdar, Samapan; Chakrabarti, J.; Ghosh, Mahua
Conformational thermodynamics guided structural reconstruction of biomolecular fragments
MOLECULAR BIOSYSTEMS, 12:444-453, 2016
abstract, full text, DOI:10.1039/c5mb00529a

Espinoza-Fonseca, L. Michel
Pathogenic mutation R959W alters recognition dynamics of dysferlin inner DysF domain
MOLECULAR BIOSYSTEMS, 12:973-981, 2016
abstract, full text, DOI:10.1039/c5mb00772k

Jang, Hyunbum; Arce, Fernando Teran; Lee, Joon; Gillman, Alan L.; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels
PROTEIN AMYLOID AGGREGATION: METHODS AND PROTOCOLS, 1345:251-268, 2016
abstract, full text, DOI:10.1007/978-1-4939-2978-8_16

Jo, Sunhwan; Qi, Yifei; Im, Wonpil
Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins
GLYCOBIOLOGY, 26:19-29, JAN 2016
abstract, full text, DOI:10.1093/glycob/cwv083

Luan, Binquan; Tien Huynh; Zhou, Ruhong
Complete wetting of graphene by biological lipids
NANOSCALE, 8:5750-5754, 2016
abstract, full text, DOI:10.1039/c6nr00202a

Gupta, Prashant Kumar; Meuwly, Markus
Ligand and interfacial dynamics in a homodimeric hemoglobin
STRUCTURAL DYNAMICS, 3 Art. No. 012003, JAN 2016
abstract, full text, DOI:10.1063/1.4940228

Baskin, Artem; Kral, Petr
Hybrid Modeling of Molecular Sensing and Catalysis in Low-dimensional Nanomaterials
MATERIALS TODAY-PROCEEDINGS, 3:396-410, 2016
abstract, full text, DOI:10.1016/j.matpr.2016.01.027

Moreira, Ines P.; Sasselli, Ivan Ramos; Cannon, Daniel A.; Hughes, Meghan; Lamprou, Dimitrios A.; Tuttle, Tell; Ulijn, Rein V.
Enzymatically activated emulsions stabilised by interfacial nanofibre networks
SOFT MATTER, 12:2623-2631, 2016
abstract, full text, DOI:10.1039/c5sm02730f

Russ, K. A.; Elvati, P.; Parsonage, T. L.; Dews, A.; Jarvis, J. A.; Ray, M.; Schneider, B.; Smith, P. J. S.; Williamson, P. T. F.; Violi, A.; Philbert, M. A.
C-60 fullerene localization and membrane interactions in RAW 264.7 immortalized mouse macrophages
NANOSCALE, 8:4134-4144, 2016
abstract, full text, DOI:10.1039/c5nr07003a

Zhao, Lina; Zhai, Jiao; Zhang, Xuejie; Gao, Xueyun; Fang, Xiaohong; Li, Jingyuan
Computational design of peptide-Au cluster probe for sensitive detection of alpha(IIb)beta(3) integrin
NANOSCALE, 8:4203-4208, 2016
abstract, full text, DOI:10.1039/c5nr09175f

St-Jacques, Antony D.; Rachel, Natalie M.; Curry, Dan R.; Gillett, Steve M. F. G.; Clouthier, Christopher M.; Keillor, Jeffrey W.; Pelletier, Joelle N.; Chica, Roberto A.
Specificity of transglutaminase-catalyzed peptide synthesis
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 123:53-61, JAN 2016
abstract, full text, DOI:10.1016/j.molcatb.2015.11.009

Pino-Angeles, Almudena; Leveritt, John M., I.I.I.; Lazaridis, Themis
Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family
PLOS COMPUTATIONAL BIOLOGY, 12 Art. No. e1004570, JAN 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004570

Van Ngo; Wang, Yibo; Haas, Stephan; Noskov, Sergei Y.; Farley, Robert A.
K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na-v Channels
PLOS COMPUTATIONAL BIOLOGY, 12 Art. No. e1004482, JAN 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004482

Karandur, Deepti; Harris, Robert C.; Pettitt, B. Montgomery
Protein collapse driven against solvation free energy without H-bonds
PROTEIN SCIENCE, 25:103-110, JAN 2016
abstract, full text, DOI:10.1002/pro.2749

Hua, Duy P.; Huang, He; Roy, Amitava; Post, Carol Beth
Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents
PROTEIN SCIENCE, 25:204-218, JAN 2016
abstract, full text, DOI:10.1002/pro.2753

Timucin, Emel; Cousido-Siah, Alexandra; Mitschler, Andre; Podjarny, Alberto; Sezerman, Osman Ugur
Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:129-142, JAN 2016
abstract, full text, DOI:10.1002/prot.24961

Dhakal, Soma; Adendorff, Matthew R.; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G.
Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis
NANOSCALE, 8:3125-3137, 2016
abstract, full text, DOI:10.1039/c5nr07263h

Lehtonen, Soili I.; Tullila, Antti; Agrawal, Nitin; Kukkurainen, Sampo; Kahkonen, Niklas; Koskinen, Masi; Nevanen, Tarja K.; Johnson, Mark S.; Airenne, Tomi T.; Kulomaa, Markku S.; Riihimaki, Tiina A.; Hytonen, Vesa P.
Artificial Avidin-Based Receptors for a Panel of Small Molecules
ACS CHEMICAL BIOLOGY, 11:211-221, JAN 2016
abstract, full text, DOI:10.1021/acschembio.5b00906

Atsmon-Raz, Yoav; Miller, Yifat
Non-Amyloid-beta Component of Human alpha-Synuclein Oligomers Induces Formation of New A beta Oligomers: Insight into the Mechanisms That Link Parkinson's and Alzheimer's Diseases
ACS CHEMICAL NEUROSCIENCE, 7:46-55, JAN 2016
abstract, full text, DOI:10.1021/acs.chemneuro.5b00204

Wilkens, Casper; Auger, Kyle D.; Anderson, Nolan T.; Meekins, David A.; Raththagala, Madushi; Abou Hachem, Maher; Payne, Christina M.; Gentry, Matthew S.; Svensson, Birte
Plant -glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose
FEBS LETTERS, 590:118-128, JAN 2016
abstract, full text, DOI:10.1002/1873-3468.12027

Autzen, Henriette Elisabeth; Musgaard, Maria
MD Simulations of P-Type ATPases in a Lipid Bilayer System
P-TYPE ATPASES: METHODS AND PROTOCOLS, 1377:459-492, 2016
abstract, full text, DOI:10.1007/978-1-4939-3179-8_40

Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 20, JAN 2016
abstract, full text, DOI:10.1007/s00894-015-2881-0

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.
Effect of nano structures on the nucleus wetting modes during water vapour condensation: from individual groove to nano-array surface
RSC ADVANCES, 6:7923-7932, 2016
abstract, full text, DOI:10.1039/c5ra23836f

Chaves, Silvina; Pera, Licia M.; Luis Avila, Cesar; Romero, Cintia M.; Baigori, Mario; Moran Vieyra, F. Eduardo; Borsarelli, Claudio D.; Chehin, Rosana N.
Towards efficient biocatalysts: photo-immobilization of a lipase on novel lysozyme amyloid-like nanofibrils
RSC ADVANCES, 6:8528-8538, 2016
abstract, full text, DOI:10.1039/c5ra19590j

Luan, Binquan; Huynh, Tien; Li, Jingyuan; Zhout, Ruhong
Nanomechanics of Protein Unfolding Outside a Generic Nanopore
ACS NANO, 10:317-323, JAN 2016
abstract, full text, DOI:10.1021/acsnano.5b04557

Dequidt, Alain; Devemy, Julien; Padua, Agilio A. H.
Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:260-268, JAN 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00612

Zhang, Qi-Lin; Yang, Rong-Yao; Jiang, Wei-Zhou; Huang, Zi-Qian
Fast water channeling across carbon nanotubes in far infrared terahertz electric fields
NANOSCALE, 8:1886-1891, 2016
abstract, full text, DOI:10.1039/c5nr07281f

Bagci, Eyup; Aydin, Emel; Mihasan, Marius; Maniu, Calin; Hritcu, Lucian
Anxiolytic and antidepressant-like effects of Ferulago angulata essential oil in the scopolamine rat model of Alzheimer's disease
FLAVOUR AND FRAGRANCE JOURNAL, 31:70-80, JAN 2016
abstract, full text, DOI:10.1002/ffj.3289

Chan, Chun; Wen, Haohua; Lu, Lanyuan; Fan, Jun
Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins
CHINESE PHYSICS B, 25 Art. No. 018707, JAN 2016
abstract, full text, DOI:10.1088/1674-1056/25/1/018707

Kotar, Anita; Tomasic, Tihomir; Zivkovic, Martina Lenarcic; Jug, Gregor; Plavec, Janez; Anderluh, Marko
STD NMR and molecular modelling insights into interaction of novel mannose-based ligands with DC-SIGN
ORGANIC & BIOMOLECULAR CHEMISTRY, 14:862-875, 2016
abstract, full text, DOI:10.1039/c5ob01916h

Borreguero, Jose M.; Lynch, Vickie E.
Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:9-17, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00878

Sedeh, Reza Sharifi; Pan, Keyao; Adendorff, Matthew Ralph; Hallatschek, Oskar; Bathe, Klaus-Juergen; Bathe, Mark
Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:261-273, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00965

Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L., I.I.I.; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:405-413, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00935

Yoo, Jejoong; Aksimentiev, Aleksei
Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:430-443, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00967

Cosenza, Chiara; Lettera, Vincenzo; Causa, Filippo; Scognamiglio, Pasqualina Liana; Battista, Edmondo; Netti, Paolo Antonio
Cell mechanosensory recognizes ligand compliance at biomaterial interface
BIOMATERIALS, 76:282-291, JAN 2016
abstract, full text, DOI:10.1016/j.biomaterials.2015.10.068

Huang, Zi-Qian; Yang, Rong-Yao; Jiang, Wei-Zhou; Zhang, Qi-Lin
Heating of Nanosized Liquid Water in High-Intensity Terahertz Pulses
CHINESE PHYSICS LETTERS, 33 Art. No. 013101, JAN 2016
abstract, full text, DOI:10.1088/0256-307X/33/1/013101

Yu, Xiaofeng; Nandekar, Prajwal; Mustafa, Ghulam; Cojocaru, Vlad; Lepesheva, Galina I.; Wade, Rebecca C.
Ligand tunnels in T-brucei and human CYP51: Insights for parasite-specific drug design
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1860:67-78, JAN 2016
abstract, full text, DOI:10.1016/j.bbagen.2015.10.015

Schadzek, Patrik; Schlingmann, Barbara; Schaarschmidt, Frank; Lindner, Julia; Koval, Michael; Heisterkamp, Alexander; Preller, Matthias; Ngezahayo, Anaclet
The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:57-66, JAN 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.10.001

Morrison, Lindsay J.; Brodbelt, Jennifer S.
Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry
ANALYST, 141:166-176, 2016
abstract, full text, DOI:10.1039/c5an01819f

Liu, Peng; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
The true nature of rotary movements in rotaxanes
CHEMICAL SCIENCE, 7:457-462, 2016
abstract, full text, DOI:10.1039/c5sc03022f

Bergmann, Myriam; Michaud, Gaelle; Visini, Ricardo; Jin, Xian; Gillon, Emilie; Stocker, Achim; Imberty, Anne; Darbre, Tamis; Reymond, Jean-Louis
Multivalency effects on Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA
ORGANIC & BIOMOLECULAR CHEMISTRY, 14:138-148, 2016
abstract, full text, DOI:10.1039/c5ob01682g

Korchowiec, Beata; Gorczyca, Marcelina; Rogalska, Ewa; Regnouf-de-Vains, Jean-Bernard; Mourer, Maxime; Korchowiec, Jacek
The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies
SOFT MATTER, 12:181-190, 2016
abstract, full text, DOI:10.1039/c5sm01891a

Shahbaaz, Mohd.; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md. Imtaiyaz
Current Advances in the Identification and Characterization of Putative Drug and Vaccine Targets in the Bacterial Genomes
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 16:1040-1069, 2016
abstract, full text, DOI:10.2174/1568026615666150825143307

Hosek, Petr; Spiwok, Vojtech
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
COMPUTER PHYSICS COMMUNICATIONS, 198:222-229, JAN 2016
abstract, full text, DOI:10.1016/j.cpc.2015.08.037

Picaud, Fabien; Boukari, Khaoula; Balme, Sebastien; Janot, Jean Marc; Henn, Francois
Selectivity against proton in cation permeable hybrid solid state membrane
COMPUTATIONAL MATERIALS SCIENCE, 111:380-386, JAN 2016
abstract, full text, DOI:10.1016/j.commatsci.2015.09.044

Harrach, Michael F.; Drossel, Barbara; Winschel, Wadim; Gutmann, Torsten; Buntkowsky, Gerd
Mixtures of Isobutyric Acid and Water Confined in Cylindrical Silica Nanopores Revisited: A Combined Solid-State NMR and Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:28961-28969, DEC 31 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b09537

Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe
Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2
PLOS ONE, 10 Art. No. e0145758, DEC 30 2015
abstract, full text, DOI:10.1371/journal.pone.0145758

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet
Energy landscape of LeuT from molecular simulations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243134, DEC 28 2015
abstract, full text, DOI:10.1063/1.4936133

MacDermaid, Christopher M.; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.; Klein, Michael L.; Fiorin, Giacomo
Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes
JOURNAL OF CHEMICAL PHYSICS, 143, DEC 28 2015
abstract, full text, DOI:10.1063/1.4937153

Wei, Zonghui; Luijten, Erik
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243146, DEC 28 2015
abstract, full text, DOI:10.1063/1.4937384

Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
Transient beta-hairpin formation in alpha-synuclein monomer revealed by coarse-grained molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243142, DEC 28 2015
abstract, full text, TCBG publications, DOI:10.1063/1.4936910

Gorham, Ronald D., Jr.; Nunez, Vicente; Lin, Jung-Hsin; Rooijakkers, Suzan H. M.; Vullev, Valentine I.; Morikis, Dirnitrios
Discovery of Small Molecules for Fluorescent Detection of Complement Activation Product C3d
JOURNAL OF MEDICINAL CHEMISTRY, 58:9535-9545, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b01062

Palese, Luigi L.
Correlation Analysis of Trp-Cage Dynamics in Folded and Unfolded States
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15568-15573, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09678

Lemkul, Justin A.; Huang, Jing; MacKerell, Alexander D., Jr.
Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid beta-Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15574-15582, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09978

Song, Yang; Nelp, Micah T.; Bandarian, Vahe; Wysocki, Vicki H.
Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information
ACS CENTRAL SCIENCE, 1:477-487, DEC 23 2015
abstract, full text, DOI:10.1021/acscentsci.5b00251

Nickels, Jonathan D.; Cheng, Xiaolin; Mostofian, Barmak; Stanley, Christopher; Lindner, Benjamin; Heberle, Frederick A.; Perticaroli, Stefania; Feirgenson, Mikhail; Egami, Takeshi; Standaert, Robert F.; Smith, Jeremy C.; Myles, Dean A. A.; Ohl, Michael; Katsaras, John
Mechanical Properties of Nanoscopic Lipid Domains
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:15772-15780, DEC 23 2015
abstract, full text, DOI:10.1021/jacs.5b08894

Sjulstok, Emil; Olsen, Jogvan Magnus Haugaard; Solov'yov, Ilia A.
Quantifying electron transfer reactions in biological systems: what interactions play the major role?
SCIENTIFIC REPORTS, 5 Art. No. 18446, DEC 22 2015
abstract, full text, DOI:10.1038/srep18446

Basu, Ipsita; Manna, Moutusi; Mukhopadhyay, Chaitali
Insights into the behavioral difference of water in the presence of GM1
FEBS LETTERS, 589:3887-3892, DEC 21 2015
abstract, full text, DOI:10.1016/j.febslet.2015.11.014

Simonin, Alexandre; Montalbetti, Nicolas; Gyimesi, Gergely; Pujol-Gimenez, Jonai; Hediger, Matthias A.
The Hydroxyl Side Chain of a Highly Conserved Serine Residue Is Required for Cation Selectivity and Substrate Transport in the Glial Glutamate Transporter GLT-1/SLC1A2
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:30464-30474, DEC 18 2015
abstract, full text, DOI:10.1074/jbc.M115.689836

Niu, Yuzhen; Pan, Dabo; Shi, Danfeng; Bai, Qifeng; Liu, Huanxiang; Yao, Xiaojun
Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations
PLOS ONE, 10 Art. No. e0145219, DEC 17 2015
abstract, full text, DOI:10.1371/journal.pone.0145219

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Thompson, D.; Saywell, A.; Mangham, B.; Champness, N. R.; Larsson, J. A.; Moriarty, P.
Physisorption Controls the Conformation and Density of States of an Adsorbed Porphyrin
JOURNAL OF PHYSICAL CHEMISTRY C, 119:27982-27994, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b08350

Walters, Peter L.; Makri, Nancy
Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:4959-4965, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b02265

Batista, Mariana R. B.; Martinez, Leandro
Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPAR gamma and Functional Implications
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15418-15429, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09824

Wang, Jianping; Yang, Fan; Zhao, Juan
Selectively Probing the Structures and Dynamics of beta-Peptide Aggregates Using the Amide-A Vibrational Marker
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15451-15459, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b10249

Villarreal, Oscar D.; Chen, Liao Y.; Whetten, Robert L.; Demeler, Borries
Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15502-15508, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09864

Jin, Xiaojie; Bai, Qifeng; Xue, Weiwei; Liu, Huanxiang; Yao, Xiaojun
Computational study on the inhibition mechanism of a cyclic peptide MaD5 to PfMATE: Insight from molecular dynamics simulation, free energy calculation and dynamical network analysis
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 149:81-88, DEC 15 2015
abstract, full text, DOI:10.1016/j.chemolab.2015.10.013

Fields, James B.; Hollingsworth, Scott A.; Chreifi, Georges; Heyden, Matthias; Arce, Anton P.; Magana-Garcia, Hugo I.; Poulos, Thomas L.; Tobias, Douglas J.
"Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations
BIOCHEMISTRY, 54:7272-7282, DEC 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00569

Hamre, Anne Grethe; Jana, Suvamay; Reppert, Nicole K.; Payne, Christina M.; Sorlie, Morten
Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase
BIOCHEMISTRY, 54:7292-7306, DEC 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00830

Chavan, Tanmay S.; Jang, Hyunbum; Khavrutskii, Lyuba; Abraham, Sherwin J.; Banerjee, Avik; Freed, Benjamin C.; Johannessen, Liv; Tarasov, Sergey G.; Gaponenko, Vadim; Nussinov, Ruth; Tarasova, Nadya I.
High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site
BIOPHYSICAL JOURNAL, 109:2602-2613, DEC 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.09.034

Chen, Cong; Zhang, Ning; Li, Weizhong; Song, Yongchen
Water Contact Angle Dependence with Hydroxyl Functional Groups on Silica Surfaces under CO2 Sequestration Conditions
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 49:14680-14687, DEC 15 2015
abstract, full text, DOI:10.1021/acs.est.5b03646

Agullo, Luis; Malhotra, Sunny; Fissolo, Nicolas; Montalban, Xavier; Comabella, Manuel
Molecular dynamics and intracellular signaling of the TNF-R1 with the R92Q mutation
JOURNAL OF NEUROIMMUNOLOGY, 289:12-20, DEC 15 2015
abstract, full text, DOI:10.1016/j.jneuroim.2015.10.003

Kolyadko, Vladimir N.; Lushchekina, Sofya V.; Vuimo, Tatiana A.; Surov, Stepan S.; Ovsepyan, Ruzanna A.; Korneeva, Vera A.; Vorobiev, Ivan I.; Orlova, Nadezhda A.; Minakhin, Leonid; Kuznedelov, Konstantin; Severinov, Konstantin V.; Ataullakhanov, Fazoil I.; Panteleev, Mikhail A.
New Infestin-4 Mutants with Increased Selectivity against Factor XIIa
PLOS ONE, 10 Art. No. e0144940, DEC 15 2015
abstract, full text, DOI:10.1371/journal.pone.0144940

Czajkowsky, Daniel M.; Sun, Jielin; Shen, Yi; Shao, Zhifeng
Single molecule compression reveals intra-protein forces drive cytotoxin pore formation
ELIFE, 4 Art. No. e08421, DEC 10 2015
abstract, full text, DOI:10.7554/eLife.08421

Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F. J.; Javanainen, Matti; Kanduc, Matej; Kulig, Waldemar; Lamber, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S.; Monticelli, Luca; Maatta, Jukka; Ollila, O. H. Samuli; Retegan, Marius; Rog, Tomasz; Santuz, Hubert; Tynkkynen, Joona
Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15075-15088, DEC 10 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04878

Simakov, Nikolay A.; White, Joseph P.; DeLeon, Robert L.; Ghadersohi, Amin; Furlani, Thomas R.; Jones, Matthew D.; Gallo, Steven M.; Patra, Abani K.
Application kernels: HPC resources performance monitoring and variance analysis
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 27:5238-5260, DEC 10 2015
abstract, full text, DOI:10.1002/cpe.3564

Koehler, Stephan; Schmid, Friederike; Settanni, Giovanni
Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces
LANGMUIR, 31:13180-13190, DEC 8 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b03371

Mori, Yoshiharu; Okumura, Hisashi
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2344-2349, DEC 5 2015
abstract, full text, DOI:10.1002/jcc.24213

Chen, Po-Han; Unger, Vinzenz; He, Xiaolin
Structure of Full-Length Human PDGFR beta Bound to Its Activating Ligand PDGF-B as Determined by Negative-Stain Electron Microscopy
JOURNAL OF MOLECULAR BIOLOGY, 427:3921-3934, DEC 4 2015
abstract, full text, DOI:10.1016/j.jmb.2015.10.003

Navarrete, Karen R.; Alderete, Joel B.; Jimenez, Veronica A.
Structural basis for drug resistance conferred by beta-tubulin mutations: a molecular modeling study on native and mutated tubulin complexes with epothilone B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:2530-2540, DEC 2 2015
abstract, full text, DOI:10.1080/07391102.2015.1063455

Hannan, Abdul; Abraham, Neethu Maria; Goyal, Siddharth; Jamir, Imlitoshi; Priyakumar, U. Deva; Mishra, Krishnaveni
Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast
NUCLEIC ACIDS RESEARCH, 43:10213-10226, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv842

Yang, Darren; Boyer, Benjamin; Prevost, Chantal; Danilowicz, Claudia; Prentiss, Mara
Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure
NUCLEIC ACIDS RESEARCH, 43:10251-10263, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv883

Sun, Ming; Li, Wen; Blomqvist, Karin; Das, Sanchaita; Hashem, Yaser; Dvorin, Jeffrey D.; Frank, Joachim
Dynamical features of the Plasmodium falciparum ribosome during translation
NUCLEIC ACIDS RESEARCH, 43:10515-10524, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv991

Papaioannou, Anastasios; Kuyucak, Serdar; Kuncic, Zdenka
Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding
PLOS ONE, 10 Art. No. e0144058, DEC 2 2015
abstract, full text, DOI:10.1371/journal.pone.0144058

Borisova, Anna S.; Eneyskaya, Elena V.; Bobrov, Kirill S.; Jana, Suvamay; Logachev, Anton; Polev, Dmitrii E.; Lapidus, Alla L.; Ibatullin, Farid M.; Saleem, Umair; Sandgren, Mats; Payne, Christina M.; Kulminskaya, Anna A.; Stahlberg, Jerry
Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from Geotrichum candidum 3C
FEBS JOURNAL, 282:4515-4537, DEC 2015
abstract, full text, DOI:10.1111/febs.13509

Ben Imeddourene, Akli; Elbahnsi, Ahmad; Gueroult, Marc; Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte
Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004631, DEC 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004631

Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; Kim, Jae In; Chang, Hyun Joon; Baek, Inchul; Eom, Kilho; Na, Sungsoo
Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations
PHYSICAL BIOLOGY, 12 Art. No. 066021, DEC 2015
abstract, full text, DOI:10.1088/1478-3975/12/6/066021

Wang, Lin; Li, Lin; Alexov, Emil
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:2186-2197, DEC 2015
abstract, full text, DOI:10.1002/prot.24935

Vass, Marton; Jojart, Balazs; Bogar, Ferenc; Paragi, Gabor; Keseru, Gyoergy M.; Tarcsay, Akos
Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:1137-1149, DEC 2015
abstract, full text, DOI:10.1007/s10822-015-9883-y

Sheng, Yinghong; Zhong, Linghao; Guo, Dahai; Lau, Gavin; Feng, Changjian
Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study
JOURNAL OF INORGANIC BIOCHEMISTRY, 153:186-196, DEC 2015
abstract, full text, DOI:10.1016/j.jinorgbio.2015.08.006

Loeffler, Hannes H.; Michel, Julien; Woods, Christopher
FESetup: Automating Setup for Alchemical Free Energy Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2485-2490, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00368

Bovigny, Christophe; Tamo, Giorgio; Lemmin, Thomas; Maino, Nicolas; Dal Peraro, Matteo
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2491-2499, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00501

Grazioso, Giovanni; Sgrignani, Jacopo; Capelli, Romina; Matera, Carlo; Dallanoce, Clelia; De Amici, Marco; Cavalli, Andrea
Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2528-2539, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00459

Ramakrishna, S.; Padhi, Siladitya; Priyakumar, U. Deva
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach
JOURNAL OF CHEMICAL SCIENCES, 127:2159-2169, DEC 2015
abstract, full text, DOI:10.1007/s12039-015-0982-z

Comer, Jeffrey; Chen, Ran; Poblete, Horacio; Vergara-Jaque, Ariela; Riviere, Jim E.
Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation
ACS NANO, 9:11761-11774, DEC 2015
abstract, full text, DOI:10.1021/acsnano.5b03592

Lapelosa, Mauro; Patapoff, Thomas W.; Zarraga, Isidro E.
Modeling of protein-anion exchange resin interaction for the human growth hormone charge variants
BIOPHYSICAL CHEMISTRY, 207:1-6, DEC 2015
abstract, full text, DOI:10.1016/j.bpc.2015.07.004

Binesh, A. R.; Kamali, R.
Molecular dynamics insights into human aquaporin 2 water channel
BIOPHYSICAL CHEMISTRY, 207:107-113, DEC 2015
abstract, full text, DOI:10.1016/j.bpc.2015.10.002

Perez-Gordones, M. C.; Serrano, M. L.; Rojas, H.; Martinez, J. C.; Uzcanga, G.; Mendoza, M.
Presence of a thapsigargin-sensitive calcium pump in Trypanosoma evansi: Immunological, physiological, molecular and structural evidences
EXPERIMENTAL PARASITOLOGY, 159:107-117, DEC 2015
abstract, full text, DOI:10.1016/j.exppara.2015.08.017

Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua
Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA)
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 153:380-390, DEC 2015
abstract, full text, DOI:10.1016/j.jphotobiol.2015.10.023

Darre, Leonardo; Domene, Carmen
Binding of Capsaicin to the TRPV1 Ion Channel
MOLECULAR PHARMACEUTICS, 12:4454-4465, DEC 2015
abstract, full text, DOI:10.1021/acs.molpharmaceut.5b00641

Das, Amit; Gerlits, Oksana; Parks, Jerry M.; Langan, Paul; Kovalevsky, Andrey; Heller, William T.
Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation
STRUCTURE, 23:2331-2340, DEC 1 2015
abstract, full text, DOI:10.1016/j.str.2015.10.005

Zhang Zidong; Zhang Jilong; Zheng Qingchuan; Kong Chuipeng; Li Zhengqiang; Zhang Hongxing; Ma Jianzhang
Theoretical Investigation on Binding Process of Allophanate to Allophanate Hydrolase
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:1023-1028, DEC 2015
abstract, full text, DOI:10.1007/s40242-015-5108-0

Kong, Ruirui; Yi, Fengshuang; Wen, Pushuai; Liu, Jianghong; Chen, Xiaoping; Ren, Jinqi; Li, Xiaofei; Shang, Yulong; Nie, Yongzhan; Wu, Kaichun; Fan, Daiming; Zhu, Li; Feng, Wei; Wu, Jane Y.
Myo9b is a key player in SLIT/ROBO-mediated lung tumor suppression
JOURNAL OF CLINICAL INVESTIGATION, 125:4407-4420, DEC 2015
abstract, full text, DOI:10.1172/JCI81673

Le, Sarah N.; Porebski, Benjamin T.; McCoey, Julia; Fodor, James; Riley, Blake; Godlewska, Marlena; Gora, Monika; Czarnocka, Barbara; Banga, J. Paul; Hoke, David E.; Kass, Itamar; Buckle, Ashley M.
Modelling of Thyroid Peroxidase Reveals Insights into Its Enzyme Function and Autoantigenicity
PLOS ONE, 10 Art. No. e0142615, DEC 1 2015
abstract, full text, DOI:10.1371/journal.pone.0142615

Pietra, Francesco
Uptake of Organohalide Pollutants, and Release of Partially Dehalogenated Products, by NpRdhA, a 'Base-Off' Cob(II)alamin-Dependent Reductive Dehalogenase from a Deep Sea Bacterium. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 12:1945-1953, DEC 2015
abstract, full text, DOI:10.1002/cbdv.201500195

Zobnina, V. G.; Chagovets, V. V.; Boryak, O. A.; Kosevich, M. V.
A mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers
JOURNAL OF ANALYTICAL CHEMISTRY, 70:1533-1541, DEC 2015
abstract, full text, DOI:10.1134/S1061934815130110

Qiu, Hu; Sarathy, Aditya; Leburton, Jean-Pierre; Schulten, Klaus
Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
NANO LETTERS, 15:8322-8330, DEC 2015
abstract, full text, TCBG publications, DOI:10.1021/acs.nanolett.5b03963

Stirnemann, Guillaume; Sterpone, Fabio
Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5573-5577, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00954

Dama, James F.; Hocky, Glen M.; Sun, Rui; Voth, Gregory A.
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5638-5650, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00907

Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.
Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5688-5695, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00606

Oehme, Daniel P.; Doblin, Monika S.; Wagner, John; Bacic, Antony; Downton, Matthew T.; Gidley, Michael J.
Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption
CELLULOSE, 22:3501-3520, DEC 2015
abstract, full text, DOI:10.1007/s10570-015-0778-9

Kamthania, Mohit; Sharma, D. K.
Screening and structure-based modeling of T-cell epitopes of Nipah virus proteome: an immunoinformatic approach for designing peptide-based vaccine
3 BIOTECH, 5:877-882, DEC 2015
abstract, full text, DOI:10.1007/s13205-015-0303-8

Liu, Xin; Li, Yajuan; Wen, Liangxue; Tao, Kun; Xiao, Qing; Cao, Weixi; Huang, Zhenglan; Gao, Miao; Li, Hui; Wang, Fang; Feng, Wenli
ABL SH3 mutant inhibits BCR-ABL activity and increases imatinib sensitivity by targeting RIN1 protein in CML cell
CANCER LETTERS, 369:222-228, DEC 1 2015
abstract, full text, DOI:10.1016/j.canlet.2015.08.017

Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas; Papadopoulos, Georgios E.
Detailed study of the dielectric function of a lysozyme solution studied with molecular dynamics simulations
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 44:599-611, DEC 2015
abstract, full text, DOI:10.1007/s00249-015-1052-7

Kolly, Gaelle S.; Mukherjee, Raju; Kilacskova, Emoeke; Abriata, Luciano A.; Raccaud, Mahe; Blasko, Jaroslav; Sala, Claudia; Dal Peraro, Matteo; Mikusova, Katarina; Cole, Stewart T.
GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
JOURNAL OF BACTERIOLOGY, 197:3686-3697, DEC 2015
abstract, full text, DOI:10.1128/JB.00628-15

Jo, Sunhwan; Jiang, Wei
A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations
COMPUTER PHYSICS COMMUNICATIONS, 197:304-311, DEC 2015
abstract, full text, DOI:10.1016/j.cpc.2015.08.030

Stetz, Gabrielle; Verkhivker, Gennady M.
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
PLOS ONE, 10 Art. No. e0143752, NOV 30 2015
abstract, full text, DOI:10.1371/journal.pone.0143752

Liang, Qiansheng; Anderson, Warren D.; Jones, Shelly T.; Souza, Caio S.; Hosoume, Juliana M.; Treptow, Werner; Covarrubias, Manuel
Positive Allosteric Modulation of Kv Channels by Sevoflurane: Insights into the Structural Basis of Inhaled Anesthetic Action
PLOS ONE, 10 Art. No. e0143363, NOV 24 2015
abstract, full text, DOI:10.1371/journal.pone.0143363

Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio
Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA
PLOS ONE, 10 Art. No. e0142774, NOV 24 2015
abstract, full text, DOI:10.1371/journal.pone.0142774

Nazaruk, Ewa; Miszta, Przemyslaw; Filipek, Slawomir; Gorecka, Ewa; Landau, Ehud M.; Bilewicz, Renata
Lyotropic Cubic Phases for Drug Delivery: Diffusion and Sustained Release from the Mesophase Evaluated by Electrochemical Methods
LANGMUIR, 31:12753-12761, NOV 24 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b03247

Simonov, Alexandr N.; Holien, Jessica K.; Yeung, Joyee Chun In; Nguyen, Ann D.; Corbin, C. Jo; Zheng, Jie; Kuznetsov, Vladimir L.; Auchus, Richard J.; Conley, Alan J.; Bond, Alan M.; Parker, Michael W.; Rodgers, Raymond J.; Martin, Lisandra L.
Mechanistic Scrutiny Identifies a Kinetic Role for Cytochrome b5 Regulation of Human Cytochrome P450c17 (CYP17A1, P450 17A1)
PLOS ONE, 10 Art. No. e0141252, NOV 20 2015
abstract, full text, DOI:10.1371/journal.pone.0141252

Cheng, Huaigang; Song, Huiping
Investigation of bio-removing metal ions from wastewater-a viewpoint of micro forces
DESALINATION AND WATER TREATMENT, 56:2118-2130, NOV 20 2015
abstract, full text, DOI:10.1080/19443994.2014.958764

Bravo-Rodriguez, Kenny; Klopries, Stephan; Koopmans, Kyra R. M.; Sundermann, Uschi; Yahiaoui, Samir; Arens, Julia; Kushnir, Susanna; Schulz, Frank; Sanchez-Garcia, Elsa
Substrate Flexibility of a Mutated Acyltransferase Domain and Implications for Polyketide Biosynthesis
CHEMISTRY & BIOLOGY, 22:1425-1430, NOV 19 2015
abstract, full text, DOI:10.1016/j.chembiol.2015.02.008

Sikdar, Samapan; Ghosh, Mahua; De Raychaudhury, Molly; Chakrabarti, J.
Quantum Chemical Studies on Stability and Chemical Activities in Calcium Ion Bound Calmodulin Loops
JOURNAL OF PHYSICAL CHEMISTRY B, 119:14652-14659, NOV 19 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09713

Heidary, Nina; Utesch, Tillmann; Zerball, Maximilian; Horch, Marius; Millo, Diego; Fritsch, Johannes; Lenz, Oliver; von Klitzing, Regine; Hildebrandt, Peter; Fischer, Anna; Mroginski, Maria Andrea; Zebger, Ingo
Orientation-Controlled Electrocatalytic Efficiency of an Adsorbed Oxygen-Tolerant Hydrogenase
PLOS ONE, 10 Art. No. e0143101, NOV 18 2015
abstract, full text, DOI:10.1371/journal.pone.0143101

Monje-Galvan, Viviana; Klauda, Jeffery B.
Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties
BIOCHEMISTRY, 54:6852-6861, NOV 17 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00718

Qi, Yifei; Cheng, Xi; Lee, Jumin; Vermaas, Josh V.; Pogorelov, Taras V.; Tajkhorshid, Emad; Park, Soohyung; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
BIOPHYSICAL JOURNAL, 109:2012-2022, NOV 17 2015
abstract, full text, DOI:10.1016/j.bpj.2015.10.008

Wu, Emilia L.; Qi, Yifei; Park, Soohyung; Mallajosyula, Sairam S.; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Im, Wonpil
Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein
BIOPHYSICAL JOURNAL, 109:2090-2100, NOV 17 2015
abstract, full text, DOI:10.1016/j.bpj.2015.10.009

Dai, Qian; Xu, Jia-Jia; Li, Hui-Ji; Yi, Hai-Bo
Ion association characteristics in MgCl2 and CaCl2 aqueous solutions: a density functional theory and molecular dynamics investigation
MOLECULAR PHYSICS, 113:3545-3558, NOV 17 2015
abstract, full text, DOI:10.1080/00268976.2015.1039618

Mancini, Daiana T.; Sen, Kakali; Barbatti, Mario; Thiel, Walter; Ramalho, Teodorico C.
Excited-State Proton Transfer Can Tune the Color of Protein Fluorescent Markers
CHEMPHYSCHEM, 16:3444-3449, NOV 16 2015
abstract, full text, DOI:10.1002/cphc.201500744

Rodrigues Abadio, Ana Karina; Kioshima, Erika Seki; Leroux, Vincent; Martins, Natalia Florencio; Maigret, Bernard; Soares Felipe, Maria Sueli
Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus
PLOS ONE, 10 Art. No. e0142926, NOV 16 2015
abstract, full text, DOI:10.1371/journal.pone.0142926

Joseph, Prem Raj B.; Mosier, Philip D.; Desai, Umesh R.; Rajarathnam, Krishna
Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions
BIOCHEMICAL JOURNAL, 472:121-133, NOV 15 2015
abstract, full text, DOI:10.1042/BJ20150059

Wang, Jianping; Yang, Fan; Shi, Jipei; Zhao, Juan
Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 185102, NOV 14 2015
abstract, full text, DOI:10.1063/1.4935579

Gambini, Luca; Rizzi, Luca; Pedretti, Alessandro; Taglialatela-Scafati, Orazio; Carucci, Mario; Pancotti, Andrea; Galli, Corinna; Read, Martin; Giurisato, Emanuele; Romeo, Sergio; Russo, Ilaria
Picomolar Inhibition of Plasmepsin V, an Essential Malaria Protease, Achieved Exploiting the Prime Region
PLOS ONE, 10 Art. No. e0142509, NOV 13 2015
abstract, full text, DOI:10.1371/journal.pone.0142509

Cheng, Yuanhua; Rao, Vijay; Tu, An-yue; Lindert, Steffen; Wang, Dan; Oxenford, Lucas; McCulloch, Andrew D.; McCammon, J. Andrew; Regnier, Michael
Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:27749-27766, NOV 13 2015
abstract, full text, DOI:10.1074/jbc.M115.683045

Meneksedag-Erol, Deniz; Bahadur, Remant K. C.; Tang, Tian; Uludag, Hasan
A Delicate Balance When Substituting a Small Hydrophobe onto Low Molecular Weight Polyethylenimine to Improve Its Nucleic Acid Delivery Efficiency
ACS APPLIED MATERIALS & INTERFACES, 7:24822-24832, NOV 11 2015
abstract, full text, DOI:10.1021/acsami.5b07929

Wang Shuangshuang; Liu Peng; Cai Wensheng; Shao Xueguang
Effect of Hydrophobicity of Threads on the Solvent-controlled Shuttling in Rotaxanes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:2211-2219, NOV 10 2015
abstract, full text, DOI:10.7503/cjcu20150620

Guo, Qing; He, Yufan; Lu, Peter
Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:13904-13909, NOV 10 2015
abstract, full text, DOI:10.1073/pnas.1506405112

Tadepalli, Sirimuvva; Kuang, Zhifeng; Jiang, Qisheng; Liu, Keng-Ku; Fisher, Marilee A.; Morrissey, Jeremiah J.; Kharasch, Evan D.; Slocik, Joseph M.; Naik, Rajesh R.; Singamaneni, Srikanth
Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices
Scientific Reports, 5 Art. No. 16206, NOV 10 2015
abstract, full text, DOI:10.1038/srep16206

Rydzewski, J.; Jakubowski, R.; Nowak, W.
Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 171103, NOV 7 2015
abstract, full text, DOI:10.1063/1.4935370

Chantreau, Vanessa; Taddese, Bruck; Munier, Mathilde; Gourdin, Louis; Henrion, Daniel; Rodien, Patrice; Chabbert, Marie
Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor
PLOS ONE, 10 Art. No. e0142250, NOV 6 2015
abstract, full text, DOI:10.1371/journal.pone.0142250

Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul
The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics
PLoS One, 10 Art. No. e0142173, NOV 6 2015
abstract, full text, DOI:10.1371/journal.pone.0142173

Xu Wei; Lan Zhong; Peng Ben-Li; Wen Rong-Fu; Ma Xue-Hu
Molecular dynamics simulation on the wetting characteristic of micro-droplet on surfaces with different free energies
ACTA PHYSICA SINICA, 64 Art. No. 216801, NOV 5 2015
abstract, full text, DOI:10.7498/aps.64.216801

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho
The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers
Journal of Physical Chemistry Letters, 6:4444-4450, NOV 5 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b02189

Grosch, Jason S.; Yang, Jing; Shen, Alice; Sereda, Yuriy V.; Ortoleva, Peter J.
Broad spectrum assessment of the epitope fluctuation-Immunogenicity hypothesis
VACCINE, 33:5945-5949, NOV 4 2015
abstract, full text, DOI:10.1016/j.vaccine.2015.06.111

Wan, Rongzheng; Wang, Chunlei; Lei, Xiaoling; Zhou, Guoquan; Fang, Haiping
Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns
PHYSICAL REVIEW LETTERS, 115 Art. No. 195901, NOV 4 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.195901

Cheng, Mary Hongying; Bahar, Ivet
Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter
STRUCTURE, 23:2171-2181, NOV 3 2015
abstract, full text, DOI:10.1016/j.str.2015.09.001

Li, Qufei; Shen, Rong; Treger, Jeremy S.; Wanderling, Sherry S.; Milewski, Wieslawa; Siwowska, Klaudia; Bezanilla, Francisco; Perozo, Eduardo
Resting state of the human proton channel dimer in a lipid bilayer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E5926-E5935, NOV 3 2015
abstract, full text, DOI:10.1073/pnas.1515043112

Gaidos, Gabriel; Panaitiu, Alexandra E.; Guo, Bingqian; Pellegrini, Maria; Mierke, Dale F.
Identification and Characterization of the Interaction Site between cFLIP(L) and Calmodulin
PLOS ONE, 10 Art. No. e0141692, NOV 3 2015
abstract, full text, DOI:10.1371/journal.pone.0141692

Chen, Qi; Luan, Zheng-Jiao; Yu, Hui-Lei; Cheng, Xiaolin; Xu, Jian-He
Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 62:319-324, NOV 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.10.015

Khakbaz, Pouyan; Klauda, Jeffery B.
Probing the importance of lipid diversity in cell membranes via molecular simulation
CHEMISTRY AND PHYSICS OF LIPIDS, 192:12-22, NOV 2015
abstract, full text, DOI:10.1016/j.chemphyslip.2015.08.003

Ballut, Lionel; Violot, Sebastien; Shivakumaraswamy, Santosh; Thota, Lakshmi Prasoona; Sathya, Manu; Kunala, Jyothirmai; Dijkstra, Bauke W.; Terreux, Raphael; Haser, Richard; Balaram, Hemalatha; Aghajari, Nushin
Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation
NATURE COMMUNICATIONS, 6 Art. No. 8930, NOV 2015
abstract, full text, DOI:10.1038/ncomms9930

Khelashvili, George; Stanley, Nathaniel; Sahai, Michelle A.; Medina, Jaime; LeVine, Michael V.; Shi, Lei; De Fabritiis, Gianni; Weinstein, Harel
Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus
ACS CHEMICAL NEUROSCIENCE, 6:1825-1837, NOV 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00179

Knapp, Bernhard; Demharter, Samuel; Esmaielbeiki, Reyhaneh; Deane, Charlotte M.
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations
BRIEFINGS IN BIOINFORMATICS, 16:1035-1044, NOV 2015
abstract, full text, DOI:10.1093/bib/bbv005

Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria J.; Alberto, Roger; Santos, Isabel; Correia, Joao D. G.
Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme
CHEMICAL BIOLOGY & DRUG DESIGN, 86:1072-1086, NOV 2015
abstract, full text, DOI:10.1111/cbdd.12575

Debnath, Utsab; Verma, Saroj; Singh, Pankaj; Rawat, Kavita; Gupta, Satish K.; Tripathi, Raj K.; Siddiqui, Hefazat H.; Katti, Seturam B.; Prabhakar, Yenamandra S.
Synthesis, Biological Evaluation and Molecular Modeling Studies of New 2,3-Diheteroaryl Thiazolidin-4-Ones as NNRTIs
CHEMICAL BIOLOGY & DRUG DESIGN, 86:1285-1291, NOV 2015
abstract, full text, DOI:10.1111/cbdd.12591

Pang, Chun-Li; Yuan, Hong-Bo; Cao, Tian-Guang; Su, Ji-Guo; Chen, Ya-Fei; Liu, Hui; Yu, Hui; Zhang, Hai-Ling; Zhan, Yong; An, Hai-Long; Han, Yue-Bin
Molecular simulation assisted identification of Ca2+ binding residues in TMEM16A
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:1035-1043, NOV 2015
abstract, full text, DOI:10.1007/s10822-015-9876-x

Santos, Lucianna Helene; Ferreira, Rafaela Salgado; Caffarena, Ernesto Raul
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors
MEMORIAS DO INSTITUTO OSWALDO CRUZ, 110:847-864, NOV 2015
abstract, full text, DOI:10.1590/0074-02760150239

Manocheewa, Siriphan; Mittler, John E.; Samudrala, Ram; Mullins, James I.
Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development
VIRUSES-BASEL, 7:5718-5735, NOV 2015
abstract, full text, DOI:10.3390/v7112901

Peng, Yunhui; Suryadi, Jimmy; Yang, Ye; Kucukkal, Tugba G.; Cao, Weiguo; Alexov, Emil
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:27270-27287, NOV 2015
abstract, full text, DOI:10.3390/ijms161126022

Sanchez-Moreno, Israel; Bordes, Isabel; Castillo, Raquel; Javier Ruiz-Perina, Jose; Moliner, Vicent; Garcia-Junceda, Eduardo
Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:27835-27849, NOV 2015
abstract, full text, DOI:10.3390/ijms161126073

Banerjee, Avik; Dasgupta, Subrata; Mukhopadhyay, Bishnu P.; Sekar, Kanagaraj
The putative role of some conserved water molecules in the structure and function of human transthyretin
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:2248-2266, NOV 2015
abstract, full text, DOI:10.1107/S1399004715016004

Galiano, Vicente; Villalain, Jose
Oleuropein aglycone in lipid bilayer membranes. A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2849-2858, NOV 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.08.007

Martin, Lisandra L.; Holien, Jessica K.; Mizrachi, Dario; Corbin, C. Jo; Conley, Alan J.; Parker, Michael W.; Rodgers, Raymond J.
Evolutionary comparisons predict that dimerization of human cytochrome P450 aromatase increases its enzymatic activity and efficiency
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY, 154:294-301, NOV 2015
abstract, full text, DOI:10.1016/j.jsbmb.2015.09.006

Kappel, Kalli; Miao, Yinglong; McCammon, J. Andrew
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
QUARTERLY REVIEWS OF BIOPHYSICS, 48:479-487, NOV 2015
abstract, full text, DOI:10.1017/S0033583515000153

Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P.; Dekker, Cees; Aksimentiev, Aleksei
Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA
ACS NANO, 9:10598-10611, NOV 2015
abstract, full text, DOI:10.1021/acsnano.5b04173

Misra, Santosh K.; Ghoshal, Goutam; Gartia, Manas R.; Wu, Zhe; De, Arun K.; Ye, Mao; Bromfield, Corinne R.; Williams, Emery M.; Singh, Kuldeep; Tangella, Krishnarao V.; Rund, Laurie; Schulten, Klaus; Schook, Lawrence B.; Ray, Partha S.; Burdette, Everette C.; Pan, Dipanjan
Trimodal Therapy: Combining Hyperthermia with Repurposed Bexarotene and Ultrasound for Treating Liver Cancer
ACS NANO, 9:10695-10718, NOV 2015
abstract, full text, TCBG publications, DOI:10.1021/acsnano.5b05974

Pietropaolo, Adriana; D'Urso, Alessandro; Purrello, Roberto; Berova, Nina
Effect of Different Z-Inducers on the Stabilization of Z Portion in BZ-DNA Sequence: Correlation Between Experimental and Simulation Data
CHIRALITY, 27:773-778, NOV 2015
abstract, full text, DOI:10.1002/chir.22502

Johnson, Matthew C.; Tatum, Kelsey B.; Lynn, Jason S.; Brewer, Tess E.; Lu, Stephen; Washburn, Brian K.; Stroupe, M. Elizabeth; Jones, Kathryn M.
Sinorhizobium meliloti Phage Phi M9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid
JOURNAL OF VIROLOGY, 89:10945-10958, NOV 2015
abstract, full text, DOI:10.1128/JVI.01353-15

Zhou, Hao; Li, Shangyang; Badger, John; Nalivaika, Ellen; Cai, Yufeng; Foulkes-Murzycki, Jennifer; Schiffer, Celia; Makowski, Lee
Modulation of HIV protease flexibility by the T80N mutation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1929-1939, NOV 2015
abstract, full text, DOI:10.1002/prot.24737

Ozbaykal, Gizem; Atilgan, Ali Rana; Atilgan, Canan
In silico mutational studies of Hsp70 disclose sites with distinct functional attributes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:2077-2090, NOV 2015
abstract, full text, DOI:10.1002/prot.24925

Scherer, Martin K.; Trendelkamp-Schroer, Benjamin; Paul, Fabian; Perez-Hernandez, Guillermo; Hoffmann, Moritz; Plattner, Nuria; Wehmeyer, Christoph; Prinz, Jan-Hendrik; Noe, Frank
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5525-5542, NOV 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00743

Luo, Jinping; Liu, Lijun; Su, Peng; Duan, Pengbo; Lu, Daihui
A piecewise lookup table for calculating nonbonded pairwise atomic interactions
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 288, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2833-8

Ramirez-Salinas, Gema L.; Garcia-Machorro, J.; Quiliano, Miguel; Zimic, Mirko; Briz, Veronica; Rojas-Hernandez, Saul; Correa-Basurto, J.
Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 292, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2835-6

Stanton, Richard A.; Nettles, James H.; Schinazi, Raymond F.
Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 282, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2826-7

Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; Durner, Ellis; Ott, Wolfgang; Bayer, Edward A.; Schulten, Klaus; Nash, Michael A.; Gaub, Hermann E.
Mapping Mechanical Force Propagation through Biomolecular Complexes
NANO LETTERS, 15:7370-7376, NOV 2015
abstract, full text, TCBG publications, DOI:10.1021/acs.nanolett.5b02727

Stegeman, John J.; Behrendt, Lars; Woodin, Bruce R.; Kubota, Akira; Lemaire, Benjamin; Pompon, Denis; Goldstone, Jared V.; Urban, Philippe
Functional characterization of zebrafish cytochrome P450 1 family proteins expressed in yeast
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:2340-2352, NOV 2015
abstract, full text, DOI:10.1016/j.bbagen.2015.07.010

Singh, Satya P.; Foley, John F.; Zhang, Hongwei H.; Hurt, Darrell E.; Richards, Jennifer L.; Smith, Craig S.; Liao, Fang; Farber, Joshua M.
Selectivity in the Use of G(i/o) Proteins Is Determined by the DRF Motif in CXCR6 and Is Cell-Type Specific
MOLECULAR PHARMACOLOGY, 88:894-910, NOV 2015
abstract, full text, DOI:10.1124/mol.115.099960

Adams, Bryn L.; Hurley, Margaret M.; Jahnke, Justin P.; Stratis-Cullum, Dimitra N.
Functional and Selective Bacterial Interfaces Using Cross-Scaffold Gold Binding Peptides
JOM, 67:2483-2493, NOV 2015
abstract, full text, DOI:10.1007/s11837-015-1662-7

Qian, Yi; Zhang, Jie; Hu, Qinglin; Xu, Ming; Chen, Yue; Hu, Guoqing; Zhao, Meirong; Liu, Sijin
Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status
BIOMATERIALS, 70:12-22, NOV 2015
abstract, full text, DOI:10.1016/j.biomaterials.2015.08.015

Li, Chun-Yang; Chen, Xiu-Lan; Shao, Xuan; Wei, Tian-Di; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Su, Hai-Nan; Song, Xiao-Yan; Shi, Mei; Zhou, Bai-Cheng; Zhang, Yu-Zhong
Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3
JOURNAL OF BACTERIOLOGY, 197:3378-3387, NOV 2015
abstract, full text, DOI:10.1128/JB.00542-15

Spiwok, Vojtech; Sucur, Zoran; Hosek, Petr
Enhanced sampling techniques in biomolecular simulations
BIOTECHNOLOGY ADVANCES, 33:1130-1140, NOV 1 2015
abstract, full text, DOI:10.1016/j.biotechadv.2014.11.011

Timucin, Ahmet Can; Bodur, Cagri; Basaga, Huveyda
SIRT1 contributes to aldose reductase expression through modulating NFAT5 under osmotic stress: In vitro and in silico insights
CELLULAR SIGNALLING, 27:2160-2172, NOV 2015
abstract, full text, DOI:10.1016/j.cellsig.2015.08.013

Ghodsi, Hossein; Darvish, Kurosh
Investigation of mechanisms of viscoelastic behavior of collagen molecule
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS, 51:194-204, NOV 2015
abstract, full text, DOI:10.1016/j.jmbbm.2015.07.015

Billesbolle, Christian B.; Kruger, Mie B.; Shi, Lei; Quick, Matthias; Li, Zheng; Stolzenberg, Sebastian; Kniazeff, Julie; Gotfryd, Kamil; Mortensen, Jonas S.; Javitch, Jonathan A.; Weinstein, Harel; Loland, Claus J.; Gether, Ulrik
Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:26725-26738, OCT 30 2015
abstract, full text, DOI:10.1074/jbc.M115.677658

Baratto, Maria Camilla; Sinicropi, Adalgisa; Linde, Dolores; Saez-Jimenez, Veronica; Sorace, Lorenzo; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Basosi, Riccardo; Pogni, Rebecca
Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13583-13592, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02961

Milanovsky, Georgy E.; Shuvalov, Vladimir A.; Semenov, Alexey Yu.; Cherepanov, Dmitry A.
Elastic Vibrations in the Photosynthetic Bacterial Reaction Center Coupled to the Primary Charge Separation: Implications from Molecular Dynamics Simulations and Stochastic Langevin Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13656-13667, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03036

Livada, Jovan; Martinie, Ryan J.; Dassama, Laura M. K.; Krebs, Carsten; Bollinger, J. Martin, Jr.; Silakov, Alexey
Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13777-13784, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04057

Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.
APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies
SCIENTIFIC REPORTS, 5 Art. No. 15648, OCT 27 2015
abstract, full text, DOI:10.1038/srep15648

Sena, Mohan Maruthi; Morrow, Christin P.; Kirkpatrick, R. James; Krishnan, Marimuthu
Supercritical Carbon Dioxide at Smectite Mineral-Water Interfaces: Molecular Dynamics and Adaptive Biasing Force Investigation of CO2/H2O Mixtures Nanoconfined in Na-Montmorillonite
CHEMISTRY OF MATERIALS, 27:6946-6959, OCT 27 2015
abstract, full text, DOI:10.1021/acs.chemmater.5b01855

Azamat, Jafar; Sardroodi, Jaber Jahanbin; Rastkar, Alireza
Molecular dynamics simulation of ion separation and water transport through boron nitride nanotubes
DESALINATION AND WATER TREATMENT, 56:1090-1098, OCT 23 2015
abstract, full text, DOI:10.1080/19443994.2014.944571

de Veer, Simon J.; Wang, Conan K.; Harris, Jonathan M.; Craik, David J.; Swedberg, Joakim E.
Improving the Selectivity of Engineered Protease Inhibitors: Optimizing the P2 Prime Residue Using a Versatile Cyclic Peptide Library
JOURNAL OF MEDICINAL CHEMISTRY, 58:8257-8268, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b01148

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Labat, Frederic; Ciofini, Ilaria; Nicolotti, Orazio; Lattanzi, Gianluca; Adamo, Carlo
Theoretical Investigation of Hole Transporter Materials for Energy Devices
JOURNAL OF PHYSICAL CHEMISTRY C, 119:23890-23898, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b08981

Adluri, Archita N. S.; Murphy, Jennifer N.; Tozer, Tiffany; Rowley, Christopher N.
Polarizable Force Field with a sigma-Hole for Liquid and Aqueous Bromomethane
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13422-13432, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09041

Kucukkal, Tugba G.; Yang, Ye; Uvarov, Olga; Cao, Weiguo; Alexov, Emil
Impact of Rett Syndrome Mutations on MeCP2 MBD Stability
BIOCHEMISTRY, 54:6357-6368, OCT 20 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00790

Farrugia, Mark A.; Wang, Beibei; Feig, Michael; Hausinger, Robert P.
Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease
BIOCHEMISTRY, 54:6392-6401, OCT 20 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00942

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernandez, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
BIOPHYSICAL JOURNAL, 109:1528-1532, OCT 20 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.015

Swedberg, Joakim E.; Schroeder, Christina I.; Mitchell, Justin M.; Durek, Thomas; Fairlie, David P.; Edmonds, David J.; Griffith, David A.; Ruggeri, Roger B.; Derksen, David R.; Loria, Paula M.; Liras, Spiros; Price, David A.; Craik, David J.
Cyclic alpha-conotoxin peptidomimetic chimeras as potent GLP-1R agonists
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 103:175-184, OCT 20 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.08.046

Park, Kyu Hyung; Kim, Pyosang; Kim, Woojae; Shimizu, Hideyuki; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho
Excited-State Dynamic Planarization of Cyclic Oligothiophenes in the Vicinity of a Ring-to-Linear Excitonic Behavioral Turning Point
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54:12711-12715, OCT 19 2015
abstract, full text, DOI:10.1002/anie.201504588

Chan, Albert H.; Yi, Sung Wook; Terwilliger, Austen L.; Maresso, Anthony W.; Jung, Michael E.; Clubb, Robert T.
Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:25461-25474, OCT 16 2015
abstract, full text, DOI:10.1074/jbc.M115.670984

Liu, Jian; Shi, Guosheng; Guo, Pan; Yang, Jinrong; Fang, Haiping
Blockage of Water Flow in Carbon Nanotubes by Ions Due to Interactions between Cations and Aromatic Rings
PHYSICAL REVIEW LETTERS, 115 Art. No. 164502, OCT 16 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.164502

Hui, Gar Kay; Wright, David W.; Vennard, Owen L.; Rayner, Lucy E.; Pang, Melisa; Yeo, See Cheng; Gor, Jayesh; Molyneux, Karen; Barratt, Jonathan; Perkins, Stephen J.
The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease
BIOCHEMICAL JOURNAL, 471:167-185, OCT 15 2015
abstract, full text, DOI:10.1042/BJ20150612

Riley, Blake T.; Broendum, Sebastian S.; Reboul, Cyril F.; Cowieson, Nathan P.; Costa, Mauricio G. S.; Kass, Itamar; Jackson, Colin; Perahia, David; Buckle, Ashley M.; McGowan, Sheena
Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC
PLOS ONE, 10 Art. No. e0140219, OCT 15 2015
abstract, full text, DOI:10.1371/journal.pone.0140219

Pavlova, Anna; Gumbart, James C.
Parametrization of Macrolide Antibiotics Using the Force Field Toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2052-2063, OCT 15 2015
abstract, full text, DOI:10.1002/jcc.24043

Kanchi, Subbarao; Suresh, Gorle; Priyakumar, U. Deva; Ayappa, K. G.; Maiti, Prabal K.
Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12990-13001, OCT 15 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b07124

Konas, Ryan M.; Daristotle, John L.; Harbor, Ndubuisi B.; Klauda, Jeffery B.
Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13134-13141, OCT 15 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06066

MacDonald, Corey A.; Boyd, Russell J.
Competing nitrile hydratase catalytic mechanisms: Is cysteine-sulfenic acid acting as a nucleophile?
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1070:48-54, OCT 15 2015
abstract, full text, DOI:10.1016/j.comptc.2015.07.010

Schneider, Miriam; Kasanetz, Fernando; Lynch, Diane L.; Friemel, Chris M.; Lassalle, Olivier; Hurst, Dow P.; Steindel, Frauke; Monory, Krisztina; Schaefer, Carola; Miederer, Isabelle; Leweke, F. Markus; Schreckenberger, Mathias; Lutz, Beat; Reggio, Patricia H.; Manzoni, Olivier J.; Spanagel, Rainer
Enhanced Functional Activity of the Cannabinoid Type-1 Receptor Mediates Adolescent Behavior
JOURNAL OF NEUROSCIENCE, 35:13975-13988, OCT 14 2015
abstract, full text, DOI:10.1523/JNEUROSCI.1937-15.2015

Di Maio, Danilo; Chandramouli, Balasubramanian; Brancato, Giuseppe
Pathways and Barriers for Ion Translocation through the 5-HT(3)A Receptor Channel
PLOS ONE, 10 Art. No. e0140258, OCT 14 2015
abstract, full text, DOI:10.1371/journal.pone.0140258

Ercius, Peter; Alaidi, Osama; Rames, Matthew J.; Ren, Gang
Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research
ADVANCED MATERIALS, 27:5638-5663, OCT 14 2015
abstract, full text, DOI:10.1002/adma.201501015

Belaz, Sorya; Rattier, Thibault; Lafite, Pierre; Moreau, Philippe; Routier, Francoise H.; Robert-Gangneux, Florence; Gangneux, Jean-Pierre; Daniellou, Richard
Identification, biochemical characterization, and in-vivo expression of the intracellular invertase BfrA from the pathogenic parasite Leishmania major
CARBOHYDRATE RESEARCH, 415:31-38, OCT 13 2015
abstract, full text, DOI:10.1016/j.carres.2015.07.001

Iglesias-Fernandez, Javier; Darre, Leonardo; Kohlmeyer, Axel; Thomas, Robert K.; Shen, Hsin-Hui; Domene, Carmen
Surfactin at the Water/Air Interface and in Solution
LANGMUIR, 31:11097-11104, OCT 13 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b02305

Medarevic, Djordje; Kachrimanis, Kyriakos; Djuric, Zorica; Ibric, Svetlana
Influence of hydrophilic polymers on the complexation of carbamazepine with hydroxypropyl-beta-cyclodextrin
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 78:273-285, OCT 12 2015
abstract, full text, DOI:10.1016/j.ejps.2015.08.001

Hernandez, Sergio; Figueroa, Daniella; Correa, Simon; Diaz, Ariel; Aguayo, Daniel; Villanueva, Rodrigo A.
Phosphorylation at the N-terminal finger subdomain of a viral RNA-dependent RNA polymerase
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 466:21-27, OCT 9 2015
abstract, full text, DOI:10.1016/j.bbrc.2015.08.082

Shakourian-Fard, Mehdi; Kamath, Ganesh; Smith, Kassiopeia; Xiong, Hui; Sankaranarayanan, Subramanian K. R. S.
Trends in Na-Ion Solvation with Alkyl-Carbonate Electrolytes for Sodium-Ion Batteries: Insights from First-Principles Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 119:22747-22759, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b04706

Gc, Jeevan B.; Gerstman, Bernard S.; Chapagain, Prem P.
The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12750-12759, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05681

Chakraborty, Debashree; Taly, Antoine; Sterpone, Fabio
Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12760-12770, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05791

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:12384-12389, OCT 6 2015
abstract, full text, DOI:10.1073/pnas.1504986112

Madsen, Jesper J.; Ohkubo, Y. Zenmei; Peters, Gunther H.; Faber, Johan H.; Tajkhorshid, Emad; Olsen, Ole H.
Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail
BIOCHEMISTRY, 54:6123-6131, OCT 6 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00417

Modi, Niraj; Ganguly, Sonalli; Barcena-Uribarri, Ivan; Benz, Roland; van den Berg, Bert; Kleinekathoefer, Ulrich
Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa
BIOPHYSICAL JOURNAL, 109:1429-1438, OCT 6 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.035

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Motta, Alessandro; Nicolotti, Orazio; Lattanzi, Gianluca
Effects of Different Self-Assembled Mono layers on Thin-Film Morphology: A Combined DFT/MD Simulation Protocol
LANGMUIR, 31:10693-10701, OCT 6 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b02761

Megow, Joerg
How Van der Waals Interactions Influence the Absorption Spectra of Pheophorbide a Complexes: A Mixed Quantum-Classical Study
CHEMPHYSCHEM, 16:3101-3107, OCT 5 2015
abstract, full text, DOI:10.1002/cphc.201500326

Kutzner, Carsten; Pall, Szilard; Fechner, Martin; Esztermann, Ansgar; de Groot, Bert L.; Grubmueller, Helmut
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1990-2008, OCT 5 2015
abstract, full text, DOI:10.1002/jcc.24030

Mendez-Luna, D.; Martinez-Archundia, M.; Maroun, Rachid C.; Ceballos-Reyes, G.; Fragoso-Vazquez, M. J.; Gonzalez-Juarez, D. E.; Correa-Basurto, J.
Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:2161-2172, OCT 3 2015
abstract, full text, DOI:10.1080/07391102.2014.994102

Suresh, Gorle; Priyakumar, U. Deva
Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme
JOURNAL OF CHEMICAL SCIENCES, 127:1701-1713, OCT 2015
abstract, full text, DOI:10.1007/s12039-015-0942-7

Kheirodin, Mohsen; Pishkenari, Hossein Nejat; Moosavi, Ali; Meghdari, Ali
Study of Biomolecules Imaging Using Molecular Dynamics Simulations
NANO, 10 Art. No. 1550096, OCT 2015
abstract, full text, DOI:10.1142/S1793292015500964

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004469, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004469

Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004568, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004568

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoit
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004368, OCT 2015
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1004368

Votapka, Lane W.; Amaro, Rommie E.
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004381, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004381

Wahle, Manuel; Wriggers, Willy
Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
PLoS Computational Biology, 11 Art. No. e1004516, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004516

Zhao, Hanchao; Palencia, Andres; Seiradake, Elena; Ghaemi, Zhaleh; Cusack, Stephen; Luthey-Schulten, Zaida; Martinis, Susan
Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism
ACS CHEMICAL BIOLOGY, 10:2277-2285, OCT 2015
abstract, full text, DOI:10.1021/acschembio.5b00291

Alcorlo, Martin; Lopez-Perrote, Andres; Delgado, Sandra; Yebenes, Hugo; Subias, Marta; Rodriguez-Gallego, Cesar; Rodriguez de Cordoba, Santiago; Llorca, Oscar
Structural insights on complement activation
FEBS JOURNAL, 282:3883-3891, OCT 2015
abstract, full text, DOI:10.1111/febs.13399

Schur, Florian K. M.; Dick, Robert A.; Hagen, Wim J. H.; Vogt, Volker M.; Briggs, John A. G.
The Structure of Immature Virus-Like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the p10 Domain in Assembly
JOURNAL OF VIROLOGY, 89:10294-10302, OCT 2015
abstract, full text, DOI:10.1128/JVI.01502-15

Kognole, Abhishek A.; Payne, Christina M.
Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules
GLYCOBIOLOGY, 25:1100-1111, OCT 2015
abstract, full text, DOI:10.1093/glycob/cwv048

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano
Conserved water molecules in bacterial serine hydroxymethyltransferases
PROTEIN ENGINEERING DESIGN & SELECTION, 28:415-426, OCT 2015
abstract, full text, DOI:10.1093/protein/gzv026

Wieteska, J. R.; Welche, P. R. L.; Tu, K. -M.; ElGamacy, Mohammad; Csanyi, G.; Payne, M. C.; Chaue, P. -L.
Isoflurane does not aggregate inside POPC bilayers at high pressure: Implications for pressure reversal of general anaesthesia
CHEMICAL PHYSICS LETTERS, 638:116-121, OCT 1 2015
abstract, full text, DOI:10.1016/j.cplett.2015.07.065

Spyrakis, Francesca; Benedetti, Paolo; Decherchi, Sergio; Rocchia, Walter; Cavalli, Andrea; Alcaro, Stefano; Ortuso, Francesco; Baroni, Massimo; Cruciani, Gabriele
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2256-2274, OCT 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00169

Suliman, FakhrEldin O.; Elbashir, Abdalla A.; Schmitz, Oliver J.
Study on the separation of ofloxacin enantiomers by hydroxylpropyl-beta-cyclodextrin as a chiral selector in capillary electrophoresis: a computational approach
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 83:119-129, OCT 2015
abstract, full text, DOI:10.1007/s10847-015-0547-2

Padariya, Monikaben; Kalathiya, Umesh; Baginski, Maciej
Structural and dynamic changes adopted by EmrE, multidrug transporter protein-Studies by molecular dynamics simulation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2065-2074, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.05.014

Chang, Kai-Ti; Anishkin, Andriy; Patwardhan, Gauri A.; Beverly, Levi J.; Siskind, Leah J.; Colombini, Marco
Ceramide channels: destabilization by Bcl-xL and role in apoptosis
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2374-2384, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.07.013

McDougle, Daniel R.; Baylon, Javier L.; Meling, Daryl D.; Kambalyal, Amogh; Grinkova, Yelena V.; Hammernik, Jared; Tajkhorshid, Emad; Das, Aditi
Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2-lipid bilayer interactions
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2460-2470, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.07.015

Marcoux, Julien; Mangione, P. Patrizia; Porcari, Riccardo; Degiacomi, Matteo T.; Verona, Guglielmo; Taylor, Graham W.; Giorgetti, Sofia; Raimondi, Sara; Sanglier-Cianferani, Sarah; Benesch, Justin L. P.; Cecconi, Ciro; Naqvi, Mohsin M.; Gillmore, Julian D.; Hawkins, Philip N.; Stoppini, Monica; Robinson, Carol V.; Pepys, Mark B.; Bellotti, Vittorio
A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis
EMBO MOLECULAR MEDICINE, 7:1337-1349, OCT 2015
abstract, full text

Allen, Stacey M.; Lim, Erin E.; Jortzik, Esther; Preuss, Janina; Chua, Hwa Huat; MacRae, James I.; Rahlfs, Stefan; Haeussler, Kristina; Downton, Matthew T.; McConville, Malcolm J.; Becker, Katja; Ralph, Stuart A.
Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target
FEBS JOURNAL, 282:3808-3823, OCT 2015
abstract, full text, DOI:10.1111/febs.13380

Liu, Peng; Shao, Xueguang; Cai, Wensheng
Deciphering the Mechanism Involved in the Switch On/Off of Molecular Pistons
CHINESE JOURNAL OF CHEMISTRY, 33:1199-1205, OCT 2015
abstract, full text, DOI:10.1002/cjoc.201500402

Harris, Robert C.; Pettitt, B. Montgomery
Examining the Assumptions Underlying Continuum-Solvent Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4593-4600, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00684

Perez, Alberto; MacCallum, Justin L.; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A.
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4770-4779, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00662

Daday, Csaba; Curutchet, Caries; Sinicropi, Adalgisa; Mennucci, Benedetta; Filippi, Claudia
Chromophore-Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4825-4839, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00650

Darre, L.; Iglesias-Fernandez, J.; Kohlmeyer, A.; Wacklin, H.; Domene, C.
Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4875-4884, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00635

Choi, Hwanho; Kang, Hongsuk; Park, Hwangseo
Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4933-4942, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00325

Ngo, Van; da Silva, Mauricio C.; Kubillus, Maximilian; Li, Hui; Roux, Benoit; Elstner, Marcus; Cui, Qiang; Salahub, Dennis R.; Noskov, Sergei Yu.
Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4992-5001, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00524

Paz, S. Alexis; Abrams, Cameron F.
Free Energy and Hidden Barriers of the beta-Sheet Structure of Prion Protein
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5024-5034, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00576

Qin, Xin; Xia, Wenjie; Sinko, Robert; Keten, Sinan
Tuning Glass Transition in Polymer Nanocomposites with Functionalized Cellulose Nanocrystals through Nanoconfinement
NANO LETTERS, 15:6738-6744, OCT 2015
abstract, full text, DOI:10.1021/acs.nanolett.5b02588

Fichou, Yann; Heyden, Matthias; Zaccai, Giuseppe; Weik, Martin; Tobias, Douglas J.
Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12580-12589, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05849

Chen, Houyang; Ruckenstein, Eli
Hydrated Ions: From Individual Ions to Ion Pairs to Ion Clusters
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12671-12676, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06837

Caddeo, Claudia; Cazia, Vasco; Bagolini, Luigi; Lusk, Mark T.; Mattoni, Alessandro
Pinpointing the Cause of Platinum Tipping on CdS Nanorods
JOURNAL OF PHYSICAL CHEMISTRY C, 119:22663-22668, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b06264

Cannon, Daniel A.; Aslikenasy, Nurit; Tuttle, Tell
Influence of Solvent in Controlling Peptide-Surface Interactions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:3944-3949, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01733

Zhang, Jiong; Barz, Bogdan; Zhang, Jingfen; Xu, Dong; Kosztin, Ioan
Selective refinement and selection of near-native models in protein structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1823-1835, OCT 2015
abstract, full text, DOI:10.1002/prot.24866

Qu, Tao; Verma, Devendra; Alucozai, Milad; Tomar, Vikas
Influence of interfacial interactions on deformation mechanism and interface viscosity in alpha-chitin-calcite interfaces
ACTA BIOMATERIALIA, 25:325-338, OCT 1 2015
abstract, full text, DOI:10.1016/j.actbio.2015.06.034

Valenzuela-Riffo, Felipe; Tapia, Gerardo; Parra-Palma, Carolina; Morales-Quintana, Luis
Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 270, OCT 2015
abstract, full text, DOI:10.1007/s00894-015-2807-x

Pradhan, Shashindra M.; Katti, Kalpana S.; Katti, Dinesh R.
Evolution of Molecular Interactions in the Interlayer of Na-Montmorillonite Swelling Clay with Increasing Hydration
INTERNATIONAL JOURNAL OF GEOMECHANICS, 15 Art. No. 04014073, OCT 2015
abstract, full text, DOI:10.1061/(ASCE)GM.1943-5622.0000412

Sawada, Yasuyuki; Sokabe, Masahiro
Molecular dynamics study on protein-water interplay in the mechanogating of the bacterial mechanosensitive channel MscL
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 44:531-543, OCT 2015
abstract, full text, DOI:10.1007/s00249-015-1065-2

Chang, Shan; He, Hong-Qiu; Shen, Lin; Wan, Hua
Understanding peptide competitive inhibition of botulinum neurotoxin a binding to SV2 protein via molecular dynamics simulations
BIOPOLYMERS, 103:597-608, OCT 2015
abstract, full text, DOI:10.1002/bip.22682

van Erp, Paul B. G.; Jackson, Ryan N.; Carter, Joshua; Golden, Sarah M.; Bailey, Scott; Wiedenheft, Blake
Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli
NUCLEIC ACIDS RESEARCH, 43:8381-8391, SEP 30 2015
abstract, full text, DOI:10.1093/nar/gkv793

Gorska, Anna; Jasinski, Maciej; Trylska, Joanna
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids
NUCLEIC ACIDS RESEARCH, 43 Art. No. e114, SEP 30 2015
abstract, full text, DOI:10.1093/nar/gkv559

Westergard, Thomas; Salari, Reza; Martin, Joseph V.; Brannigan, Grace
Interactions of L-3,5,4 '-Triiodothyronine, Allopregnanolone, and Ivermectin with the GABA(A) Receptor: Evidence for Overlapping Intersubunit Binding Modes
PLOS ONE, 10 Art. No. e0139072, SEP 30 2015
abstract, full text, DOI:10.1371/journal.pone.0139072

Zisis, Themistoklis; Freddolino, Peter L.; Turunen, Petri; van Teeseing, Muriel C. F.; Rowan, Alan E.; Blank, Kerstin G.
Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation
BIOCHEMISTRY, 54:5969-5979, SEP 29 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00586

Davare, Monika A.; Vellore, Nadeem A.; Wagner, Jacob P.; Eide, Christopher A.; Goodman, James R.; Drilon, Alexander; Deininger, Michael W.; O'Hare, Thomas; Druker, Brian J.
Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E5381-E5390, SEP 29 2015
abstract, full text, DOI:10.1073/pnas.1515281112

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong
y Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations
PLOS ONE, 10 Art. No. e0139081, SEP 28 2015
abstract, full text, DOI:10.1371/journal.pone.0139081

He, Xiaoxia; Shen, Yan; Hung, Francisco R.; Santiso, Erik E.
Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124506, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931654

La Penna, G.; Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.
A first-principle calculation of the XANES spectrum of Cu2+ in water
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124508, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931808

Rydzewski, J.; Nowak, W.
Memetic algorithms for ligand expulsion from protein cavities
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124101, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931181

Karim, Christine B.; Espinoza-Fonseca, L. Michel; James, Zachary M.; Hanse, Eric A.; Gaynes, Jeffrey S.; Thomas, David D.; Kelekar, Ameeta
Structural Mechanism for Regulation of Bcl-2 protein Noxa by phosphorylation
SCIENTIFIC REPORTS, 5 Art. No. 14557, SEP 28 2015
abstract, full text, DOI:10.1038/srep14557

Tanaka, Naoto; Dutrow, Emily V.; Miyadera, Keiko; Delemotte, Lucie; MacDermaid, Christopher M.; Reinstein, Shelby L.; Crumley, William R.; Dixon, Christopher J.; Casal, Margret L.; Klein, Michael L.; Aguirre, Gustavo D.; Tanaka, Jacqueline C.; Guziewicz, Karina E.
Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment
PLOS ONE, 10 Art. No. e0138943, SEP 25 2015
abstract, full text, DOI:10.1371/journal.pone.0138943

Bockus, Andrew T.; Schwochert, Joshua A.; Pye, Cameron R.; Townsend, Chad E.; Sok, Vong; Bednarek, Maria A.; Lokey, R. Scott
Going Out on a Limb: Delineating The Effects of beta-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues
JOURNAL OF MEDICINAL CHEMISTRY, 58:7409-7418, SEP 24 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00919

Meher, Biswa Ranjan; Dixit, Anshuman; Bousfield, George R.; Lushington, Gerald H.
Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. e0137897, SEP 24 2015
abstract, full text, DOI:10.1371/journal.pone.0137897

Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra
Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12365-12380, SEP 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05496

Chon, Nara Lee; Osterberg, J. Ryan; Henderson, Jack; Khan, Hanif M.; Reuter, Nathalie; Knight, Jefferson D.; Lin, Hai
Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions
BIOCHEMISTRY, 54:5696-5711, SEP 22 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00422

Gamiz-Hernandez, Ana P.; Angelova, Iva Neycheva; Send, Robert; Sundholm, Dage; Kaila, Ville R. I.
Protein-Induced Color Shift of Carotenoids in beta-Crustacyanin
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54:11564-11566, SEP 21 2015
abstract, full text, DOI:10.1002/anie.201501609

Chatterjee, Abhijit; Bhattacharya, Swati
Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 114109, SEP 21 2015
abstract, full text, DOI:10.1063/1.4930976

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.
Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization
NUCLEIC ACIDS RESEARCH, 43:7675-7687, SEP 18 2015
abstract, full text, DOI:10.1093/nar/gkv761

Marquez-Miranda, Valeria; Belen Camarada, Maria; Araya-Duran, Ingrid; Varas-Concha, Ignacio; Eduardo Almonacid, Daniel; Danilo Gonzalez-Nilo, Fernando
Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers
PLOS ONE, 10 Art. No. e0138392, SEP 18 2015
abstract, full text, DOI:10.1371/journal.pone.0138392

Lorch, Sebastian; Capponi, Sara; Pieront, Florian; Bondar, Ana-Nicoleta
Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12172-12181, SEP 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06594

Lammi, Carmen; Zanoni, Chiara; Arnoldi, Anna; Vistoli, Giulio
Two Peptides from Soy beta-Conglycinin Induce a Hypocholesterolemic Effect in HepG2 Cells by a Statin-Like Mechanism: Comparative in Vitro and in Silico Modeling Studies
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 63:7945-7951, SEP 16 2015
abstract, full text, DOI:10.1021/acs.jafc.5b03497

Kim, Steve S.; Kuang, Zhifeng; Ngo, Yen H.; Farmer, Barry L.; Naik, Rajesh R.
Biotic-Abiotic Interactions: Factors that Influence Peptide-Graphene Interactions
ACS APPLIED MATERIALS & INTERFACES, 7:20447-20453, SEP 16 2015
abstract, full text, DOI:10.1021/acsami.5b06434

Imbrici, P.; Maggi, L.; Mangiatordi, G. F.; Dinardo, M. M.; Altamura, C.; Brugnoni, R.; Alberga, D.; Pinter, G. Lauria; Ricci, G.; Siciliano, G.; Micheli, R.; Annicchiarico, G.; Lattanzi, G.; Nicolotti, O.; Morandi, L.; Bernasconi, P.; Desaphy, J. -F.; Mantegazza, R.; Camerino, D. Conte
ClC-1 mutations in myotonia congenita patients: insights into molecular gating mechanisms and genotype-phenotype correlation
JOURNAL OF PHYSIOLOGY-LONDON, 593:4181-4199, SEP 15 2015
abstract, full text, DOI:10.1113/JP270358

Ribeiro, Andre A. S. T.; Ortiz, Vanessa
MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 109:1110-1116, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.013

Earnest, Tyler M.; Lai, Jonathan; Chen, Ke; Hallock, Michael J.; Williamson, James R.; Luthey-Schulten, Zaida
Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly
BIOPHYSICAL JOURNAL, 109:1117-1135, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.030

Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Yurtsever, Mine; Noskov, Sergei Y.; Durdagi, Serdar
Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDE delta Inhibitors
BIOPHYSICAL JOURNAL, 109:1163-1168, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.001

Floquet, Nicolas; Costa, Mauricio G. S.; Batista, Paulo R.; Renault, Pedro; Bisch, Paulo M.; Raussin, Florent; Martinez, Jean; Morris, May C.; Perahia, David
Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes
BIOPHYSICAL JOURNAL, 109:1179-1189, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.003

Sumbul, Fidan; Acuner-Ozbabacan, Saliha Ece; Haliloglu, Turkan
Allosteric Dynamic Control of Binding
BIOPHYSICAL JOURNAL, 109:1190-1201, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.011

Sharma, Vivek; Belevich, Galina; Gamiz-Hernandez, Ana P.; Rog, Tomasz; Vattulainen, Ilpo; Verkhovskaya, Marina L.; Wikstrom, Marten; Hummer, Gerhard; Kaila, Ville R. I.
Redox-induced activation of the proton pump in the respiratory complex I
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:11571-11576, SEP 15 2015
abstract, full text, DOI:10.1073/pnas.1503761112

Koldso, Heidi; Andersen, Ole Juul; Nikolajsen, Camilla Lund; Scavenius, Carsten; Sorensen, Charlotte S.; Underhaug, Jarl; Runager, Kasper; Nielsen, Niels Chr.; Enghild, Jan J.; Schiott, Birgit
Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor beta-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants
BIOCHEMISTRY, 54:5546-5556, SEP 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00473

Nakano, Shogo; Okazaki, Seiji; Ishitsubo, Erika; Kawahara, Nobuhiro; Komeda, Hidenobu; Tokiwa, Hiroaki; Asano, Yasuhisa
Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B
SCIENTIFIC REPORTS, 5 Art. No. 13836, SEP 15 2015
abstract, full text, DOI:10.1038/srep13836

Chinappi, Mauro; Luchian, Tudor; Cecconi, Fabio
Nanopore tweezers: Voltage-controlled trapping and releasing of analytes
PHYSICAL REVIEW E, 92 Art. No. 032714, SEP 15 2015
abstract, full text, DOI:10.1103/PhysRevE.92.032714

Piazzetta, Paolo; Marino, Tiziana; Russo, Nino
Theoretical investigation on the restoring step of the carbonic anhydrase catalytic cycle for natural and promiscuous substrates
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 582:101-106, SEP 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.03.022

Zuo, Zhicheng; Wang, Beibei; Weng, Jingwei; Wang, Wenning
Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB
SCIENTIFIC REPORTS, 5 Art. No. 13905, SEP 14 2015
abstract, full text, DOI:10.1038/srep13905

Sokhan, V. P.; Jones, A.; Cipcigan, F. S.; Crain, J.; Martyna, G. J.
Molecular-Scale Remnants of the Liquid-Gas Transition in Supercritical Polar Fluids
PHYSICAL REVIEW LETTERS, 115 Art. No. 117801, SEP 11 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.117801

Poma, Adolfo B.; Chwastyk, Mateusz; Cieplak, Marek
Polysaccharide-Protein Complexes in a Coarse-Grained Model
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12028-12041, SEP 10 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06141

Lin, Wayne; Insley, Thomas; Tuttle, Marcus D.; Zhu, Lingyang; Berthold, Deborah A.; Kral, Petr; Rienstra, Chad M.; Murphy, Catherine J.
Control of Protein Orientation on Gold Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY C, 119:21035-21043, SEP 10 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b07701

Chen, Qiang; Kinde, Monica N.; Arjunan, Palaniappa; Wells, Marta M.; Cohen, Aina E.; Xu, Yan; Tang, Pei
Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC
SCIENTIFIC REPORTS, 5 Art. No. 13833, SEP 8 2015
abstract, full text, DOI:10.1038/srep13833

Viciano, Ignacio; Castillo, Raquel; Marti, Sergio
QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1736-1747, SEP 5 2015
abstract, full text, DOI:10.1002/jcc.23967

Zheng, Lijun; Farrell, David M.; Fulton, Ruth M.; Bagg, Eve E.; Salcedo, Ernesto; Manino, Meridee; Britt, Steven G.
Analysis of Conserved Glutamate and Aspartate Residues in Drosophila Rhodopsin 1 and Their Influence on Spectral Tuning
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:21951-21961, SEP 4 2015
abstract, full text, DOI:10.1074/jbc.M115.677765

Wang, Xinlei; Vukovic, Lela; Koh, Hye Ran; Schulten, Klaus; Myong, Sua
Dynamic profiling of double-stranded RNA binding proteins
NUCLEIC ACIDS RESEARCH, 43:7566-7576, SEP 3 2015
abstract, full text, TCBG publications, DOI:10.1093/nar/gkv726

Markegard, Cade B.; Mazaheripour, Arnir; Jocson, Jonah-Micah; Burke, Anthony M.; Dickson, Mary N.; Gorodetsky, Alon A.; Nguyen, Hung D.
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11459-11465, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03874

Gleed, Mitchell L.; Ioannidis, Harris; Kolocouris, Antonios; Busath, David D.
Resistance-Mutation (N31) Effects on Drug Orientation and Channel Hydration in Amantadine-Bound Influenza A M2
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11548-11559, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05808

Parikh, Niyati D.; Klimov, Dmitri K.
Molecular Mechanisms of Alzheimer's Biomarker FDDNP Binding to A beta Amyloid Fibril
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11568-11580, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06112

Thibault, J. C.; Roe, D. R.; Eilbeck, K.; Cheatham, T. E., I.I.I.; Facelli, J. C.
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 26:577-593, SEP 2 2015
abstract, full text, DOI:10.1080/1062936X.2015.1076515

Saxena, A. K.; Devillers, J.; Bhunia, S. S.; Bro, E.
Modelling inhibition of avian aromatase by azole pesticides
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 26:757-782, SEP 2 2015
abstract, full text, DOI:10.1080/1062936X.2015.1090749

Hylton, Rebecca K.; Tizzard, Graham J.; Threlfall, Terence L.; Ellis, Amy L.; Coles, Simon J.; Seaton, Colin C.; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L.
Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:11095-11104, SEP 2 2015
abstract, full text, DOI:10.1021/jacs.5b05938

Campomanes, Pablo; Rothlisberger, Ursula; Alfonso-Prieto, Mercedes; Rovira, Carme
The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:11170-11178, SEP 2 2015
abstract, full text, DOI:10.1021/jacs.5b06796

Noto, Rosina; Randazzo, Loredana; Raccosta, Samuele; Caccia, Sonia; Moriconi, Claudia; Miranda, Elena; Martorana, Vincenzo; Manno, Mauro
The stability and activity of human neuroserpin are modulated by a salt bridge that stabilises the reactive centre loop
SCIENTIFIC REPORTS, 5 Art. No. 13666, SEP 2 2015
abstract, full text, DOI:10.1038/srep13666

Tarus, Bogdan; Bertrand, Helene; Zedda, Gloria; Di Primo, Carmelo; Quideau, Stephane; Slama-Schwok, Anny
Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1899-1912, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.979230

Wang, Fangfang; Yang, Wei; Shi, Yonghui; Le, Guowei
3D-QSAR, molecular docking and molecular dynamics studies of a series of ROR gamma t inhibitors
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1929-1940, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.980321

Banerjee, Avik; Mukhopadhyay, Bishnu P.
An insight to the conserved water mediated dynamics of catalytic His88 and its recognition to thyroxin and RBP binding residues in human transthyretin
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1973-1988, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.984632

Moradi, Mahmoud; Enkavi, Giray; Tajkhorshid, Emad
Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate: phosphate antiporter
NATURE COMMUNICATIONS, 6 Art. No. 8393, SEP 2015
abstract, full text, DOI:10.1038/ncomms9393

Uporov, Igor V.; Forlemu, Neville Y.; Nori, Rahul; Aleksandrov, Tsvetan; Sango, Boris A.; Mbote, Yvonne E. Bongfen; Pothuganti, Sandeep; Thomasson, Kathryn A.
Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:21237-21276, SEP 2015
abstract, full text, DOI:10.3390/ijms160921237

Hu, Dong; Gur, Mert; Zhou, Zhuan; Gamper, Armin; Hung, Mien-Chie; Fujita, Naoya; Lan, Li; Bahar, Ivet; Wan, Yong
Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis
NATURE COMMUNICATIONS, 6 Art. No. 8419, SEP 2015
abstract, full text, DOI:10.1038/ncomms9419

Echeverria, Ignacia; Liu, Yunlong; Gabelli, Sandra B.; Amzel, L. Mario
Oncogenic mutations weaken the interactions that stabilize the p110 alpha-p85 alpha heterodimer in phosphatidylinositol 3-kinase alpha
FEBS JOURNAL, 282:3528-3542, SEP 2015
abstract, full text, DOI:10.1111/febs.13365

Koehler, Stephan; Schmid, Friederike; Settanni, Giovanni
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004346, SEP 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004346

Azamat, Jafar; Sattary, Batoul Shirforush; Khataee, Alireza; Joo, Sang Woo
Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 61:13-20, SEP 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.06.012

Suresh, Gorle; Priyakumar, U. Deva
Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 61:150-159, SEP 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.07.009

Macalino, Stephani Joy Y.; Gosu, Vijayakumar; Hong, Sunhye; Choi, Sun
Role of computer-aided drug design in modern drug discovery
ARCHIVES OF PHARMACAL RESEARCH, 38:1686-1701, SEP 2015
abstract, full text, DOI:10.1007/s12272-015-0640-5

Mendes, Celso L.; Bode, Brett; Bauer, Gregory H.; Enos, Jeremy; Beldica, Cristina; Kramer, William T.
Deployment and testing of the sustained petascale Blue Waters system
JOURNAL OF COMPUTATIONAL SCIENCE, 10:327-337, SEP 2015
abstract, full text, DOI:10.1016/j.jocs.2015.03.007

Liu, Xiaorong; Beugelsdijk, Alex; Chen, Jianhan
Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL
BIOPHYSICAL JOURNAL, 109:1049-1057, SEP 1 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.043

Carswell, Casey L.; Henault, Camille M.; Murlidaran, Sruthi; Therien, J. P. Daniel; Juranka, Peter F.; Surujballi, Julian A.; Brannigan, Grace; Baenziger, John E.
Role of the Fourth Transmembrane alpha Helix in the Allosteric Modulation of Pentameric Ligand-Gated Ion Channels
STRUCTURE, 23:1655-1664, SEP 1 2015
abstract, full text, DOI:10.1016/j.str.2015.06.020

Shadrina, Maria S.; Peslherbe, Gilles H.; English, Ann M.
Quaternary-Linked Changes in Structure and Dynamics That Modulate O-2 Migration within Hemoglobin's Gas Diffusion Tunnels
BIOCHEMISTRY, 54:5268-5278, SEP 1 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00368

Shadrina, Maria S.; Peslherbe, Gilles H.; English, Ann M.
O-2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7
BIOCHEMISTRY, 54:5279-5289, SEP 1 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00369

Iacovelli, Federico; Falconi, Mattia
Decoding the conformation-linked functional properties of nucleic acids by the use of computational tools
FEBS JOURNAL, 282:3298-3310, SEP 2015
abstract, full text, DOI:10.1111/febs.13315

Sun, Dawei; Flock, Tilman; Deupi, Xavier; Maeda, Shoji; Matkovic, Milos; Mendieta, Sandro; Mayer, Daniel; Dawson, Roger J. P.; Schertler, Gebhard F. X.; Babu, M. Madan; Veprintsev, Dmitry B.
Probing G alpha(i1) protein activation at single-amino acid resolution
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 22:686-U64, SEP 2015
abstract, full text, DOI:10.1038/nsmb.3070

Tan, Bowen; Zhou, Yijie; Song, Zhilei; Peng, Yinxuan; Wu, Fang; Kang, Yue; Liu, Xiaomin; Zeng, Li; Huang, Tingting; Liu, Zongying; Xiong, Lili; Guo, Zhiyun; Cui, Jian; Mao, Canquan
Modeling and Virtual Screening of Antisense Peptides Targeting the Divergent Region of Tumor-Associated MT1-MMP Protein
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 36:2198-2207, SEP 2015
abstract, full text, DOI:10.1002/bkcs.10421

Rodriguez, Roberto A.; Yu, Lili; Chen, Liao Y.
Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4427-4438, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00340

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+, and Rb+ via Water-Mediated Hydrogen Bonding
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4473-4485, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00508

Qi, Yifei; Ingolfsson, Helgi I.; Cheng, Xi; Lee, Jumin; Marrink, Siewert J.; Im, Wonpil
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4486-4494, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00513

Yang, Jing; Calero, Carles; Bonomi, Massimiliano; Marti, Jordi
Specific Ion Binding at Phospholipid Membrane Surfaces
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4495-4499, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00540

Lockhart, Christopher; O'Connor, James; Armentrout, Steven; Klimov, Dmitri K.
Greedy replica exchange algorithm for heterogeneous computing grids
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 243, SEP 2015
abstract, full text, DOI:10.1007/s00894-015-2763-5

Sung, Shen-Shu
Peptide folding driven by Van der Waals interactions
PROTEIN SCIENCE, 24:1383-1388, SEP 2015
abstract, full text, DOI:10.1002/pro.2710

Hamed, Elham; Ma, Dan; Keten, Sinan
Effect of Polymer Conjugation Site on Stability and Self-Assembly of Coiled Coils
BIONANOSCIENCE, 5:140-149, SEP 2015
abstract, full text, DOI:10.1007/s12668-015-0172-y

Ramya, L.; Gautham, N.; Chaloin, Laurent; Kajava, Andrey V.
Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1654-1664, SEP 2015
abstract, full text, DOI:10.1002/prot.24851

Katti, Dinesh R.; Srinivasamurthy, Lakshmikanth; Katti, Kalpana S.
Molecular modeling of initiation of interlayer swelling in Na-montmorillonite expansive clay
CANADIAN GEOTECHNICAL JOURNAL, 52:1385-1395, SEP 2015
abstract, full text, DOI:10.1139/cgj-2014-0309

Parasuraman, Ponnusamy; Murugan, Veeramani; Selvin, Jeyasigamani F. A.; Gromiha, M. Michael; Fukui, Kazuhiko; Veluraja, Kasinadar
Theoretical investigation on the glycan-binding specificity of Agrocybe cylindracea galectin using molecular modeling and molecular dynamics simulation studies
JOURNAL OF MOLECULAR RECOGNITION, 28:528-538, SEP 2015
abstract, full text, DOI:10.1002/jmr.2468

Lewis, Martin A.; Hunihan, Lisa; Watson, John; Gentles, Robert G.; Hu, Shuanghua; Huang, Yazhong; Bronson, Joanne; Macor, John E.; Beno, Brett R.; Ferrante, Meredith; Hendricson, Adam; Knox, Ronald J.; Molski, Thaddeus F.; Kong, Yan; Cvijic, Mary Ellen; Rockwell, Kristin L.; Weed, Michael R.; Cacace, Angela M.; Westphal, Ryan S.; Alt, Andrew; Brown, Jeffrey M.
Discovery of D1 Dopamine Receptor Positive Allosteric Modulators: Characterization of Pharmacology and Identification of Residues that Regulate Species Selectivity
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 354:340-349, SEP 2015
abstract, full text, DOI:10.1124/jpet.115.224071

Dai, Yuejie; Zhen, Jing; Zhang, Xiuli; Zhong, Yonghui; Liu, Shaodan; Sun, Ziyue; Guo, Yue; Wu, Qingli
Analysis of the complex formation, interaction and electron transfer pathway between the "open" conformation of NADPH-cytochrome P450 reductase and aromatase
STEROIDS, 101:116-124, SEP 2015
abstract, full text, DOI:10.1016/j.steroids.2015.06.006

Marcinkowski, Lukasz; Kloskowski, Adam; Czub, Jacek; Namiesnik, Jacek; Warminska, Dorota
Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide - volumetric and compressibility studies
JOURNAL OF CHEMICAL THERMODYNAMICS, 88:36-43, SEP 2015
abstract, full text, DOI:10.1016/j.jct.2015.04.006

Alishahi, Marzieh; Kamali, Reza; Abouali, Omid
Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility behaviour
EUROPEAN PHYSICAL JOURNAL E, 38 Art. No. 92, AUG 31 2015
abstract, full text, DOI:10.1140/epje/i2015-15092-5

Nieto, Carlos T.; Gonzalez-Nunez, Veronica; Rodriguez, Raquel E.; Diez, David; Garrido, Narciso M.
Design, synthesis, pharmacological evaluation and molecular dynamics of beta-amino acids morphan-derivatives as novel ligands for opioid receptors
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 101:150-162, AUG 28 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.06.025

Chen, Xi; Hnida, Kathrin; Graewert, Melissa Ann; Andersen, Jan Terje; Iversen, Rasmus; Tuukkanen, Anne; Svergun, Dmitri; Sollid, Ludvig M.
Structural Basis for Antigen Recognition by Transglutaminase 2-specific Autoantibodies in Celiac Disease
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:21365-21375, AUG 28 2015
abstract, full text, DOI:10.1074/jbc.M115.669895

Xi, Yi-Bo; Chen, Xiang-Jun; Zhao, Wei-Jie; Yan, Yong-Bin
Congenital Cataract-Causing Mutation G129C in gamma C-Crystallin Promotes the Accumulation of Two Distinct Unfolding Intermediates That Form Highly Toxic Aggregates
JOURNAL OF MOLECULAR BIOLOGY, 427:2765-2781, AUG 28 2015
abstract, full text, DOI:10.1016/j.jmb.2015.07.001

Anishkin, Andriy; Vanegas, Juan M.; Rogers, David M.; Lorenzi, Philip L.; Chan, Wai Kin; Purwaha, Preeti; Weinstein, John N.; Sukharev, Sergei; Rempe, Susan B.
Catalytic Role of the Substrate Defines Specificity of Therapeutic L-Asparaginase
JOURNAL OF MOLECULAR BIOLOGY, 427:2867-2885, AUG 28 2015
abstract, full text, DOI:10.1016/j.jmb.2015.06.017

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10998-11009, AUG 27 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01687

Mondal, Padmabati; Biswas, Mithun; Goldau, Thomas; Heckel, Alexander; Burghardt, Irene
In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11275-11286, AUG 27 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03118

Ramirez-Salinas, G. Lizbeth; Michel Espinoza-Fonseca, L.
Atomistic Characterization of the First Step of Calcium Pump Activation Associated with Proton Countertransport
BIOCHEMISTRY, 54:5235-5241, AUG 25 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00672

Heim, Erin N.; Marston, Jez L.; Federman, Ross S.; Edwards, Anne P. B.; Karabadzhak, Alexander G.; Petti, Lisa M.; Engelman, Donald M.; DiMaio, Daniel
Biologically active LIL proteins built with minimal chemical diversity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E4717-E4725, AUG 25 2015
abstract, full text, DOI:10.1073/pnas.1514230112

Sondergaard, Siri; Aznauryan, Mikayel; Haustrup, Emil K.; Schiott, Birgit; Birkedal, Victoria; Corry, Ben
Dynamics of Fluorescent Dyes Attached to G-Quadruplex DNA and their Effect on FRET Experiments
CHEMPHYSCHEM, 16:2562-2570, AUG 24 2015
abstract, full text, DOI:10.1002/cphc.201500271

Sriwimol, Wilaiwan; Aroonkesorn, Aratee; Sakdee, Somsri; Kanchanawarin, Chalermpol; Uchihashi, Takayuki; Ando, Toshio; Angsuthanasombat, Chanan
Potential Prepore Trimer Formation by the Bacillus thuringiensis Mosquito-specific Toxin MOLECULAR INSIGHTS INTO A CRITICAL PREREQUISITE OF MEMBRANE-BOUND MONOMERS
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:20793-20803, AUG 21 2015
abstract, full text, DOI:10.1074/jbc.M114.627554

Sanchez-Badillo, Joel; Gallo, Marco; Alvarado, Sandra; Glossman-Mitnik, Daniel
Solvation Thermodynamic Properties of Hydrogen Sulfide in [C(4)mim][PF6], [C(4)mim][BF4], and (C(4)mim][Cl] Ionic Liquids, Determined by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10727-10737, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06525

Shi, Wei; Siefert, Nicholas S.; Morreale, Bryan D.
Molecular Simulations of CO2, H-2, H2O, and H2S Gas Absorption into Hydrophobic Poly(dimethylsiloxane) (PDMS) Solvent: Solubility and Surface Tension
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19253-19265, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b05806

Gorny, Krzysztof; Raczynski, Przemyslaw; Dendzik, Zbigniew; Gburski, Zygmunt
Odd-Even Effects in the Dynamics of Liquid Crystalline Thin Films on the Surface of Single Walled Carbon and Silicon Carbide Nanotubes: Computer Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19266-19271, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b05961

Lee, One-Sun; Carignano, Marcelo A.
Exfoliation of Electrolyte-Intercalated Graphene: Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19415-19422, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b03217

Tan, Bikan; Hodak, Miroslav; Lu, Wenchang; Bernholc, J.
Charge transport in DNA nanowires connected to carbon nanotubes
PHYSICAL REVIEW B, 92 Art. No. 075429, AUG 19 2015
abstract, full text, DOI:10.1103/PhysRevB.92.075429

Luitz, Manuel; Bomblies, Rainer; Ostermeir, Katja; Zacharias, Martin
Exploring biomolecular dynamics and interactions using advanced sampling methods
JOURNAL OF PHYSICS-CONDENSED MATTER, 27 Art. No. 323101, AUG 19 2015
abstract, full text, DOI:10.1088/0953-8984/27/32/323101

Pluhackova, Kristyna; Boeckmann, Rainer A.
Biomembranes in atomistic and coarse-grained simulations
JOURNAL OF PHYSICS-CONDENSED MATTER, 27 Art. No. 323103, AUG 19 2015
abstract, full text, DOI:10.1088/0953-8984/27/32/323103

Jones, Paul R.; Hao, Xiuqing; Cruz-Chu, Eduardo R.; Rykaczewski, Konrad; Nandy, Krishanu; Schutzius, Thomas M.; Varanasi, Kripa K.; Megaridis, Constantine M.; Walther, Jens H.; Koumoutsakos, Petros; Espinosa, Horacio D.; Patankar, Neelesh A.
Sustaining dry surfaces under water
SCIENTIFIC REPORTS, 5 Art. No. 12311, AUG 18 2015
abstract, full text, DOI:10.1038/srep12311

Watly, Joanna; Simonovsky, Eyal; Barbosa, Nuno; Spodzieja, Marta; Wieczorek, Robert; Rodziewicz-Motowidlo, Sylwia; Miller, Yifat; Kozlowski, Henryk
African Viper Poly-His Tag Peptide Fragment Efficiently Binds Metal Ions and Is Folded into an alpha-Helical Structure
INORGANIC CHEMISTRY, 54:7692-7702, AUG 17 2015
abstract, full text, DOI:10.1021/acs.inorgchem.5b01029

Mino-Galaz, German A.; Gutierrez, Gonzalo
Hydrogen bonds and asymmetrical heat diffusion in alpha-helices. A computational analysis
CHEMICAL PHYSICS LETTERS, 635:16-22, AUG 16 2015
abstract, full text, DOI:10.1016/j.cplett.2015.06.041

Raczynski, Przemyslaw; Raczynska, Violetta; Gorny, Krzysztof; Gburski, Zygmunt
Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 580:22-30, AUG 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.06.008

MacDonald, Corey A.; Boyd, Russell J.
Computational insights into the suicide inhibition of Plasmodium falciparum Fk506-binding protein 35
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 25:3221-3225, AUG 15 2015
abstract, full text, DOI:10.1016/j.bmcl.2015.05.079

Mahdavi, Somayeh; Kuyucak, Serdar
Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels
PLOS ONE, 10 Art. No. e0133000, AUG 14 2015
abstract, full text, DOI:10.1371/journal.pone.0133000

Zidar, Nace; Macut, Helena; Tomasic, Tihomir; Brvar, Matjaz; Montalvao, Sofia; Tammela, Paivi; Solmajer, Tom; Masic, Lucija Peterlin; Ilas, Janez; Kikelj, Danijel
N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation
JOURNAL OF MEDICINAL CHEMISTRY, 58:6179-6194, AUG 13 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00775

Kurnikov, Igor V.; Kurnikova, Maria
Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10275-10286, AUG 13 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01295

La Penna, Giovanni; Hureau, Christelle; Faller, Peter
Learning chemistry with multiple first-principles simulations
MOLECULAR SIMULATION, 41:780-787, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.927064

Koishi, Takahiro; Takeichi, Hironori
An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid
MOLECULAR SIMULATION, 41:801-807, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.923569

Nomura, Kentaro; Oikawa, Minoru; Kawai, Atsushi; Narumi, Tetsu; Yasuoka, Kenji
GPU-accelerated replica exchange molecular simulation on solid-liquid phase transition study of Lennard-Jones fluids
MOLECULAR SIMULATION, 41:874-880, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.954572

Kang, Hojin; Klauda, Jeffery B.
Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers
MOLECULAR SIMULATION, 41:948-954, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.926548

Mori, Yoshiharu; Okumura, Hisashi
Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide
MOLECULAR SIMULATION, 41:1035-1040, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.938071

Sadeghian, Keyarash; Ochsenfeld, Christian
Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:9824-9831, AUG 12 2015
abstract, full text, DOI:10.1021/jacs.5b01449

Kostopoulou, Ourania N.; Magoulas, George E.; Papadopoulos, Georgios E.; Mouzaki, Athanasia; Dinos, George P.; Papaioannou, Dionissios; Kalpaxis, Dimitrios L.
Synthesis and Evaluation of Chloramphenicol Homodimers: Molecular Target, Antimicrobial Activity, and Toxicity against Human Cells
PLOS ONE, 10 Art. No. e0134526, AUG 12 2015
abstract, full text, DOI:10.1371/journal.pone.0134526

Raina, Deepak; Agarwal, Praveen; Lee, James; Bharti, Ajit; McKnight, C. James; Sharma, Pankaj; Kharbanda, Surender; Kufe, Donald
Characterization of the MUC1-C Cytoplasmic Domain as a Cancer Target
PLOS ONE, 10 Art. No. e0135156, AUG 12 2015
abstract, full text, DOI:10.1371/journal.pone.0135156

Nagy-Smith, Katelyn; Moore, Eric; Schneider, Joel; Tycko, Robert
Molecular structure of monomorphic peptide fibrils within a kinetically trapped hydrogel network
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:9816-9821, AUG 11 2015
abstract, full text, DOI:10.1073/pnas.1509313112

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stephanie; Aspuru-Guzik, Alan; Kleinekathoefer, Ulrich
Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9995-10004, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03654

Atsmon-Raz, Yoav; Miller, Yifat
A Proposed Atomic Structure of the Self-Assembly of the Non-Amyloid-beta Component of Human alpha-Synuclein As Derived by Computational Tools
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10005-10015, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03760

Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro
All-Atom Molecular Dynamics Simulation of Protein Translocation through an alpha-Hemolysin Nanopore
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2963-2968, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01077

Vasilevskaya, Tatiana; Khrenova, Maria G.; Nemukhin, Alexander V.; Thiel, Walter
Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1621-1630, AUG 5 2015
abstract, full text, DOI:10.1002/jcc.23977

Goh, Boon Chong; Perilla, Juan R.; England, Matthew R.; Heyrana, Katrina J.; Craven, Rebecca C.; Schulten, Klaus
Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis
STRUCTURE, 23:1414-1425, AUG 4 2015
abstract, full text, TCBG publications, DOI:10.1016/j.str.2015.05.017

Baday, Sefer; Orabi, Esam A.; Wang, Shihao; Lamoureux, Guillaume; Berneche, Simon
Mechanism of NH4+ Recruitment and NH3 Transport in Rh Proteins
STRUCTURE, 23:1550-1557, AUG 4 2015
abstract, full text, DOI:10.1016/j.str.2015.06.010

Jahed, Zeinab; Shams, Hengameh; Mofrad, Mohammad R. K.
A Disulfide Bond Is Required for the Transmission of Forces through SUN-KASH Complexes
BIOPHYSICAL JOURNAL, 109:501-509, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.057

Liu, Yufeng; Ke, Meng; Gong, Haipeng
Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter
BIOPHYSICAL JOURNAL, 109:542-551, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.037

Leioatts, Nicholas; Romo, Tod D.; DaniaL, Shairy Azmy; Grossfield, Alan
Retinal Conformation Changes Rhodopsin's Dynamic Ensemble
BIOPHYSICAL JOURNAL, 109:608-617, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.046

Wells, Stephen A.; van der Kamp, Marc W.; McGeagh, John D.; Mulholland, Adrian J.
Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions
PLOS ONE, 10 Art. No. e0133372, AUG 4 2015
abstract, full text, DOI:10.1371/journal.pone.0133372

Diaz-Franulic, Ignacio; Sepulveda, Romina V.; Navarro-Quezada, Nieves; Gonzalez-Nilo, Fernando; Naranjo, David
Pore dimensions and the role of occupancy in unitary conductance of Shaker K channels
JOURNAL OF GENERAL PHYSIOLOGY, 146:133-146, AUG 2015
abstract, full text, DOI:10.1085/jgp.201411353

Geninatti, Thomas; Hood, R. Lyle; Bruno, Giacomo; Jain, Priya; Nicolov, Eugenia; Ziemys, Arturas; Grattoni, Alessandro
Sustained Administration of Hormones Exploiting Nanoconfined Diffusion through Nanochannel Membranes
MATERIALS, 8:5276-5288, AUG 2015
abstract, full text, DOI:10.3390/ma8085241

Theis, Jeanne L.; Zimmermann, Michael T.; Evans, Jared M.; Eckloff, Bruce W.; Wieben, Eric D.; Qureshi, Muhammad Y.; O'Leary, Patrick W.; Olson, Timothy M.
Recessive MYH6 Mutations in Hypoplastic Left Heart With Reduced Ejection Fraction
CIRCULATION-CARDIOVASCULAR GENETICS, 8:564-571, AUG 2015
abstract, full text, DOI:10.1161/CIRCGENETICS.115.001070

Yuchi, Zhiguang; Yuen, Siobhan M. Wong King; Lau, Kelvin; Underhill, Ainsley Q.; Cornea, Razvan L.; Fessenden, James D.; Van Petegem, Filip
Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant
NATURE COMMUNICATIONS, 6 Art. No. 7947, AUG 2015
abstract, full text, DOI:10.1038/ncomms8947

Ierich, Jessica C. M.; Oliveira, Guedmiller S.; Vig, Ana C. A.; Amarante, Adriano M.; Franca, Eduardo F.; Leite, Fabio L.; Mascarenhas, Yvonne P.
A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:1702-1709, AUG 2015
abstract, full text, DOI:10.5935/0103-5053.20150144

Tepavcevic, Sanja; Liu, Yuzi; Zhou, Dehua; Lai, Barry; Maser, Jorg; Zuo, Xiaobing; Chan, Henry; Kral, Petr; Johnson, Christopher S.; Stamenkovic, Vojislav; Markovic, Nenad M.; Rajh, Tijana
Nanostructured Layered Cathode for Rechargeable Mg-Ion Batteries
ACS NANO, 9:8194-8205, AUG 2015
abstract, full text, DOI:10.1021/acsnano.5b02450

Tse, Amanda; Verkhivker, Germady M.
Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:1645-1662, AUG 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00240

Verma, Saroj; Debnath, Utsab; Agarwal, Pooja; Srivastava, Kumkum; Prabhakar, Yenamandra S.
In Silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:1708-1719, AUG 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00392

Kumar, Rajendra; Grubmueller, Helmut
do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations
BIOINFORMATICS, 31:2583-2585, AUG 1 2015
abstract, full text, DOI:10.1093/bioinformatics/btv190

Omar, Sara Ibrahim; Tuszynski, Jack
Ranking the Binding Energies of p53 Mutant Activators and Their ADMET Properties
CHEMICAL BIOLOGY & DRUG DESIGN, 86:163-172, AUG 2015
abstract, full text, DOI:10.1111/cbdd.12480

Paoletta, Silvia; Sabbadin, Davide; von Kuegelgen, Ivar; Hinz, Sonja; Katritch, Vsevolod; Hoffmann, Kristina; Abdelrahman, Aliaa; Strassburger, Jens; Baqi, Younis; Zhao, Qiang; Stevens, Raymond C.; Moro, Stefano; Mueller, Christa E.; Jacobson, Kenneth A.
Modeling ligand recognition at the P2Y(12) receptor in light of X-ray structural information
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:737-756, AUG 2015
abstract, full text, DOI:10.1007/s10822-015-9858-z

Xu, Jinxing; Yuan, Haoliang; Ran, Ting; Zhang, Yanmin; Liu, Haichun; Lu, Shuai; Xiong, Xiao; Xu, Anyang; Jiang, Yulei; Lu, Tao; Chen, Yadong
A selectivity study of sodium-dependent glucose cotransporter 2/sodium-dependent glucose cotransporter 1 inhibitors by molecular modeling
JOURNAL OF MOLECULAR RECOGNITION, 28:467-479, AUG 2015
abstract, full text, DOI:10.1002/jmr.2464

Kong, Ren; Chang, Shan; Xia, Weiming; Wong, Stephen T. C.
Molecular dynamics simulation study reveals potential substrate entry path into gamma-secretase/presenilin-1
JOURNAL OF STRUCTURAL BIOLOGY, 191:120-129, AUG 2015
abstract, full text, DOI:10.1016/j.jsb.2015.07.001

Li Zan; Qi XiaoLe; Ren XianGang; Cui Lei; Wang XiaoMei; Zhu Ping
Molecular characteristics and evolutionary analysis of a very virulent infectious bursal disease virus
SCIENCE CHINA-LIFE SCIENCES, 58:731-738, AUG 2015
abstract, full text, DOI:10.1007/s11427-015-4900-x

Pietra, Francesco
On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 12:1163-1171, AUG 2015
abstract, full text, DOI:10.1002/cbdv.201400362

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3829-3843, AUG 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00503

Domene, Carmen; Jorgensen, Christian; Vanommeslaeghe, Kenno; Schofield, Christopher J.; MacKerell, Alexander, Jr.
Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3946-3954, AUG 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00411

Morales-Quintana, Luis; Alejandra Moya-Leon, Maria; Herrera, Raul
Computational study enlightens the structural role of the alcohol acyltransferase DFGWG motif
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 216, AUG 2015
abstract, full text, DOI:10.1007/s00894-015-2762-6

Barraza, Luis F.; Jimenez, Veronica A.; Alderete, Joel B.
Effect of PEGylation on the Structure and Drug Loading Capacity of PAMAM-G4 Dendrimers: A Molecular Modeling Approach on the Complexation of 5-Fluorouracil with Native and PEGylated PAMAM-G4
MACROMOLECULAR CHEMISTRY AND PHYSICS, 216:1689-1701, AUG 2015
abstract, full text, DOI:10.1002/macp.201500179

Cvijetic, Ilija N.; Tanc, Muhammet; Juranic, Ivan O.; Verbic, Tatjana Z.; Supuran, Claudiu T.; Drakulic, Branko J.
5-Aryl-1H-pyrazole-3-carboxylic acids as selective inhibitors of human carbonic anhydrases IX and XII
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4649-4659, AUG 1 2015
abstract, full text, DOI:10.1016/j.bmc.2015.05.052

Halder, Swagata; Surolia, Avadhesha; Mukhopadhyay, Chaitali
Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations
GLYCOCONJUGATE JOURNAL, 32:371-384, AUG 2015
abstract, full text, DOI:10.1007/s10719-015-9601-y

Rydzewski, Jakub; Strzalka, Wojciech; Nowak, Wieslaw
Nanomechanics of PCNA: A protein-made DNA sliding clamp
CHEMICAL PHYSICS LETTERS, 634:236-242, AUG 1 2015
abstract, full text, DOI:10.1016/j.cplett.2015.06.027

Jain, Amisha; Tripathi, Pranav; Shrotriya, Aniket; Chaudhary, Ritu; Singh, Ajeet
In silico analysis and modeling of putative T cell epitopes for vaccine design of Toscana virus
3 BIOTECH, 5:497-503, AUG 2015
abstract, full text, DOI:10.1007/s13205-014-0247-4

Mansour-Hendili, Lamisse; Blanchard, Anne; Le Pottier, Nelly; Roncelin, Isabelle; Lourdel, Stephane; Treard, Cyrielle; Gonzalez, Wendy; Vergara-Jaque, Ariela; Morin, Gilles; Colin, Estelle; Holder-Espinasse, Muriel; Bacchetta, Justine; Baudouin, Veronique; Benoit, Stephane; Berard, Etienne; Bourdat-Michel, Guylhene; Bouchireb, Karim; Burtey, Stephane; Cailliez, Mathilde; Cardon, Gerard; Cartery, Claire; Champion, Gerard; Chauveau, Dominique; Cochat, Pierre; Dahan, Karin; De la Faille, Renaud; Debray, Francois-Guillaume; Dehoux, Laurenne; Deschenes, Georges; Desport, Estelle; Devuyst, Olivier; Dieguez, Stella; Emma, Francesco; Fischbach, Michel; Fouque, Denis; Fourcade, Jacques; Francois, Helene; Gilbert-Dussardier, Brigitte; Hannedouche, Thierry; Houillier, Pascal; Izzedine, Hassan; Janner, Marco; Karras, Alexandre; Knebelmann, Bertrand; Lavocat, Marie-Pierre; Lemoine, Sandrine; Leroy, Valerie; Loirat, Chantal; Macher, Marie-Alice; Martin-Coignard, Dominique; Morin, Denis; Niaudet, Patrick; Nivet, Hubert; Nobili, Francois; Novo, Robert; Faivre, Laurence; Rigothier, Claire; Roussey-Kesler, Gwenaelle; Salomon, Remi; Schleich, Andreas; Sellier-Leclerc, Anne-Laure; Soulami, Kenza; Tiple, Aurelien; Ulinski, Tim; Vanhille, Philippe; Van Regemorter, Nicole; Jeunemaitre, Xavier; Vargas-Poussou, Rosa
Mutation Update of the CLCN5 Gene Responsible for Dent Disease 1
HUMAN MUTATION, 36:743-752, AUG 2015
abstract, full text, DOI:10.1002/humu.22804

Fiesel, Fabienne C.; Caulfield, Thomas R.; Moussaud-Lamodiere, Elisabeth L.; Ogaki, Kotaro; Dourado, Daniel F. A. R.; Flores, Samuel C.; Ross, Owen A.; Springer, Wolfdieter
Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin
HUMAN MUTATION, 36:774-786, AUG 2015
abstract, full text, DOI:10.1002/humu.22808

Slack, Ryan L.; Spiriti, Justin; Ahn, Jinwoo; Parniak, Michael A.; Zuckerman, Daniel M.; Ishima, Rieko
Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1526-1538, AUG 2015
abstract, full text, DOI:10.1002/prot.24843

Azamat, Jafar; Ebrahimzadeh, Alireza Rastkar; Sardroodi, Jaber Jahanbin; Gholinezhad, Leila
Molecular Dynamics Simulation of Nanoporous Graphene as Membrane for Ion Separation Under Induced Electric Field
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 12:1512-1518, AUG 2015
abstract, full text, DOI:10.1166/jctn.2015.3922

Sun, Qian; Zhu, Tao; Wang, Chang-yu; Ma, Ding
Binding of human SWI1 ARID domain to DNA without sequence specificity: A molecular dynamics study
JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY-MEDICAL SCIENCES, 35:469-476, AUG 2015
abstract, full text, DOI:10.1007/s11596-015-1455-9

Ferrante, Andrea; Templeton, Megan; Hoffman, Megan; Castellini, Margaret J.
The Thermodynamic Mechanism of Peptide-MHC Class II Complex Formation Is a Determinant of Susceptibility to HLA-DM
JOURNAL OF IMMUNOLOGY, 195:1251-1261, AUG 1 2015
abstract, full text, DOI:10.4049/jimmunol.1402367

Fossati, Sara Maria; Candiani, Simona; Noedl, Marie-Therese; Maragliano, Luca; Pennuto, Maria; Domingues, Pedro; Benfenati, Fabio; Pestarino, Mario; Zullo, Letizia
Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?
MOLECULAR NEUROBIOLOGY, 52:45-56, AUG 2015
abstract, full text, DOI:10.1007/s12035-014-8842-2

Sencanski, Milan; Dosen-Micovic, Ljiljana; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana
Theoretical insight into sulfur aromatic interactions with extension to D-2 receptor activation mechanism
STRUCTURAL CHEMISTRY, 26:1139-1149, AUG 2015
abstract, full text, DOI:10.1007/s11224-015-0574-z

Wu, Sangwook; Shim, Joong-Youn; Lee, Chang Jun; Pedersen, Lee G.
Do the crystallographic forms of prethrombin-2 revert to a single form in solution?
BIOPHYSICAL CHEMISTRY, 203:28-32, AUG-SEP 2015
abstract, full text, DOI:10.1016/j.bpc.2015.05.005

Sharma, Vivek; Ala-Vannesluoma, Pauliina; Vattulainen, Ilpo; Wikstrom, Marten; Rog, Tomasz
Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1847:690-697, AUG 2015
abstract, full text, DOI:10.1016/j.bbabio.2015.04.007

Gao, Weimin; She, Fenghua; Zhang, Juan; Dumee, Ludovic F.; He, Li; Hodgson, Peter D.; Kong, Lingxue
Understanding water and ion transport behaviour and permeability through poly(amide) thin film composite membrane
JOURNAL OF MEMBRANE SCIENCE, 487:32-39, AUG 1 2015
abstract, full text, DOI:10.1016/j.memsci.2015.03.052

Li, Jing; Newhall, Jillian; Ishiyama, Noboru; Gottardi, Cara; Ikura, Mitsuhiko; Leckband, Deborah E.; Tajkhorshid, Emad
Structural Determinants of the Mechanical Stability of alpha-Catenin
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:18890-18903, JUL 31 2015
abstract, full text, DOI:10.1074/jbc.M115.647941

Hamre, Anne Grethe; Jana, Suvamay; Holen, Matilde Mengkrog; Mathiesen, Geir; Vaeljamaee, Priit; Payne, Christina M.; Sorlie, Morten
Thermodynamic Relationships with Processivity in Serratia marcescens Family 18 Chitinases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9601-9613, JUL 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03817

Hsiao, Ya-Wen; Hedstrom, Magnus
Molecular Dynamics Simulations of NaCl Permeation in Bihydrated Montmorillonite Inter layer Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 119:17352-17361, JUL 30 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b01169

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 045106, JUL 28 2015
abstract, full text, DOI:10.1063/1.4927568

Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.
Free energy of ion hydration: Interface susceptibility and scaling with the ion size
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 044511, JUL 28 2015
abstract, full text, DOI:10.1063/1.4927570

Chiodo, Letizia; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni
A Structural Model of the Human alpha 7 Nicotinic Receptor in an Open Conformation
PLOS ONE, 10 Art. No. e0133011, JUL 24 2015
abstract, full text, DOI:10.1371/journal.pone.0133011

Rosler, Kirsten S.; Mercier, Evan; Andrews, Ian C.; Wieden, Hans-Joachim
Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:18650-18661, JUL 24 2015
abstract, full text, DOI:10.1074/jbc.M114.598227

Gosselin-Badaroudine, Pascal; Moreau, Adrien; Delemotte, Lucie; Cens, Thierry; Collet, Claude; Rousset, Matthieu; Charnet, Pierre; Klein, Michael L.; Chahine, Mohamed
Characterization of the honeybee AmNa(V)1 channel and tools to assess the toxicity of insecticides
SCIENTIFIC REPORTS, 5 Art. No. 12475, JUL 23 2015
abstract, full text, DOI:10.1038/srep12475

Rodriguez, Javier; Dolores Elola, M.
Molecular Dynamics Simulations of Ibuprofen Release from pH-Gated Silica Nanochannels
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8868-8878, JUL 23 2015
abstract, full text, DOI:10.1021/jp505585g

Rahaman, Obaidur; Kalimeri, Maria; Melchionna, Simone; Henin, Jerome; Sterpone, Fabio
Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8939-8949, JUL 23 2015
abstract, full text, DOI:10.1021/jp507571u

Martinez, Anna Victoria; Malolepsza, Edyta; Dominguez, Laura; Lu, Qing; Straub, John E.
Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA(2) in AOT Reverse Micelles
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9084-9090, JUL 23 2015
abstract, full text, DOI:10.1021/jp508813n

Silveira, Rodrigo L.; Skaf, Munir S.
Molecular Dynamics Simulations of Family 7 Cellobiohydrolase Mutants Aimed at Reducing Product Inhibition
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9295-9303, JUL 23 2015
abstract, full text, DOI:10.1021/jp509911m

Yu, Hao; Yzeiri, Irena; Hou, Binyang; Chen, Chiu-Hao; Bu, Wei; Vanysek, Petr; Chen, Yu-Sheng; Lin, Binhua; Kral, Petr; Schlossman, Mark L.
Electric Field Effect on Phospholipid Monolayers at an Aqueous-Organic Liquid-Liquid Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9319-9334, JUL 23 2015
abstract, full text, DOI:10.1021/jp5098525

Li, Hui; Ngo, Van; Da Siva, Mauricio Chagas; Salahub, Dennis R.; Callahan, Karen; Roux, Benoit; Noskov, Sergei Yu.
Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9401-9416, JUL 23 2015
abstract, full text, DOI:10.1021/jp510560k

Ahmad, Ashfaq; Cai, Yongfei; Chen, Xingqiang; Shuai, Jianwei; Han, Aidong
Conformational Dynamics of Response Regulator RegX3 from Mycobacterium tuberculosis
PLOS ONE, 10 Art. No. e0133389, JUL 22 2015
abstract, full text, DOI:10.1371/journal.pone.0133389

Huang, Jun; Jones, Bryan J.; Kazlauskas, Romas J.
Stabilization of an alpha/beta-Hydrolase by Introducing Pro line Residues: Salicylic Acid Binding Protein 2 from Tobacco
BIOCHEMISTRY, 54:4330-4341, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00333

McCormick, James W.; Vogel, Pia D.; Wise, John G.
Multiple Drug Transport Pathways through Human P-Glycoprotein
BIOCHEMISTRY, 54:4374-4390, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00018

Gonzalez, Walter G.; Arango, Andres S.; Miksovska, Jaroslava
Amphiphilic Residues 29-44 of DREAM N-Termini Mediate Calmodulin:DREAM Complex Formation
BIOCHEMISTRY, 54:4391-4403, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00251

Capponi, Sara; Heyden, Matthias; Bondar, Ana-Nicoleta; Tobias, Douglas J.; White, Stephen H.
Anomalous behavior of water inside the SecY translocon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:9016-9021, JUL 21 2015
abstract, full text, DOI:10.1073/pnas.1424483112

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe
Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:17642-17654, JUL 17 2015
abstract, full text, DOI:10.1074/jbc.M115.651877

Song, Hyun Deok; Zhu, Fangqiang
Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter
PLOS ONE, 10 Art. No. e0133388, JUL 17 2015
abstract, full text, DOI:10.1371/journal.pone.0133388

Chen, Yu; Bauer, Benedikt W.; Rapoport, Tom A.; Gumbart, James C.
Conformational Changes of the Clamp of the Protein Translocation ATPase SecA
JOURNAL OF MOLECULAR BIOLOGY, 427:2348-2359, JUL 17 2015
abstract, full text, DOI:10.1016/j.jmb.2015.05.003

Espinoza-Fonseca, L. Michel; Autry, Joseph M.; Thomas, David D.
Sarcolipin and phospholamban inhibit the calcium pump by populating a similar metal ion-free intermediate state
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 463:37-41, JUL 17 2015
abstract, full text, DOI:10.1016/j.bbrc.2015.05.012

Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca
Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly
PLOS ONE, 10 Art. No. e0132706, JUL 16 2015
abstract, full text, DOI:10.1371/journal.pone.0132706

Chen, Chuanying; Esadze, Alexandre; Zandarashvili, Levani; Dan Nguyen; Pettitt, B. Montgomery; Iwahara, Junji
Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2733-2737, JUL 16 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01134

de Veer, Simon J.; Swedberg, Joakim E.; Akcan, Muharrem; Rosengren, K. Johan; Brattsand, Maria; Craik, David J.; Harris, Jonathan M.
Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition
BIOCHEMICAL JOURNAL, 469:243-253, JUL 15 2015
abstract, full text, DOI:10.1042/BJ20150412

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. e0132356, JUL 15 2015
abstract, full text, DOI:10.1371/journal.pone.0132356

Lemkul, Justin A.; Roux, Benoit; van der Spoel, David; MacKerell, Alexander D., Jr.
Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1473-1479, JUL 15 2015
abstract, full text, DOI:10.1002/jcc.23937

Bermudez, Marcel; Wolber, Gerhard
Structure versus function-The impact of computational methods on the discovery of specific GPCR-ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:3907-3912, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.026

Trujillo, Kevin; Paoletta, Silvia; Kiselev, Evgeny; Jacobson, Kenneth A.
Molecular modeling of the human P2Y(14) receptor: A template for structure-based design of selective agonist ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4056-4064, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.042

Deganutti, Giuseppe; Cuzzolin, Alberto; Ciancetta, Antonella; Moro, Stefano
Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A(3) adenosine receptor positive allosteric modulator LUF6000
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4065-4071, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.039

Chen, Chen; Liu, Yonglan; Zhang, Jin; Zhang, Mingzhen; Zheng, Jie; Teng, Yong; Liang, Guizhao
A quantitative sequence-aggregation relationship predictor applied as identification of self-assembled hexapeptides
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 145:7-16, JUL 15 2015
abstract, full text, DOI:10.1016/j.chemolab.2015.04.009

Nguyen, Lam T.; Gumbart, James C.; Beeby, Morgan; Jensen, Grant J.
Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E3689-E3698, JUL 14 2015
abstract, full text, DOI:10.1073/pnas.1504281112

Chen, Junmei; Hinckley, Jesse D.; Haberichter, Sandra; Jacobi, Paula; Montgomery, Robert; Flood, Veronica H.; Wong, Randall; Interlandi, Gianluca; Chung, Dominic W.; Lopez, Jose A.; Di Paola, Jorge
Variable content of von Willebrand factor mutant monomer drives the phenotypic variability in a family with von Willebrand disease
BLOOD, 126:262-269, JUL 9 2015
abstract, full text, DOI:10.1182/blood-2014-11-613935

Garcia-Gimenez, Elena; Alcaraz, Antonio; Aguilella-Arzo, Marcel; Aguilella, Vicente M.
Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8475-8479, JUL 9 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03547

Katti, Dinesh R.; Sharma, Anurag; Pradhan, Shashindra Man; Katti, Kalpana S.
Carbon nanotube proximity influences rice DNA
CHEMICAL PHYSICS, 455:17-22, JUL 9 2015
abstract, full text, DOI:10.1016/j.chemphys.2015.03.015

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi
Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 015101, JUL 7 2015
abstract, full text, DOI:10.1063/1.4923010

Weber, Adrian C. J.; Burnell, E. Elliott; Meerts, W. Leo; de Lange, Cornelis A.; Dong, Ronald Y.; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio
Communication: Molecular dynamics and H-1 NMR of n-hexane in liquid crystals
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 011103, JUL 7 2015
abstract, full text, DOI:10.1063/1.4923253

van den Biggelaar, Maartje; Madsen, Jesper J.; Faber, Johan H.; Zuurveld, Marleen G.; van der Zwaan, Carmen; Olsen, Ole H.; Stennicke, Henning R.; Mertens, Koen; Meijer, Alexander B.
Factor VIII Interacts with the Endocytic Receptor Low-density Lipoprotein Receptor-related Protein 1 via an Extended Surface Comprising "Hot-Spot" Lysine Residues
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:16463-16476, JUL 3 2015
abstract, full text, DOI:10.1074/jbc.M115.650911

Vasco, Aldrin V.; Perez, Carlos S.; Morales, Fidel E.; Garay, Hilda E.; Vasilev, Dimitar; Gavin, Jose A.; Wessjohann, Ludger A.; Rivera, Daniel G.
Macrocyclization of Peptide Side Chains by the Ugi Reaction: Achieving Peptide Folding and Exocyclic N-Functionalization in One Shot
JOURNAL OF ORGANIC CHEMISTRY, 80:6697-6707, JUL 3 2015
abstract, full text, DOI:10.1021/acs.joc.5b00858

Kaware, Ravindra; Desai, Salil
Molecular dynamics modeling of water nanodroplet spreading on topographically patterned silicon dioxide and silicon nitride substrates
IIE TRANSACTIONS, 47:767-782, JUL 3 2015
abstract, full text, DOI:10.1080/0740817X.2014.973983

Alsamarah, Abdelaziz; LaCuran, Alecander E.; Oelschlaeger, Peter; Hao, Jijun; Luo, Yun
Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity
PLOS ONE, 10 Art. No. e0132221, JUL 2 2015
abstract, full text, DOI:10.1371/journal.pone.0132221

Zhang, Yuqi; Young, Ryan M.; Thazhathveetil, Arun K.; Singh, Arunoday P. N.; Liu, Chaoren; Berlin, Yuri A.; Grozema, Ferdinand C.; Lewis, Frederick D.; Ratner, Mark A.; Renaud, Nicolas; Siriwong, Khatcharin; Voityuk, Alexander A.; Wasielewski, Michael R.; Beratan, David N.
Conformationally Gated Charge Transfer in DNA Three-Way Junctions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2434-2438, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00863

Mottin, Melina; Souza, Paulo C. T.; Skaf, Munir S.
Molecular Recognition of PPAR gamma by Kinase Cdk5/p25: Insights from a Combination of Protein-Protein Docking and Adaptive Biasing Force Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8330-8339, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04269

Duboue-Dijon, Elise; Laage, Damien
Characterization of the Local Structure in Liquid Water by Various Order Parameters
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8406-8418, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02936

Ambrosia, Matthew Stanley; Jang, Joonkyung; Ha, Man Yeong
Static and dynamic hydrophobicity on a nano-sized groove/ridge surface
COMPUTERS & FLUIDS, 114:75-83, JUL 2 2015
abstract, full text, DOI:10.1016/j.compfluid.2015.02.010

Chwastyk, Mateusz; Bernaola, Adolfo Poma; Cieplak, Marek
Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome
PHYSICAL BIOLOGY, 12 Art. No. 046002, JUL 2015
abstract, full text, DOI:10.1088/1478-3975/12/4/046002

Petukh, Marharyta; Li, Minghui; Alexov, Emil
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004276, JUL 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004276

Ramirez-Sarmiento, Cesar A.; Noel, Jeffrey K.; Valenzuela, Sandro L.; Artsimovitch, Irina
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004379, JUL 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004379

Li, Rongzhong; Macnamara, Lindsay M.; Leuchter, Jessica D.; Alexander, Rebecca W.; Cho, Samuel S.
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:15872-15902, JUL 2015
abstract, full text, DOI:10.3390/ijms160715872

Goryashchenko, Alexander S.; Khrenova, Maria G.; Bochkova, Anna A.; Ivashina, Tatiana V.; Vinokurov, Leonid M.; Savitsky, Alexander P.
Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:16642-16654, JUL 2015
abstract, full text, DOI:10.3390/ijms160716642

Schwerdt, Julian G.; MacKenzie, Katrin; Wright, Frank; Oehme, Daniel; Wagner, John M.; Harvey, Andrew J.; Shirley, Neil J.; Burton, Rachel A.; Schreiber, Miriam; Halpin, Claire; Zimmer, Jochen; Marshall, David F.; Waugh, Robbie; Fincher, Geoffrey B.
Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses
PLANT PHYSIOLOGY, 168:968-983, JUL 2015
abstract, full text, DOI:10.1104/pp.15.00140

Zeng Yan; Zhang Yong; Song XianQiang; Ji QingHua; Ye Sheng; Zhang RongGuang; Lou JiZhong
The conformational states of talin autoinhibition complex and its activation under forces
SCIENCE CHINA-LIFE SCIENCES, 58:694-703, JUL 2015
abstract, full text, DOI:10.1007/s11427-015-4873-9

Malmstrom, Robert D.; Kornev, Alexandr P.; Taylor, Susan S.; Amaro, Rommie E.
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
NATURE COMMUNICATIONS, 6 Art. No. 7588, JUL 2015
abstract, full text, DOI:10.1038/ncomms8588

Castillo, Juan P.; Rui, Huan; Basilio, Daniel; Das, Avisek; Roux, Benoit; Latorre, Ramon; Bezanilla, Francisco; Holmgren, Miguel
Mechanism of potassium ion uptake by the Na+/K+-ATPase
NATURE COMMUNICATIONS, 6 Art. No. 7622, JUL 2015
abstract, full text, DOI:10.1038/ncomms8622

Clemens, Jonathon B.; Kibar, Osman; Chachisvilis, Mirianas
A molecular propeller effect for chiral separation and analysis
NATURE COMMUNICATIONS, 6 Art. No. 7868, JUL 2015
abstract, full text, DOI:10.1038/ncomms8868

Tamura, Koichi; Hayashi, Shigehiko
Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2900-2917, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00120

Chen, Nanhao; Zhao, Yuan; Lu, Jianing; Wu, Ruibo; Cao, Zexing
Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3180-3188, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00045

Wan, Shunzhou; Knapp, Bernhard; Wright, David W.; Deane, Charlotte M.; Coveney, Peter V.
Rapid, Precise, and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3346-3356, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00179

Moral, M.; Son, W. -J.; Sancho-Garcia, J. C.; Oivier, Y.; Muccioli, L.
Cost-Effective Force Field Tailored for Solid-Phase Simulations of OLED Materials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3383-3392, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00164

Di Marino, Daniele; Chillemi, Giovanni; De Rubeis, Silvia; Tramontano, Anna; Achsel, Tilmann; Bagni, Claudia
MD and Docking Studies Reveal That the Functional Switch of CYFIP1 is Mediated by a Butterfly-like Motion
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3401-3410, JUL 2015
abstract, full text, DOI:10.1021/ct500431h

Cortes-Ciriano, Isidro; Bouvier, Guillaume; Nilges, Michael; Maragliano, Luca; Malliavin, Therese E.
Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3446-3454, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00153

Walczewska-Szewc, Katarzyna; Depazes, Evelyne; Corry, Ben
Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3455-3465, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00205

Park, Soohyung; Beayen, Andrew H.; Klauda, Jeffery B.; Im, Wonpil
How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3466-3477, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00232

Kimanius, Dari; Pettersson, Ingrid; Schluckebier, Gerd; Lindahl, Erik; Andersson, Magnus
SAXS-Guided Metadynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3491-3498, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00299

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3499-3509, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00356

Xu, Xuefei; Zheng, Jingjing; Truhlar, Donald G.
Ultraviolet Absorption Spectrum of Malonaldehyde in Water Is Dominated by Solvent-Stabilized Conformations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:8026-8029, JUL 1 2015
abstract, full text, DOI:10.1021/jacs.5b04845

Ficici, Emel; Andricioaei, Ioan; Howorka, Stefan
Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance
NANO LETTERS, 15:4822-4828, JUL 2015
abstract, full text, DOI:10.1021/acs.nanolett.5b01960

Arias, Hugo R.; Feuerbach, Dominik; Ortells, Marcelo
Functional and structural interaction of (-)-lobeline with human alpha 4 beta 2 and alpha 4 beta 4 nicotinic acetylcholine receptor subtypes
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 64:15-24, JUL 2015
abstract, full text, DOI:10.1016/j.biocel.2015.03.003

Mucic, Ivana D.; Nikolic, Milan R.; Stojanovic, Srdan D.
Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies
PROTOPLASMA, 252:947-958, JUL 2015
abstract, full text, DOI:10.1007/s00709-014-0727-8

Gao, Yi; Olsen, Kenneth W.
Drug-Polymer Interactions at Water-Crystal Interfaces and Implications for Crystallization Inhibition: Molecular Dynamics Simulations of Amphiphilic Block Copolymer Interactions with Tolazamide Crystals
JOURNAL OF PHARMACEUTICAL SCIENCES, 104:2132-2141, JUL 2015
abstract, full text, DOI:10.1002/jps.24442

Mascayano, Carolina; Espinosa, Victoria; Sepulveda-Boza, Silvia; Hoobler, Eric K.; Perry, Steve; Diaz, Giovanni; Holman, Theodore R.
Enzymatic Studies of Isoflavonoids as Selective and Potent Inhibitors of Human Leukocyte 5-Lipo-Oxygenase
CHEMICAL BIOLOGY & DRUG DESIGN, 86:894-901, JUL 2015
abstract, full text, DOI:10.1111/cbdd.12469

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5:310-323, JUL-AUG 2015
abstract, full text, DOI:10.1002/wcms.1220

Mangiatordi, Giuseppe Felice; Alberga, Domenico; Siragusa, Lydia; Goracci, Laura; Lattanzi, Gianluca; Nicolotti, Orazio
Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1462-1471, JUL 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.03.019

Garate, Jose Antonio; Stoecki, Johannes; del Carmen Fernandez-Alonso, Maria; Artner, Daniel; Haegman, Mira; Oostenbrink, Chris; Jimenez-Barbero, Jesus; Beyaert, Rudi; Heine, Holger; Kosma, Paul; Zamyatina, Alla
Anti-endotoxic activity and structural basis for human MD-2 center dot TLR4 antagonism of tetraacylated lipid A mimetics based on beta GlcN(1 <-> 1)alpha GlcN scaffold
INNATE IMMUNITY, 21:490-503, JUL 2015
abstract, full text, DOI:10.1177/1753425914550426

Weng, Lindong; Elliott, Gloria D.
Distinctly Different Glass Transition Behaviors of Trehalose Mixed with Na2HPO4 or NaH2PO4: Evidence for its Molecular Origin
PHARMACEUTICAL RESEARCH, 32:2217-2228, JUL 2015
abstract, full text, DOI:10.1007/s11095-014-1610-1

Sharpe, Laura J.; Rao, Geetha; Jones, Peter M.; Glancey, Elizabeth; Aleidi, Shereen M.; George, Anthony M.; Brown, Andrew J.; Gelissen, Ingrid C.
Cholesterol sensing by the ABCG1 lipid transporter: Requirement of a CRAC motif in the final transmembrane domain
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1851:956-964, JUL 2015
abstract, full text, DOI:10.1016/j.bbalip.2015.02.016

Glaser, Jens; Trung Dac Nguyen; Anderson, Joshua A.; Lui, Pak; Spiga, Filippo; Millan, Jaime A.; Morse, David C.; Glotzer, Sharon C.
Strong scaling of general-purpose molecular dynamics simulations on GPUs
COMPUTER PHYSICS COMMUNICATIONS, 192:97-107, JUL 2015
abstract, full text, DOI:10.1016/j.cpc.2015.02.028

Brown, Aaron H.; Walsh, Tiffany R.
An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture
COMPUTER PHYSICS COMMUNICATIONS, 192:278-281, JUL 2015
abstract, full text, DOI:10.1016/j.cpc.2015.02.025

Guerra, Fernando P.; Reyes, Luz; Vergara-Jaque, Ariela; Campos-Hernandez, Carola; Gutierrez, Adelina; Perez-Diaz, Jorge; Perez-Diaz, Ricardo; Blaudez, Damien; Ruiz-Lara, Simon
Populus deltoides Kunitz trypsin inhibitor 3 confers metal tolerance and binds copper, revealing a new defensive role against heavy metal stress
ENVIRONMENTAL AND EXPERIMENTAL BOTANY, 115:28-37, JUL 2015
abstract, full text, DOI:10.1016/j.envexpbot.2015.02.005

Hu, Benfeng; Ge, Zhenpeng; Li, Xiaoyi
Interface Adsorption Taking the Most Advantageous Conformation for Electron Transfer Between Graphene and Cytochrome c
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 15:4863-4869, JUL 2015
abstract, full text, DOI:10.1166/jnn.2015.9853

Prigozhin, Maxim B.; Chao, Shu-Han; Sukenik, Shahar; Pogorelov, Taras V.; Gruebele, Martin
Mapping fast protein folding with multiple-site fluorescent probes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:7966-7971, JUN 30 2015
abstract, full text, DOI:10.1073/pnas.1422683112

Drake, Justin A.; Pettitt, B. Montgomery
Force field-dependent solution properties of glycine oligomers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1275-1285, JUN 30 2015
abstract, full text, DOI:10.1002/jcc.23934

Cluxton, Christopher D.; Caffrey, Brian E.; Kinsella, Gemma K.; Moynagh, Paul N.; Fares, Mario A.; Fallon, Padraic G.
Functional conservation of an ancestral Pellino protein in helminth species
SCIENTIFIC REPORTS, 5 Art. No. 11687, JUN 29 2015
abstract, full text, DOI:10.1038/srep11687

Takemoto, Mizuki; Kato, Hideaki E.; Koyama, Michio; Ito, Jumpei; Kamiya, Motoshi; Hayashi, Shigehiko; Maturana, Andres D.; Deisseroth, Karl; Ishitani, Ryuichiro; Nureki, Osamu
Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening
PLOS ONE, 10 Art. No. e0131094, JUN 26 2015
abstract, full text, DOI:10.1371/journal.pone.0131094

Caceres-Delpiano, Javier; Teneb, Jaime; Mansilla, Rodrigo; Garcia, Apolinaria; Salas-Burgos, Alexis
Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study
BMC STRUCTURAL BIOLOGY, 15 Art. No. 11, JUN 26 2015
abstract, full text, DOI:10.1186/s12900-015-0038-0

Fuerst, Oliver; Lin, Yibin; Granell, Meritxell; Leblanc, Gerard; Padros, Esteve; Lorenz-Fonfria, Victor A.; Cladera, Josep
The Melibiose Transporter of Escherichia coli CRITICAL CONTRIBUTION OF LYS-377 TO THE STRUCTURAL ORGANIZATION OF THE INTERACTING SUBSTRATE BINDING SITES
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:16261-16271, JUN 26 2015
abstract, full text, DOI:10.1074/jbc.M115.642678

Baylon, Javier L.; Tajkhorshid, Emad
Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7882-7893, JUN 25 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02135

Cao, Ruyin; Wu, Shanshan
In silico properties characterization of water-soluble gamma-cyclodextrin bi-capped C-60 complex: Free energy and geometrical insights for stability and solubility
CARBOHYDRATE POLYMERS, 124:188-195, JUN 25 2015
abstract, full text, DOI:10.1016/j.carbpol.2015.02.014

Nishihara, Yasutaka; Kitao, Akio
Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:7737-7742, JUN 23 2015
abstract, full text, DOI:10.1073/pnas.1502991112

Boczek, Edgar E.; Reefschlaeger, Lasse G.; Dehling, Marco; Struller, Tobias J.; Haeusler, Elisabeth; Seidl, Andreas; Kaila, Ville R. I.; Buchner, Johannes
Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E3189-E3198, JUN 23 2015
abstract, full text, DOI:10.1073/pnas.1424342112

Luan, Binquan; Huynh, Tien; Zhou, Ruhong
Simplified TiO2 force fields for studies of its interaction with biomolecules
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 234102, JUN 21 2015
abstract, full text, DOI:10.1063/1.4922618

Gu, Ying; Zhou, Hong; Gan, Yichao; Zhang, Jiawei; Chen, Jianghua; Gan, Xiaoxian; Li, Hongzhi; Zheng, Weiwei; Meng, Zhipeng; Ma, Xiaoxiao; Wang, Xichun; Xu, Xiaohua; Xu, Ganyu; Lu, Xiaoya; Liang, Yun; Zhang, Xuzhao; Lu, Xinliang; Huang, Wendong; Xu, Rongzhen
Small-molecule induction of phospho-eIF4E sumoylation and degradation via targeting its phosphorylated serine 209 residue
ONCOTARGET, 6:15111-15121, JUN 20 2015
abstract, full text

Gao, Feng; Kight, Alicia D.; Henderson, Rory; Jayanthi, Srinivas; Patel, Parth; Murchison, Marissa; Sharma, Priyanka; Goforth, Robyn L.; Kumar, Thallapuranam Krishnaswamy Suresh; Henry, Ralph L.; Heyes, Colin D.
Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:15462-15474, JUN 19 2015
abstract, full text, DOI:10.1074/jbc.M114.624346

Amin, Muhamed; Vogt, Leslie; Szejgis, Witold; Vassiliev, Serguei; Brudvig, Gary W.; Bruce, Doug; Gunner, M. R.
Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7366-7377, JUN 18 2015
abstract, full text, DOI:10.1021/jp510948e

Plehn, Thomas; Ziemann, Dirk; Megow, Joerg; May, Volkhard
Frenkel to Wannier-Mott Exciton Transition: Calculation of FRET Rates for a Tubular Dye Aggregate Coupled to a CdSe Nanocrystal
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7467-7472, JUN 18 2015
abstract, full text, DOI:10.1021/jp5111696

Kokhan, Oleksandr; Ponomarenko, Nina S.; Pokkuluri, P. Raj; Schiffer, Marianne; Mulfort, Karen L.; Tiede, David. M.
Bidirectional Photoinduced Electron Transfer in Ruthenium(II)-Tris-bipyridyl-Modified PpcA, a Multi-heme c-Type Cytochrome from Geobacter sulfurreducens
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7612-7624, JUN 18 2015
abstract, full text, DOI:10.1021/jp511558f

Holland, Bryan W.; Berry, Mark D.; Gray, C. G.; Tomberli, Bruno
A Permeability Study of O-2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers
PLOS ONE, 10 Art. No. e0122468, JUN 18 2015
abstract, full text, DOI:10.1371/journal.pone.0122468

Guvench, Olgun
Revealing the mechanisms of protein disorder and N-glycosylation in CD44-hyaluronan binding using molecular simulation
FRONTIERS IN IMMUNOLOGY, 6:1-9, JUN 16 2015
abstract, full text, DOI:10.3389/fimmu.2015.00305

Tse, Amanda; Verkhivker, Gennady M.
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
PLOS ONE, 10 Art. No. e0130203, JUN 15 2015
abstract, full text, DOI:10.1371/journal.pone.0130203

Shen Zhuang-Lin; He Gao-Hong; Zhang Ning; Hao Ce
Molecular Dynamics Simulation of Reverse-Osmotic Salt Rejection and Water Transport through Double-Walled Carbon Nanotube
ACTA PHYSICO-CHIMICA SINICA, 31:1025-1034, JUN 15 2015
abstract, full text, DOI:10.3866/PKU.WHXB201504141

Tian, He; Sakmar, Thomas P.; Huber, Thomas
Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR
CHEMBIOCHEM, 16:1314-1322, JUN 15 2015
abstract, full text, DOI:10.1002/cbic.201500030

Weng, Lindong; Chen, Cong; Li, Weizhong
Calorimetric and molecular simulation study on unfrozen water characteristics in aqueous sugar solutions: implications for biopreservation
MOLECULAR SIMULATION, 41:691-698, JUN 13 2015
abstract, full text, DOI:10.1080/08927022.2014.917299

Li, Junwei; Lu, Shouqin; Liu, Yuzhi; Pang, Chunli; Chen, Yafei; Zhang, Suhua; Yu, Hui; Long, Mian; Zhang, Hailin; Logothetis, Diomedes E.; Zhan, Yong; An, Hailong
Identification of the Conformational transition pathway in PIP2 Opening Kir Channels
SCIENTIFIC REPORTS, 5 Art. No. 11289, JUN 11 2015
abstract, full text, DOI:10.1038/srep11289

Espinoza-Fonseca, L. Michel; Ramirez-Salinas, G. Lizbeth
Microsecond Molecular Simulations Reveal a Transient Proton Pathway in the Calcium Pump
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:7055-7058, JUN 10 2015
abstract, full text, DOI:10.1021/jacs.5b03814

Wirth, Anna Jean; Liu, Yaxin; Prigozhin, Maxim B.; Schulten, Klaus; Gruebele, Martin
Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:7152-7159, JUN 10 2015
abstract, full text, TCBG publications, DOI:10.1021/jacs.5b02474

Yao, Kai; Tan, Pengli; Luo, Yinchan; Feng, Liangzhu; Xu, Ligeng; Liu, Zhuang; Li, Youyong; Peng, Rui
Graphene Oxide Selectively Enhances Thermostability of Trypsin
ACS APPLIED MATERIALS & INTERFACES, 7:12270-12277, JUN 10 2015
abstract, full text, DOI:10.1021/acsami.5b03118

Cheng, Mary Hongying; Block, Ethan; Hu, Feizhuo; Cobanoglu, Murat Can; Sorkin, Alexander; Bahar, Ivet
Insights into the modulation of dopamine transporter function by amphetamine, orphenadrine, and cocaine binding
FRONTIERS IN NEUROLOGY, 6 Art. No. UNSP 134, JUN 9 2015
abstract, full text, DOI:10.3389/fneur.2015.00134

Bakalis, Evangelos; Hoefinger, Siegfried; Venturini, Alessandro; Zerbetto, Francesco
Crossover of two power laws in the anomalous diffusion of a two lipid membrane
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 215102, JUN 7 2015
abstract, full text, DOI:10.1063/1.4921891

Wang, Conan K.; Northfield, Susan E.; Swedberg, Joakim E.; Colless, Barbara; Chaousis, Stephanie; Price, David A.; Liras, Spiros; Craik, David J.
Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 97:202-213, JUN 5 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.04.049

Cao Ping; Luo Cheng-Lin; Chen Gui-Hu; Han Dian-Rong; Zhu Xing-Feng; Dai Ya-Fei
Flux controllable pumping of water molecules in a double-walled carbon nanotube
ACTA PHYSICA SINICA, 64 Art. No. 116101, JUN 5 2015
abstract, full text, DOI:10.7498/aps.64.116101

Mei, Ye; Simmonett, Andrew C.; Pickard, Frank C.; DiStasio, Robert A., Jr.; Brooks, Bernard R.; Shao, Yihan
Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions
JOURNAL OF PHYSICAL CHEMISTRY A, 119:5865-5882, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpca.5b03159

Gorczyca, Marcelina; Korchowiec, Beata; Korchowiec, Jacek; Trojan, Sonia; Rubio-Magnieto, Jenifer; Luis, Santiago V.; Rogalska, Ewa
A Study of the Interaction between a Family of Gemini Amphiphilic Pseudopeptides and Model Monomolecular Film Membranes Formed with a Cardiolipin
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6668-6679, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02575

Schonbeck, Christian; Li, Hui; Han, Bao-Hang; Laursen, Bo W.
Solvent Effects and Driving Forces in Pillararene Inclusion Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6711-6720, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02515

Muecksch, Christian; Roesch, Christina; Mueller-Renno, Christine; Ziegler, Christiane; Urbassek, Herbert M.
Consequences of Hydrocarbon Contamination for Wettability and Protein Adsorption on Graphite Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 119:12496-12501, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b02948

Balme, Sebastien; Picaud, Fabien; Manghi, Manoel; Palmeri, John; Bechelany, Mikhael; Cabello-Aguilar, Simon; Abou-Chaaya, Adib; Miele, Philippe; Balanzat, Emmanuel; Janot, Jean Marc
Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation
SCIENTIFIC REPORTS, 5 Art. No. 10135, JUN 3 2015
abstract, full text, DOI:10.1038/srep10135

Farhi, Emmanuel; Ferran, Ghislain; Haeck, Wim; Pellegrini, Eric; Calzavara, Yoann
Light and heavy water dynamic structure factor for neutron transport codes
JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY, 52:844-856, JUN 3 2015
abstract, full text, DOI:10.1080/00223131.2014.984002

Suzuki, Takashi; Suzuki, Miho; Ogino, Shinji; Umemoto, Ryo; Nishida, Noritaka; Shimada, Ichio
Mechanical force effect on the two-state equilibrium of the hyaluronan-binding domain of CD44 in cell rolling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:6991-6996, JUN 2 2015
abstract, full text, DOI:10.1073/pnas.1423520112

Ieong, Pek; Amaro, Rommie E.; Li, Wilfred W.
Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin
BIOPHYSICAL JOURNAL, 108:2704-2712, JUN 2 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.025

Kinde, Monica N.; Chen, Qiang; Lawless, Matthew J.; Mowrey, David D.; Xu, Jiawei; Saxena, Sunil; Xu, Yan; Tang, Pei
Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC
STRUCTURE, 23:995-1004, JUN 2 2015
abstract, full text, DOI:10.1016/j.str.2015.03.017

Park, Hahnbeom; DiMaio, Frank; Baker, David
The Origin of Consistent Protein Structure Refinement from Structural Averaging
STRUCTURE, 23:1123-1128, JUN 2 2015
abstract, full text, DOI:10.1016/j.str.2015.03.022

Gong Lin-Chen; Zhou Xin; Ouyang Zhong-Can
Reweighted ensemble dynamics simulations: Theory, improvement, and application
CHINESE PHYSICS B, 24 Art. No. 060202, JUN 2015
abstract, full text, DOI:10.1088/1674-1056/24/6/060202

Priya, Prerna; Maity, Atanu; Majumdar, Sarmistha; Dastidar, Shubhra Ghosh
Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 59:1-13, JUN 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.02.005

Supunyabut, Chirayut; Fuklang, Sunit; Sompornpisut, Pornthep
Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 59:81-91, JUN 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.04.003

Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad
Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. UNSP e1004287, JUN 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004287

Kai, Tianhan; Zhang, Lin; Wang, Xiaoying; Jing, Aihua; Zhao, Bingqing; Yu, Xiang; Zheng, Jie; Zhou, Feimeng
Tabersonine Inhibits Amyloid Fibril Formation and Cytotoxicity of A beta(1-42)
ACS CHEMICAL NEUROSCIENCE, 6:879-888, JUN 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00015

Woll, Kellie A.; Weiser, Brian P.; Liang, Qiansheng; Meng, Tao; McKinstry-Wu, Andrew; Pinch, Benika; Dailey, William P.; Gao, Wei Dong; Covarrubias, Manuel; Eckenhoff, Roderic G.
Role for the Propofol Hydroxyl in Anesthetic Protein Target Molecular Recognition
ACS CHEMICAL NEUROSCIENCE, 6:927-935, JUN 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00078

Mortier, Jeremie; Rakers, Christin; Bermudez, Marcel; Murgueitio, Manuela S.; Riniker, Sereina; Wolber, Gerhard
The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes
DRUG DISCOVERY TODAY, 20:686-702, JUN 2015
abstract, full text, DOI:10.1016/j.drudis.2015.01.003

Guerra, Federico; Bondar, Ana-Nicoleta
Dynamics of the Plasma Membrane Proton Pump
JOURNAL OF MEMBRANE BIOLOGY, 248:443-453, JUN 2015
abstract, full text, DOI:10.1007/s00232-014-9732-2

Vermaas, Josh V.; Baylon, Javier L.; Arcario, Mark J.; Muller, Melanie P.; Wu, Zhe; Pogorelov, Taras V.; Tajkhorshid, Emad
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution
JOURNAL OF MEMBRANE BIOLOGY, 248:563-582, JUN 2015
abstract, full text, DOI:10.1007/s00232-015-9806-9

Vanatta, Dan K.; Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S.
A network of molecular switches controls the activation of the two-component response regulator NtrC
NATURE COMMUNICATIONS, 6 Art. No. 7283, JUN 2015
abstract, full text, DOI:10.1038/ncomms8283

Pontiggia, F.; Pachov, D. V.; Clarkson, M. W.; Villali, J.; Hagan, M. F.; Pande, V. S.; Kern, D.
Free energy landscape of activation in a signalling protein at atomic resolution
NATURE COMMUNICATIONS, 6 Art. No. 7284, JUN 2015
abstract, full text, DOI:10.1038/ncomms8284

Chintapalli, Sree V.; Bhardwaj, Gaurav; Patel, Reema; Shah, Natasha; Patterson, Randen L.; van Rossum, Damian B.; Anishkin, Andriy; Adams, Sean H.
Molecular Dynamic Simulations Reveal the Structural Determinants of Fatty Acid Binding to Oxy-Myoglobin
PLOS ONE, 10 Art. No. e0128496, JUN 1 2015
abstract, full text, DOI:10.1371/journal.pone.0128496

Elder, Robert M.; Pfaendtner, Jim; Jayaraman, Arthi
Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA
BIOMACROMOLECULES, 16:1862-1869, JUN 2015
abstract, full text, DOI:10.1021/acs.biomac.5b00469

Ioannidis, Dimitris; Papadopoulos, Georgios E.; Anastassopoulos, Georgios; Kortsaris, Alexandros; Anagnostopoulos, Konstantinos
Structural properties and interaction energies affecting drug design. An approach combining molecular simulations, statistics, interaction energies and neural networks
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 56:7-12, JUN 2015
abstract, full text, DOI:10.1016/j.compbiolchem.2015.02.016

Ramming, Thomas; Okumura, Masaki; Kanemura, Shingo; Baday, Sefer; Birk, Julia; Moes, Suzette; Spiess, Martin; Jenoe, Paul; Berneche, Simon; Inaba, Kenji; Appenzeller-Herzog, Christian
A PDI-catalyzed thiol-disulfide switch regulates the production of hydrogen peroxide by human Ero1
FREE RADICAL BIOLOGY AND MEDICINE, 83:361-372, JUN 2015
abstract, full text, DOI:10.1016/j.freeradbiomed.2015.02.011

Smith, David J.; Shah, Jindal K.; Maginn, Edward J.
Molecular Dynamics Simulation Study of the Association of Lidocainium Docusate and Its Derivatives in Aqueous Solution
MOLECULAR PHARMACEUTICS, 12:1893-1901, JUN 2015
abstract, full text, DOI:10.1021/mp5005993

Lagardere, Louis; Lipparini, Filippo; Polack, Etienne; Stamm, Benjamin; Cances, Eric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2589-2599, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00171

Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesen, Bjorn; Kasson, Peter M.; Lindahl, Erik
Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2600-2608, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00234

Jefferys, Elizabeth; Sands, Zara A.; Shi, Jiye; Sansom, Mark S. P.; Fowler, Philip W.
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2743-2754, JUN 2015
abstract, full text, DOI:10.1021/ct501111d

Costa, Mauricio G. S.; Batista, Paulo R.; Bisch, Paulo M.; Perahia, David
Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2755-2767, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00003

Meyer, Tim; Knapp, Ernst-Walter
pK(a) Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2827-2840, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00123

Devi, Meena J.
Molecular simulations of mixed self-assembled monolayer coated gold nanoparticles in water
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 149, JUN 2015
abstract, full text, DOI:10.1007/s00894-015-2684-3

Guan, Li-Jun; Ohtsuka, Jun; Okai, Masahiko; Miyakawa, Takuya; Mase, Tomoko; Zhi, Yuehua; Hou, Feng; Ito, Noriyuki; Iwasaki, Akira; Yasohara, Yoshihiko; Tanokura, Masaru
A new target region for changing the substrate specificity of amine transaminases
SCIENTIFIC REPORTS, 5 Art. No. 10753, JUN 1 2015
abstract, full text, DOI:10.1038/srep10753

Zhan, Yingqian Ada; Ytreberg, F. Marty
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 575:22-29, JUN 1 2015
abstract, full text, DOI:10.1016/j.abb.2015.03.021

Li, Yang; Gong, Haipeng
Theoretical and simulation studies on voltage-gated sodium channels
PROTEIN & CELL, 6:413-422, JUN 2015
abstract, full text, DOI:10.1007/s13238-015-0152-6

Caliman, Alisha D.; Swift, Sara E.; Wang, Yi; Miao, Yinglong; McCammon, J. Andrew
Investigation of the conformational dynamics of the apo A(2A) adenosine receptor
PROTEIN SCIENCE, 24:1004-1012, JUN 2015
abstract, full text, DOI:10.1002/pro.2681

Mironov, Vladimir A.; Khrenova, Maria G.; Lychko, Leonora A.; Nemukhin, Alexander V.
Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1046-1053, JUN 2015
abstract, full text, DOI:10.1002/prot.24802

Kapoor, Abhijeet; Travesset, Alex
Differential dynamics of RAS isoforms in GDP- and GTP-bound states
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1091-1106, JUN 2015
abstract, full text, DOI:10.1002/prot.24805

Abdizadeh, Haleh; Atilgan, Ali Rana; Atilgan, Canan
Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20:705-718, JUN 2015
abstract, full text, DOI:10.1007/s00775-015-1256-4

Morales-Camilo, Nicole; Salas, Cristian O.; Sanhueza, Claudia; Espinosa-Bustos, Christian; Sepulveda-Boza, Silvia; Reyes-Parada, Miguel; Gonzalez-Nilo, Fernando; Caroli-Rezende, Marcos; Fierro, Angelica
Synthesis, Biological Evaluation, and Molecular Simulation of Chalcones and Aurones as Selective MAO-B Inhibitors
CHEMICAL BIOLOGY & DRUG DESIGN, 85:685-695, JUN 2015
abstract, full text, DOI:10.1111/cbdd.12458

Zima, Vlastimil; Witschas, Katja; Hynkova, Anna; Zimova, Lucie; Barvik, Ivan; Vlachova, Viktorie
Structural modeling and patch-clamp analysis of pain-related mutation TRPA1-N855S reveal inter-subunit salt bridges stabilizing the channel open state
NEUROPHARMACOLOGY, 93:294-307, JUN 2015
abstract, full text, DOI:10.1016/j.neuropharm.2015.02.018

Bishop, Kevin P.; Constable, Steve; Faruk, Nabil F.; Roy, Pierre-Nicholas
OpenMM accelerated MMTK
COMPUTER PHYSICS COMMUNICATIONS, 191:203-208, JUN 2015
abstract, full text, DOI:10.1016/j.cpc.2015.01.025

Stolzenberg, Sebastian; Quick, Matthias; Zhao, Chunfeng; Gotfryd, Kamil; Khelashvili, George; Gether, Ulrik; Loland, Claus J.; Javitch, Jonathan A.; Noskov, Sergei; Weinstein, Harel; Shi, Lei
Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter: Sodium Symporters
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:13992-14003, MAY 29 2015
abstract, full text, DOI:10.1074/jbc.M114.625343

Abriata, Luciano A.; Dal Peraro, Matteo
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
SCIENTIFIC REPORTS, 5 Art. No. 10549, MAY 29 2015
abstract, full text, DOI:10.1038/srep10549

Karacheytsev, Maksym V.; Gladchenko, Galina O.; Andrushchenko, Valery; Leontiev, Victor S.; Karachevtsev, Victor A.
Hybridization of Homopolynucleotides with Different Base Ordering on the Carbon Nanotube Surface
JOURNAL OF PHYSICAL CHEMISTRY C, 119:11991-12001, MAY 28 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b02114

Blank, Iris D.; Sadeghian, Keyarash; Ochsenfeld, Christian
A Base-Independent Repair Mechanism for DNA Glycosylase-No Discrimination Within the Active Site
SCIENTIFIC REPORTS, 5 Art. No. 10369, MAY 27 2015
abstract, full text, DOI:10.1038/srep10369

Mendoza-Martinez, Cesar; Correa-Basurto, Jose; Nieto-Meneses, Rocio; Marquez-Navarro, Adrian; Aguilar-Suarez, Rocio; Dinora Montero-Cortes, Miriam; Nogueda-Torres, Benjamin; Suarez-Contreras, Erick; Galindo-Sevilla, Norma; Rojas-Rojas, Angela; Rodriguez-Lezama, Alejandro; Hernandez-Luis, Francisco
Design, synthesis and biological evaluation of quinazoline derivatives as anti-trypanosomatid and anti-plasmodial agents
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 96:296-307, MAY 26 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.04.028

Bacolla, Albino; Zhu, Xiao; Chen, Hanning; Howells, Katy; Cooper, David N.; Vasquez, Karen M.
Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes
NUCLEIC ACIDS RESEARCH, 43:5065-5080, MAY 26 2015
abstract, full text, DOI:10.1093/nar/gkv364

Karain, Wael I.; Qaraeen, Nael I.
Weighted protein residue networks based on joint recurrences between residues
BMC BIOINFORMATICS, 16 Art. No. 173, MAY 26 2015
abstract, full text, DOI:10.1186/s12859-015-0621-1

Merget, Benjamin; Sotriffer, Christoph A.
Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations
PLOS ONE, 10 Art. No. e0127009, MAY 21 2015
abstract, full text, DOI:10.1371/journal.pone.0127009

Yu, Yi; Fan, Jianfen; Yan, Mang; Xu, Jian; Zhang, Mingming
Tilt Behavior of an Octa-Peptide Nanotube in POPE and Affects on the Transport Characteristics of Channel Water
JOURNAL OF PHYSICAL CHEMISTRY A, 119:4723-4734, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpca.5b01380

Faller, Christina E.; Guvench, Olgun
Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6063-6073, MAY 21 2015
abstract, full text, DOI:10.1021/jp511431q

Hadi-Alijanvand, Hamid; Rouhani, Maryam
Journey of Poly-Nucleotides through OmpF Porin
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6113-6128, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00763

Vermaas, Josh V.; Crowley, Michael F.; Beckham, Gregg T.; Payne, Christina M.
Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6129-6143, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00778

Mino-Galaz, German A.
Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6179-6189, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5602228

Padhi, Siladitya; Priyakumar, U. Deva
Ion Hydration Dynamics in Conjunction with a Hydrophobic Gating Mechanism Regulates Ion Permeation in p7 Viroporin from Hepatitis C Virus
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6204-6210, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02759

Izgu, Enver Cagri; Fahrenbach, Albert C.; Zhang, Na; Li, Li; Zhang, Wen; Larsen, Aaron T.; Blain, J. Craig; Szostak, Jack W.
Uncovering the Thermodynamics of Monomer Binding for RNA Replication
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:6373-6382, MAY 20 2015
abstract, full text, DOI:10.1021/jacs.5b02707

Ureta-Zanartu, M. Soledad; Mascayano, Carolina; Gutierrez, Claudio
On the dramatic increase with chain length of the oxidazability of linear saturated aliphatic alcohols on gold in alkaline media
ELECTROCHIMICA ACTA, 165:232-238, MAY 20 2015
abstract, full text, DOI:10.1016/j.electacta.2015.02.230

Patra, Swarna M.; Chakraborty, Sudip; Shahane, Ganesh; Prasanna, Xavier; Sengupta, Durba; Maiti, Prabal K.; Chattopadhyay, Amitabha
Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation
MOLECULAR MEMBRANE BIOLOGY, 32:127-137, MAY 19 2015
abstract, full text, DOI:10.3109/09687688.2015.1096971

Modarres, Hassan Pezeshgi; Dorokhov, Boris D.; Popov, Vladimir O.; Ravin, Nikolai V.; Skryabin, Konstantin G.; Dal Peraro, Matteo
Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
BIOCHEMISTRY, 54:3076-3085, MAY 19 2015
abstract, full text, DOI:10.1021/bi501227b

Biocca, Silvia; Iacovelli, Federico; Matarazzo, Sara; Vindigni, Giulia; Oteri, Francesco; Desideri, Alessandro; Falconi, Mattia
Molecular mechanism of statin-mediated LOX-1 inhibition
CELL CYCLE, 14:1583-1595, MAY 19 2015
abstract, full text, DOI:10.1080/15384101.2015.1026486

Khadka, Nawal K.; Cheng, Xiaolin; Ho, Chian Sing; Katsaras, John; Pan, Jianjun
Interactions of the Anticancer Drug Tamoxifen with Lipid Membranes
BIOPHYSICAL JOURNAL, 108:2492-2501, MAY 19 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.010

Bykhovskaia, Maria
Calcium Binding Promotes Conformational Flexibility of the Neuronal Ca2+ Sensor Synaptotagmin
BIOPHYSICAL JOURNAL, 108:2507-2520, MAY 19 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.007

Pavsic, Miha; Ilc, Gregor; Vidmar, Tilen; Plavec, Janez; Lenarcic, Brigita
The cytosolic tail of the tumor marker protein Trop2-a structural switch triggered by phosphorylation
SCIENTIFIC REPORTS, 5 Art. No. 10324, MAY 18 2015
abstract, full text, DOI:10.1038/srep10324

Stachiewicz, Anna; Molski, Andrzej
A Coarse-Grained MARTINI-Like Force Field for DNA Unzipping in Nanopores
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:947-956, MAY 15 2015
abstract, full text, DOI:10.1002/jcc.23874

Krieger, Elmar; Vriend, Gert
New Ways to Boost Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:996-1007, MAY 15 2015
abstract, full text, DOI:10.1002/jcc.23899

Bureau, Hailey R.; Merz, Dale R., Jr.; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto
Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents
PLOS ONE, 10 Art. No. e0127034, MAY 13 2015
abstract, full text, DOI:10.1371/journal.pone.0127034

Lu, Songsong; Xin, Ying; Tang, Xiaolong; Yue, Feng; Wang, Huihui; Bai, Yucheng; Niu, Yonggang; Chen, Qiang
Differences in Hematological Traits between High- and Low-Altitude Lizards (Genus Phrynocephalus)
PLOS ONE, 10 Art. No. e0125751, MAY 8 2015
abstract, full text, DOI:10.1371/journal.pone.0125751

Zhang, Yu-Hang; Shetty, Keerthi; Surleac, Marius D.; Petrescu, Andrei J.; Schatz, David G.
Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:11802-11817, MAY 8 2015
abstract, full text, DOI:10.1074/jbc.M115.638627

Impellizzeri, Agata Antonina Rita; Pappalardo, Matteo; Basile, Livia; Manfra, Ornella; Andressen, Kjetil Wessel; Krobert, Kurt Allen; Messina, Angela; Levy, Finn Olav; Guccione, Salvatore
Identification of essential residues for binding and activation in the human 5-HT7(a) serotonin receptor by molecular modeling and site-directed mutagenesis
FRONTIERS IN BEHAVIORAL NEUROSCIENCE, 9 Art. No. 92, MAY 8 2015
abstract, full text, DOI:10.3389/fnbeh.2015.00092

Bonome, Emma Letizia; Lepore, Rosalba; Raimondo, Domenico; Cecconi, Fabio; Tramontano, Anna; Chinappi, Mauro
Multistep Current Signal in Protein Translocation through Graphene Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5815-5823, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02172

Jahiruddin, Sk; Datta, Ayan
What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5839-5845, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03293

Landry, Markita P.; Vukovic, Lela; Kruss, Sebastian; Bisker, Gili; Landry, Alexandra M.; Islam, Shahrin; Jain, Rishabh; Schulten, Klaus; Strano, Michael S.
Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 119:10048-10058, MAY 7 2015
abstract, full text, TCBG publications, DOI:10.1021/jp511448e

Ruiz, Luis; Benjamin, Ari; Sullivan, Matthew; Keten, Sinan
Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:1514-1520, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00252

Sieradzan, Adam K.
Introduction of Periodic Boundary Conditions into UNRES Force Field
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:940-946, MAY 5 2015
abstract, full text, DOI:10.1002/jcc.23864

Cui, Fengchao; Yang, Kecheng; Li, Yunqi
Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation
PLOS ONE, 10 Art. No. e0125848, MAY 4 2015
abstract, full text, DOI:10.1371/journal.pone.0125848

Azamat, Jafar; Khataee, Alireza; Joob, Sang Woo
Molecular dynamics simulation of trihalomethanes separation from water by functionalized nanoporous graphene under induced pressure
CHEMICAL ENGINEERING SCIENCE, 127:285-292, MAY 4 2015
abstract, full text, DOI:10.1016/j.ces.2015.01.048

Ko, Jeong-Ahn; Ambrosia, Matthew; Ha, Man Yeong
A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces
COMPUTERS & FLUIDS, 112:19-34, MAY 2 2015
abstract, full text, DOI:10.1016/j.compfluid.2015.02.005

Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.; Wagner, John; Gidley, Michael J.; Bacic, Antony
Unique Aspects of the Structure and Dynamics of Elementary I beta Cellulose Microfibrils Revealed by Computational Simulations
PLANT PHYSIOLOGY, 168:3-U654, MAY 2015
abstract, full text, DOI:10.1104/pp.114.254664

Wall, Jonathan S.; Martin, Emily B.; Richey, Tina; Stuckey, Alan C.; Macy, Sallie; Wooliver, Craig; Williams, Angela; Foster, James S.; McWilliams-Koeppen, Penney; Uberbacher, Ed; Cheng, Xiaolin; Kennel, Stephen J.
Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis
MOLECULES, 20:7657-7682, MAY 2015
abstract, full text, DOI:10.3390/molecules20057657

Sinko, Robert; Keten, Sinan
Traction-separation laws and stick-slip shear phenomenon of interfaces between cellulose nanocrystals
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS, 78:526-539, MAY 2015
abstract, full text, DOI:10.1016/j.jmps.2015.02.012

Fukuda, Masahiro; Takeda, Hironori; Kato, Hideaki E.; Doki, Shintaro; Ito, Koichi; Maturana, Andres D.; Ishitani, Ryuichiro; Nureki, Osamu
Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
NATURE COMMUNICATIONS, 6 Art. No. 7097, MAY 2015
abstract, full text, DOI:10.1038/ncomms8097

Kato, Hideaki E.; Kamiya, Motoshi; Sugo, Seiya; Ito, Jumpei; Taniguchi, Reiya; Orito, Ayaka; Hirata, Kunio; Inutsuka, Ayumu; Yamanaka, Akihiro; Maturana, Andres D.; Ishitani, Ryuichiro; Sudo, Yuki; Hayashi, Shigehiko; Nureki, Osamu
Atomistic design of microbial opsin-based blue-shifted optogenetics tools
NATURE COMMUNICATIONS, 6 Art. No. 7177, MAY 2015
abstract, full text, DOI:10.1038/ncomms8177

Calvaresi, Matteo; Furini, Simone; Domene, Carmen; Bottoni, Andrea; Zerbetto, Francesco
Blocking the Passage: C-60 Geometrically Clogs K+ Channels
ACS NANO, 9:4827-4834, MAY 2015
abstract, full text, DOI:10.1021/nn506164s

Yan, Xiliang; Fan, Jianfen; Yu, Yi; Xu, Jian; Zhang, Mingming
Transport Behavior of a Single Ca2+, K+, and Na+ in a Water-Filled Transmembrane Cyclic Peptide Nanotube
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:998-1011, MAY 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00025

Rashid, M. Harunur; Heinzelmann, Germano; Kuyucak, Serdar
Calculation of free energy changes due to mutations from alchemical free energy simulations
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 14 Art. No. 1550023, MAY 2015
abstract, full text, DOI:10.1142/S0219633615500236

Zheng, Wenjun; Qin, Feng
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
JOURNAL OF GENERAL PHYSIOLOGY, 145:443-456, MAY 2015
abstract, full text, DOI:10.1085/jgp.201411335

Akcapinar, Gunseli Bayram; Venturini, Alessandro; Martelli, Pier Luigi; Casadio, Rita; Sezerman, Ugur O.
Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches
PROTEIN ENGINEERING DESIGN & SELECTION, 28:127-135, MAY 2015
abstract, full text, DOI:10.1093/protein/gzv012

Wassenaar, Tsjerk A.; Ingolfsson, Helgi I.; Boeckmann, Rainer A.; Tieleman, D. Peter; Marrink, Siewert J.
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2144-2155, MAY 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00209

Jo, Sunhwan; Chipot, Christophe; Roux, Benoit
Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2234-2244, MAY 2015
abstract, full text, DOI:10.1021/ct501034w

Feng, Zhiwei; Ma, Shifan; Hu, Guanxing; Xie, Xiang-Qun
Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family
AAPS JOURNAL, 17:737-753, MAY 2015
abstract, full text, DOI:10.1208/s12248-015-9742-8

Feig, Michael; Harada, Ryuhei; Mori, Takaharu; Yu, Isseki; Takahashi, Koichi; Sugita, Yuji
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 58:1-9, MAY 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.02.004

Hill, Benjamin L.; Wong, Jennifer; May, Brian M.; Huerta, Fidel B.; Manley, Tara E.; Sullivan, Peter R. F.; Olsen, Kenneth W.; Ballicora, Miguel A.
Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase
PROTEIN SCIENCE, 24:714-728, MAY 2015
abstract, full text, DOI:10.1002/pro.2644

Khoa Pham; Dhulipala, Gangadhar; Gonzalez, Walter G.; Gerstman, Bernard S.; Regmi, Chola; Chapagain, Prem P.; Miksovska, Jaroslava
Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator
PROTEIN SCIENCE, 24:741-751, MAY 2015
abstract, full text, DOI:10.1002/pro.2646

Harrison, Reed E. S.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex
PROTEIN SCIENCE, 24:789-802, MAY 2015
abstract, full text, DOI:10.1002/pro.2650

Samadani, Ramin; Zhang, Jun; Brophy, Amanda; Oashi, Taiji; Priyakumar, U. Deva; Raman, E. Prabhu; St John, Franz J.; Jung, Kwan-Young; Fletcher, Steven; Pozharski, Edwin; MacKerell, Alexander D., Jr.; Shapiro, Paul
Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf
BIOCHEMICAL JOURNAL, 467:425-438, MAY 1 2015
abstract, full text, DOI:10.1042/BJ20131571

Nanda, Hirsh; Heinrich, Frank; Loesche, Mathias
Membrane association of the PTEN tumor suppressor: Neutron scattering and MD simulations reveal the structure of protein-membrane complexes
METHODS, 77-78:136-146, MAY 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.014

Prakash, Priyanka; Hancock, John F.; Gorfe, Alemayehu A.
Binding hotspots on K-ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:898-909, MAY 2015
abstract, full text, DOI:10.1002/prot.24786

Sharp, Kim A.; O'Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua
On the relationship between NMR-derived amide order parameters and protein backbone entropy changes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:922-930, MAY 2015
abstract, full text, DOI:10.1002/prot.24789

Khelashvili, George; Doktorova, Milka; Sahai, Michelle A.; Johner, Niklaus; Shi, Lei; Weinstein, Harel
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2-containing membranes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:952-969, MAY 2015
abstract, full text, DOI:10.1002/prot.24792

Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Li, Hung-Sheng; Hou, Tsai-Yi; Chu, Wen-Yuan; Shen, Po-Chuan; Chen, Ying-Yu; Tan, Chun-Jui; Hu, Jia-Cheng; Chiu, Chih-Chiang
Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1234-1247, MAY 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.02.016

Akcapinar, Gunseli Bayram; Kappel, Lisa; Sezerman, Osman Ugur; Seidl-Seiboth, Verena
Molecular diversity of LysM carbohydrate-binding motifs in fungi
CURRENT GENETICS, 61:103-113, MAY 2015
abstract, full text, DOI:10.1007/s00294-014-0471-9

Jackson, Brian C.; Reigan, Philip; Miller, Bettina; Thompson, David C.; Vasiliou, Vasilis
Human ALDH1B1 Polymorphisms may Affect the Metabolism of Acetaldehyde and All-trans retinaldehyde-In Vitro Studies and Computational Modeling
PHARMACEUTICAL RESEARCH, 32:1648-1662, MAY 2015
abstract, full text, DOI:10.1007/s11095-014-1564-3

Gaete-Eastman, Carlos; Morales-Quintana, Luis; Herrera, Raul; Alejandra Moya-Leon, Maria
In-silico analysis of the structure and binding site features of an alpha-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 115, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2656-7

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel
A theoretical study of the unfolding pathway of reduced Human serum albumin
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 106, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2659-4

Begau, Christoph; Sutmann, Godehard
Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations
COMPUTER PHYSICS COMMUNICATIONS, 190:51-61, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2015.01.009

Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru
Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS
COMPUTER PHYSICS COMMUNICATIONS, 190:120-128, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2014.11.017

Vanommeslaeghe, K.; MacKerell, A. D., Jr.
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:861-871, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.08.004

Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
Enhanced sampling techniques in molecular dynamics simulations of biological systems
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:872-877, MAY 2015
abstract, full text, TCBG publications, DOI:10.1016/j.bbagen.2014.10.019

Batchelor, Matthew; Gowdy, James; Paci, Emanuele
Effect of external pulling forces on the length distribution of peptides
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:903-910, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.019

Lynch, Gillian C.; Perkyns, John S.; Bao Linh Nguyen; Pettitt, B. Montgomery
Solvation and cavity occupation in biomolecules
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:923-931, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.020

Cazade, Pierre-Andre; Berezovska, Ganna; Meuwly, Markus
Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:996-1005, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.008

Simonson, Thomas; Aleksandrov, Alexey; Satpati, Priyadarshi
Electrostatic free energies in translational GTPases: Classic allostery and the rest
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1006-1016, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.07.006

Grauffel, Cedric; Stote, Roland H.; Dejaegere, Annick
Molecular dynamics for computational proteomics of methylated histone H3
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1026-1040, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.015

Babcock, Jeremiah J.; Brancaleon, Lorenzo
The Effect of Local Dynamics of Atto 390-Labeled Lysozyme on Fluorescence Anisotropy Modeling
BIOPOLYMERS, 103:285-295, MAY 2015
abstract, full text, DOI:10.1002/bip.22596

Fernandez-Millan, Pablo; Lazaro, Melisa; Cansiz-Arda, Sirin; Gerhold, Joachim M.; Rajala, Nina; Schmitz, Claus-A.; Silva-Espina, Cristina; Gil, David; Bernado, Pau; Valle, Mikel; Spelbrink, Johannes N.; Sola, Maria
The hexameric structure of the human mitochondrial replicative helicase Twinkle
NUCLEIC ACIDS RESEARCH, 43:4284-4295, APR 30 2015
abstract, full text, DOI:10.1093/nar/gkv189

Pan, Xiaoliang; Schwartz, Steven D.
Free Energy Surface of the Michaelis Complex of Lactate Dehydrogenase: A Network Analysis of Microsecond Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5430-5436, APR 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01840

Meneksedag-Erol, Deniz; Tang, Tian; Uudag, Hasan
Probing the Effect of miRNA on siRNA-PEI Polyplexes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5475-5486, APR 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.jb00415

Park, Min-Sun
Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1
PLOS ONE, 10 Art. No. e0125361, APR 28 2015
abstract, full text, DOI:10.1371/journal.pone.0125361

Czajkowsky, Daniel M.; Andersen, Jan Terje; Fuchs, Anja; Wilson, Timothy J.; Mekhaiel, David; Colonna, Marco; He, Jianfeng; Shao, Zhifeng; Mitchell, Daniel A.; Wu, Gang; Dell, Anne; Haslam, Stuart; Lloyd, Katy A.; Moore, Shona C.; Sandlie, Inger; Blundell, Patricia A.; Pleass, Richard J.
Developing the IVIG biomimetic, Hexa-Fc, for drug and vaccine applications
SCIENTIFIC REPORTS, 5 Art. No. 9526, APR 27 2015
abstract, full text, DOI:10.1038/srep09526

Wang, Zhe; Yu, Tao; Sang, Jian-Ping; Zou, Xian-Wu; Yan, Chengfei; Zou, Xiaoqin
Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5124-5131, APR 23 2015
abstract, full text, DOI:10.1021/jp511300u

Khrenova, Maria G.; Nemukhin, Alexander V.; Domratcheva, Tatiana
Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5176-5183, APR 23 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01299

Esque, Jeremy; Cecchini, Marco
Accurate Calculation of Conformational Free Energy Differences in Explicit Water: The Confinement-Solvation Free Energy Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5194-5207, APR 23 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01632

Leonarski, Filip; Trylska, Joanna
RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models
BIOPHYSICAL JOURNAL, 108:1843-1847, APR 21 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.023

Weber, Daniel K.; Yao, Shenggen; Rojko, Nejc; Anderluh, Gregor; Lybrand, Terry P.; Downton, Matthew T.; Wagner, John; Separovic, Frances
Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 108:1987-1996, APR 21 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.024

Procacci, Piero
Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 154117, APR 21 2015
abstract, full text, DOI:10.1063/1.4918558

Kang, Hyun-Ah; Shin, Ho-Chul; Kalantzi, Alexandra-Styliani; Toseland, Christopher P.; Kim, Hyun-Min; Gruber, Stephan; Dal Peraro, Matteo; Oh, Byung-Ha
NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination
NUCLEIC ACIDS RESEARCH, 43:3841-3856, APR 20 2015
abstract, full text, DOI:10.1093/nar/gkv172

Thomas, Michael; Enciso, Marta; Hilder, Tamsyn A.
Insertion Mechanism and Stability of Boron Nitride Nanotubes in Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4929-4936, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00102

Chialvo, Ariel A.; Moucka, Filip; Vlcek, Lukas; Nezbeda, Ivo
Vapor-Liquid Equilibrium and Polarization Behavior of the GCP Water Model: Gaussian Charge-on-Spring versus Dipole Self-Consistent Field Approaches to Induced Polarization
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5010-5019, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00595

Aoun, B.; Sharma, V. K.; Pellegrini, E.; Mitra, S.; Johnson, M.; Mukhopadhyay, R.
Structure and Dynamics of Ionic Micelles: MD Simulation and Neutron Scattering Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5079-5086, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00020

Gouge, Jerome; Rosario, Sandrine; Romain, Felix; Poitevin, Frederic; Beguin, Pierre; Delarue, Marc
Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
EMBO JOURNAL, 34:1126-1142, APR 15 2015
abstract, full text, DOI:10.15252/embj.201489643

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.
Pairwise amino acid secondary structural propensities
PHYSICAL REVIEW E, 91 Art. No. 042709, APR 15 2015
abstract, full text, DOI:10.1103/PhysRevE.91.042709

Yuan, Yunyun; Zaidi, Saheem A.; Stevens, David L.; Scoggins, Krista L.; Mosier, Philip D.; Kellogg, Glen E.; Dewey, William L.; Selley, Dana E.; Zhang, Yan
Design, syntheses, and pharmacological characterization of 17-cyclopropylmethyl-3,14 beta-dihydroxy-4,5 alpha-epoxy-6 alpha-(isoquinoline-3 '-carboxamido)morphinan analogues as opioid receptor ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:1701-1715, APR 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.02.055

Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.
A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. UNSP e0121092, APR 13 2015
abstract, full text, DOI:10.1371/journal.pone.0121092

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB
FRONTIERS IN MICROBIOLOGY, 6 Art. No. UNSP 302, APR 13 2015
abstract, full text, DOI:10.3389/fmicb.2015.00302

Krammer, Eva-Maria; Giang Thi Vu; Homble, Fabrice; Prevost, Martine
Dual Mechanism of Ion Permeation through VDAC Revealed with Inorganic Phosphate Ions and Phosphate Metabolites
PLOS ONE, 10 Art. No. e0121746, APR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0121746

Jang, Hyunbum; Abraham, Sherwin J.; Chavan, Tanmay S.; Hitchinson, Ben; Khavrutskii, Lyuba; Tarasova, Nadya I.; Nussinov, Ruth; Gaponenko, Vadim
Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:9465-9477, APR 10 2015
abstract, full text, DOI:10.1074/jbc.M114.620724

Kuttel, Michelle M.; Jackson, Graham E.; Mafata, Mpho; Ravenscroft, Neil
Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A
CARBOHYDRATE RESEARCH, 406:27-33, APR 10 2015
abstract, full text, DOI:10.1016/j.carres.2014.12.013

Preti, Delia; Baraldi, Pier Giovanni; Saponaro, Giulia; Romagnoli, Romeo; Tabrizi, Mojgan Aghazadeh; Baraldi, Stefania; Cosconati, Sandro; Bruno, Agostino; Novellino, Ettore; Vincenzi, Fabrizio; Ravani, Annalisa; Borea, Pier Andrea; Varani, Katia
Design, Synthesis, and Biological Evaluation of Novel 2-((2-4-(Substituted)phenylpiperazin-1-yl)ethyl)amino)-5 '-N-ethylcarboxamidoadenosines as Potent and Selective Agonists of the A(2A) Adenosine Receptor
JOURNAL OF MEDICINAL CHEMISTRY, 58:3253-3267, APR 9 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00215

Semino, Rocio; Rodriguez, Javier
Molecular Dynamics Study of Ionic Liquids Complexation within beta-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4865-4872, APR 9 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00909

Denisov, Ilia G.; Grinkova, Yelena V.; Baylon, Javier L.; Tajkhorshid, Emad; Sligar, Stephen G.
Mechanism of Drug-Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer
BIOCHEMISTRY, 54:2227-2239, APR 7 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00079

Michel Espinoza-Fonseca, L.; Autry, Joseph M.; Lizbeth Ramirez-Salinas, G.; Thomas, David D.
Atomic-Level Mechanisms for Phospholamban Regulation of the Calcium Pump
BIOPHYSICAL JOURNAL, 108:1697-1708, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.004

Davis, Brittny C.; Brown, Jodian A.; Thorpe, Ian F.
Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase
BIOPHYSICAL JOURNAL, 108:1785-1795, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.005

Miao, Yinglong; Caliman, Alisha D.; McCammon, J. Andrew
Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor
BIOPHYSICAL JOURNAL, 108:1796-1806, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.003

Lockhart, Christopher; Klimov, Dmitri K.
Calcium Enhances Binding of A beta Monomer to DMPC Lipid Bilayer
BIOPHYSICAL JOURNAL, 108:1807-1818, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.001

Tsutakawa, Susan E.; Yan, Chunli; Xu, Xiaojun; Weinacht, Christopher P.; Freudenthal, Bret D.; Yang, Kun; Zhuang, Zhihao; Washington, M. Todd; Tainer, John A.; Ivanov, Ivaylo
Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response
STRUCTURE, 23:724-733, APR 7 2015
abstract, full text, DOI:10.1016/j.str.2015.02.008

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Accuracy Assessment of the Linear Poisson-Boltzmann Equation and Reparametrization of the OBC Generalized Born Model for Nucleic Acids and Nucleic Acid-Protein Complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:585-596, APR 5 2015
abstract, full text, DOI:10.1002/jcc.23832

Elmes, Matthew W.; Kaczocha, Martin; Berger, William T.; Leung, KwanNok; Ralph, Brian P.; Wang, Liqun; Sweeney, Joseph M.; Miyauchi, Jeremy T.; Tsirka, Stella E.; Ojima, Iwao; Deutsch, Dale G.
Fatty Acid-binding Proteins (FABPs) Are Intracellular Carriers for Delta(9)-Tetrahydrocannabinol (THC) and Cannabidiol (CBD)
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:8711-8721, APR 3 2015
abstract, full text, DOI:10.1074/jbc.M114.618447

Gillet, Jean-Numa
Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:690-705, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.907544

Jimenez, Veronica A.; Alderete, Joel B.; Navarrete, Karen R.
Structural insight into epothilones antitumor activity based on the conformational preferences and tubulin binding modes of epothilones A and B obtained from molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:789-803, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.911702

Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
Molecular dynamics simulations of large macromolecular complexes
CURRENT OPINION IN STRUCTURAL BIOLOGY, 31:64-74, APR 2015
abstract, full text, TCBG publications, DOI:10.1016/j.sbi.2015.03.007

Tian, Jian; Woodard, Jaie C.; Whitney, Anna; Shakhnovich, Eugene I.
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004207, APR 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004207

Rismanian, M.; Saidi, M. S.; Firoozabadi, B.
Na+ permeation through its protein channels, from molecular dynamics to continuum modeling
SCIENTIA IRANICA, 22:459-466, APR 2015
abstract, full text

Tan, Pengli; Feng, Zhiwei; Zhang, Liling; Hou, Tingjun; Li, Youyong
The mechanism of proton translocation in respiratory complex I from molecular dynamics
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 35:170-179, APR 2015
abstract, full text, DOI:10.3109/10799893.2014.942464

Bae, Euiyoung; Moon, Sojin; Phillips, George N., Jr.
Molecular dynamics simulation of a psychrophilic adenylate kinase
JOURNAL OF THE KOREAN SOCIETY FOR APPLIED BIOLOGICAL CHEMISTRY, 58:209-212, APR 2015
abstract, full text, DOI:10.1007/s13765-015-0033-y

Lee, Myeongsang; Chang, Hyun Joon; Kim, Donghoi; Lee, Yongwoo; Suh, Heesu; Ahn, Namjo; Yoon, Gwonchan; Na, Sungsoo
Relationship between structural composition and material properties of polymorphic hIAPP fibrils
BIOPHYSICAL CHEMISTRY, 199:1-8, APR 2015
abstract, full text, DOI:10.1016/j.bpc.2015.02.002

Pietra, Francesco
Restoring Histone Deacetylase Activity by Waste Product Release. A View from Molecular Mechanics Simulations with Mammalian HDAC8
CHEMISTRY & BIODIVERSITY, 12:503-512, APR 2015
abstract, full text, DOI:10.1002/cbdv.201400314

Wan, Hua; Chang, Shan; Hu, Jian-ping; Tian, Yuan-xin; Tian, Xu-hong
Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:784-794, APR 2015
abstract, full text, DOI:10.1021/ci500705j

Belmonte, Luca; Moran, Oscar
On the interactions between nucleotide binding domains and membrane spanning domains in cystic fibrosis transmembrane regulator: A molecular dynamic study
BIOCHIMIE, 111:19-29, APR 2015
abstract, full text, DOI:10.1016/j.biochi.2015.01.010

Myklebust, Line M.; Van Damme, Petra; Stove, Svein I.; Doerfel, Max J.; Abboud, Angele; Kalvik, Thomas V.; Grauffel, Cedric; Jonckheere, Veronique; Wu, Yiyang; Swensen, Jeffrey; Kaasa, Hanna; Liszczak, Glen; Marmorstein, Ronen; Reuter, Nathalie; Lyon, Gholson J.; Gevaert, Kris; Arnesen, Thomas
Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects
HUMAN MOLECULAR GENETICS, 24:1956-1976, APR 1 2015
abstract, full text, DOI:10.1093/hmg/ddu611

Bao Linh Nguyen; Pettitt, B. Montgomery
Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1399-1409, APR 2015
abstract, full text, DOI:10.1021/ct501116v

Chen, Liao Y.
Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1928-1938, APR 2015
abstract, full text, DOI:10.1021/ct501162f

Lehman, William; Medlock, Greg; Li, Xiaochuan (Edward); Suphamungmee, Worawit; Tu, An-Yue; Schmidtmann, Anja; Ujfalusi, Zoltan; Fischer, Stefan; Moore, Jeffrey R.; Geeves, Michael A.; Regnier, Michael
Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domain
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 571:10-15, APR 1 2015
abstract, full text, DOI:10.1016/j.abb.2015.02.026

Mitra, Suranjita; Mukhopadhyay, Bidhan Chandra; Mandal, Anisur Rahaman; Arukha, Ananta Prasad; Chakrabarty, Kuheli; Das, Gourab Kanti; Chakrabartty, Pran Krishna; Biswas, Swadesh Ranjan
Cloning, overexpression, and characterization of a novel alkali-thermostable xylanase from Geobacillus sp WBI
JOURNAL OF BASIC MICROBIOLOGY, 55:527-537, APR 2015
abstract, full text, DOI:10.1002/jobm.201400495

Tarasevich, Barbara J.; Philo, John S.; Maluf, Nasib Karl; Krueger, Susan; Buchko, Garry W.; Lin, Genyao; Shaw, Wendy J.
The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution
JOURNAL OF STRUCTURAL BIOLOGY, 190:81-91, APR 2015
abstract, full text, DOI:10.1016/j.jsb.2014.10.007

Pedretti, Alessandro; Mazzolari, Angelica; Ricci, Chiara; Vistoli, Giulio
Enhancing the Reliability of GPCR Models by Accounting for Flexibility of Their Pro-Containing Helices: the Case of the Human mAChR1 Receptor
MOLECULAR INFORMATICS, 34:216-227, APR 2015
abstract, full text, DOI:10.1002/minf.201400159

Kaczor, Agnieszka A.; Guixa-Gonzalez, Ramon; Carrio, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana
Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors
MOLECULAR INFORMATICS, 34:246-255, APR 2015
abstract, full text, DOI:10.1002/minf.201400088

Jorgensen, Christian; Darre, Leonardo; Vanommeslaeghe, Kenno; Omoto, Kiyoyuki; Pryde, David; Domene, Carmen
In Silico Identification of PAP-1 Binding Sites in the Kv1.2 Potassium Channel
MOLECULAR PHARMACEUTICS, 12:1299-1307, APR 2015
abstract, full text, DOI:10.1021/acs.molpharmaceut.5b00023

Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang
Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71:779-789, APR 2015
abstract, full text, DOI:10.1107/S1399004715001169

Johnson, Jennifer L.; Entzminger, Kevin C.; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P., Jr.; Morales, Ivan A.; Sheppard, Aly; Gumbart, James C.; Maynard, Jennifer A.; Lieberman, Raquel L.
Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71:896-906, APR 2015
abstract, full text, DOI:10.1107/S1399004715001856

Comitani, Federico; Melis, Claudio; Molteni, Carla
Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations
BIOCHEMICAL SOCIETY TRANSACTIONS, 43:151-156, APR 2015
abstract, full text, DOI:10.1042/BST20140259

Montanez, Mara I.; Najera, Francisco; Mayorga, Cristobalina; Ruiz-Sanchez, Antonio J.; Vida, Yolanda; Collado, Daniel; Blanca, Miguel; Torres, Maria J.; Perez-Inestrosa, Ezequiel
Recognition of multiepitope dendrimeric antigens by human immunoglobulin E
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE, 11:579-588, APR 2015
abstract, full text, DOI:10.1016/j.nano.2015.01.006

Dokainish, Hisham M.; Gauld, James W.
Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B)
ACS CATALYSIS, 5:2195-2202, APR 2015
abstract, full text, DOI:10.1021/cs501707h

Kwon, Tae Woo; Ambrosia, Matthew Stanley; Jang, Joonkyoung; Ha, Man Yeong
Dynamic hydrophobicity of heterogeneous pillared surfaces at the nano-scale
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1663-1671, APR 2015
abstract, full text, DOI:10.1007/s12206-015-0338-0

Nguyen, Phuong T. V.; Yu, Haibo; Keller, Paul A.
Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:1-8, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.001

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo; Yin, Binfeng
Removal of trihalomethanes from aqueous solution through armchair carbon nanotubes: A molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:70-75, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.008

Behera, Pabitra Mohan; Behera, Deepak Kumar; Satpati, Suresh; Agnihotri, Geetanjali; Nayak, Sanghamitra; Padhi, Payodhar; Dixit, Anshuman
Molecular modeling and identification of novel glucokinase activators through stepwise virtual screening
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:122-130, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.012

Viricel, Clement; Ahmed, Marawan; Barakat, Khaled
Human PD-1 binds differently to its human ligands: A comprehensive modeling study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:131-142, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.015

Dong, Sijia S.; Abrol, Ravinder; Goddard, William A.
The Predicted Ensemble of Low-Energy Conformations of Human Somatostatin Receptor Subtype 5 and the Binding of Antagonists
CHEMMEDCHEM, 10:650-661, APR 2015
abstract, full text, DOI:10.1002/cmdc.201500023

Aitha, Mahesh; Moritz, Lindsay; Sahu, Indra D.; Sanyurah, Omar; Roche, Zahilyn; McCarrick, Robert; Lorigan, Gary A.; Bennett, Brian; Crowder, Michael W.
Conformational dynamics of metallo-beta-lactamase CcrA during catalysis investigated by using DEER spectroscopy
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20:585-594, APR 2015
abstract, full text, DOI:10.1007/s00775-015-1244-8

D'Avino, Gabriele; Muccioli, Luca; Zannoni, Claudio
From Chiral Islands to Smectic Layers: A Computational Journey Across Sexithiophene Morphologies on C-60
ADVANCED FUNCTIONAL MATERIALS, 25:1985-1995, APR 1 2015
abstract, full text, DOI:10.1002/adfm.201402609

Sfyroera, Georgia; Ricklin, Daniel; Reis, Edimara S.; Chen, Hui; Wu, Emilia L.; Kaznessis, Yiannis N.; Ekdahl, Kristina N.; Nilsson, Bo; Lambris, John D.
Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity
JOURNAL OF IMMUNOLOGY, 194:3305-3316, APR 1 2015
abstract, full text, DOI:10.4049/jimmunol.1402781

Qu, Tao; Verma, Devendra; Shahidi, Mehran; Pichler, Bernhard; Hellmich, Christian; Tomar, Vikas
Mechanics of organic-inorganic biointerfaces-Implications for strength and creep properties
MRS BULLETIN, 40:349-358, APR 2015
abstract, full text, DOI:10.1557/mrs.2015.70

Mernea, Maria; Ionescu, Alina; Vasile, Ionut; Nica, Cristina; Stoian, Gheorghe; Dascalu, Traian; Mihailescu, Dan Florin
In vitro human serum albumin glycation monitored by Terahertz spectroscopy
OPTICAL AND QUANTUM ELECTRONICS, 47:961-973, APR 2015
abstract, full text, DOI:10.1007/s11082-015-0129-y

Mornon, Jean-Paul; Hoffmann, Brice; Jonic, Slavica; Lehn, Pierre; Callebaut, Isabelle
Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics
CELLULAR AND MOLECULAR LIFE SCIENCES, 72:1377-1403, APR 2015
abstract, full text, DOI:10.1007/s00018-014-1749-2

Alaybeyoglu, Begum; Sariyar Akbulut, Berna; Ozkirimli, Elif
A novel chimeric peptide with antimicrobial activity
JOURNAL OF PEPTIDE SCIENCE, 21:294-301, APR 2015
abstract, full text, DOI:10.1002/psc.2739

Zhang, Peng; Deng, Yuefan; Feng, Rui; Luo, Xingguo; Wu, Jiangxing
Evaluation of Various Networks Configurated by Adding Bypass or Torus Links
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 26:984-996, APR 2015
abstract, full text, DOI:10.1109/TPDS.2014.2315201

Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.
Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics
JOM, 67:733-743, APR 2015
abstract, full text, DOI:10.1007/s11837-015-1361-4

Zhang, Pu-pu; Zhao, Li; Long, Shi-yang; Tian, Pu
The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 72, APR 2015
abstract, full text, DOI:10.1007/s00894-015-2625-1

Sensoy, Ozge; Weinstein, Hare
A mechanistic role of Helix 8 in GPCRs: Computational modeling of the dopamine D2 receptor interaction with the GIPC1-PDZ-domain
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:976-983, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.002

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.
Molecular basis of endosomal-membrane association for the dengue virus envelope protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1041-1052, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.018

Trung Dac Nguyen; Plimpton, Steven J.
Accelerating dissipative particle dynamics simulations for soft matter systems
COMPUTATIONAL MATERIALS SCIENCE, 100:173-180, APR 1 2015
abstract, full text, DOI:10.1016/j.commatsci.2014.10.068

Feroz, Shevin R.; Teoh, Yue Jun; Mohamad, Saharuddin B.; Hong, Sok Lai; Malek, Sri Na.; Tayyab, Saad
Interaction of flavokawain B with lysozyme: A photophysical and molecular simulation study
JOURNAL OF LUMINESCENCE, 160:101-109, APR 2015
abstract, full text, DOI:10.1016/j.jlumin.2014.11.053

Garcia, Pamela Soto; Dario Moreau, Alberto Luis; Magalhaes Ierich, Jessica Cristiane; Araujo Vig, Ana Carolina; Higa, Akemi Martins; Oliveira, Guedmiller S.; Abdalla, Fabio Camargo; Hausen, Moema; Leite, Fabio L.
A Nanobiosensor Based on 4-Hydroxyphenylpyruvate Dioxygenase Enzyme for Mesotrione Detection
IEEE SENSORS JOURNAL, 15:2106-2113, APR 2015
abstract, full text, DOI:10.1109/JSEN.2014.2371773

Vermaas, Josh V.; Taguchi, Alexander T.; Dikanov, Sergei A.; Wraight, Colin A.; Tajkhorshid, Emad
Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides
BIOCHEMISTRY, 54:2104-2116, MAR 31 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00033

Chandramouli, Balasubramanian; Di Maio, Danilo; Mancini, Giordano; Barone, Vincenzo; Brancato, Giuseppe
Breaking the Hydrophobicity of the MscL Pore: Insights into a Charge-Induced Gating Mechanism
PLOS ONE, 10 Art. No. e0120196, MAR 31 2015
abstract, full text, DOI:10.1371/journal.pone.0120196

Ho, Jianghai; Perez-Aguilar, Jose Manuel; Gao, Lu; Saven, Jeffery G.; Matsunami, Hiroaki; Eckenhoff, Roderic G.
Molecular recognition of ketamine by a subset of olfactory G protein-coupled receptors
SCIENCE SIGNALING, 8 Art. No. ra33, MAR 31 2015
abstract, full text, DOI:10.1126/scisignal.2005912

Lai, Pin-Kuang; Lin, Shiang-Tai
Internal Coordinate Density of State from Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:507-517, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23822

Padhi, Siladitya; Ramakrishna, Siddabattula; Priyakumar, U. Deva
Prediction of the Structures of Helical Membrane Proteins Based on a Minimum Unfavorable Contacts Approach
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:539-552, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23828

Martinez, Leandro
Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis
PLOS ONE, 10 Art. No. e0119264, MAR 27 2015
abstract, full text, DOI:10.1371/journal.pone.0119264

Loerbroks, Claudia; Boulanger, Eliot; Thiel, Walter
Solvent Influence on Cellulose 1,4-beta-Glycosidic Bond Cleavage: A Molecular Dynamics and Metadynarnics Study
CHEMISTRY-A EUROPEAN JOURNAL, 21:5477-5487, MAR 27 2015
abstract, full text, DOI:10.1002/chem.201405507

Sanchez-Rodriguez, Jorge E.; Khalili-Araghi, Fatemeh; Miranda, Pablo; Roux, Benoit; Holmgren, Miguel; Bezanilla, Francisco
A Structural Rearrangement of the Na+/K+-ATPase Traps Ouabain within the External Ion Permeation Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:1335-1344, MAR 27 2015
abstract, full text, DOI:10.1016/j.jmb.2015.01.011

Girdhar, Anuj; Sathe, Chaitanya; Schulten, Klaus; Leburton, Jean-Pierre
Tunable graphene quantum point contact transistor for DNA detection and characterization
NANOTECHNOLOGY, 26 Art. No. 134005, MAR 27 2015
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/26/13/134005

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4428-4440, MAR 26 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00683

Rheault, Jean-Francois; Gagne, Eve; Guertin, Michel; Lamoureux, Guillaume; Auger, Michele; Laguee, Patrick
Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study
BIOCHEMISTRY, 54:2073-2084, MAR 24 2015
abstract, full text, DOI:10.1021/bi5010624

Guo, Jiqing; Cheng, Yen May; Lees-Miller, James P.; Perissinotti, Laura L.; Claydon, Tom W.; Hull, Christina M.; Thouta, Samrat; Roach, Daniel E.; Durdagi, Serdar; Noskov, Sergei Y.; Duff, Henry J.
NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation
BIOPHYSICAL JOURNAL, 108:1400-1413, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.055

Morgan, Brittany R.; Deveau, Laura M.; Massi, Francesca
Probing the Structural and Dynamical Effects of the Charged Residues of the TZF Domain of TIS11d
BIOPHYSICAL JOURNAL, 108:1503-1515, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.039

Burmann, Bjoern M.; Holdbrook, Daniel A.; Callon, Morgane; Bond, Peter J.; Hiller, Sebastian
Revisiting the Interaction between the Chaperone Skp and Lipopolysaccharide
BIOPHYSICAL JOURNAL, 108:1516-1526, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.029

Plascencia-Villa, German; Torrente, Daniel; Marucho, Marcelo; Jose-Yacaman, Miguel
Biodirected Synthesis and Nanostructural Characterization of Anisotropic Gold Nanoparticles
LANGMUIR, 31:3527-3536, MAR 24 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b00084

Ren, Baiping; Gao, Huipeng; Cao, Yafeng; Jia, Lingyun
In Silico understanding of the cyclodextrin-phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes
JOURNAL OF HAZARDOUS MATERIALS, 285:148-156, MAR 21 2015
abstract, full text, DOI:10.1016/j.jhazmat.2014.12.001

Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli
A Model of Lipid-Free Apolipoprotein A-I Revealed by Iterative Molecular Dynamics Simulation
PLOS ONE, 10 Art. No. e0120233, MAR 20 2015
abstract, full text, DOI:10.1371/journal.pone.0120233

Andrijchenko, Natalya N.; Ermilov, Alexander Yu.; Khriachtchev, Leonid; Rasanen, Markku; Nemukhin, Alexander V.
Toward Molecular Mechanism of Xenon Anesthesia: A Link to Studies of Xenon Complexes with Small Aromatic Molecules
JOURNAL OF PHYSICAL CHEMISTRY A, 119:2517-2521, MAR 19 2015
abstract, full text, DOI:10.1021/jp508800k

Shilov, Ignat Yu.
Molecular dynamics simulation of dielectric constant and cluster structure of liquid methanol: the role of cluster-cluster dipole correlations
MOLECULAR PHYSICS, 113:570-576, MAR 19 2015
abstract, full text, DOI:10.1080/00268976.2014.960496

Mehta, Jatin; Asthana, Shailendra; Mandal, Chandi Charan; Saxena, Sunita
A Molecular Analysis Provides Novel Insights into Androgen Receptor Signalling in Breast Cancer
PLOS ONE, 10 Art. No. e0120622, MAR 17 2015
abstract, full text, DOI:10.1371/journal.pone.0120622

Blair, Jessica M. A.; Bavro, Vassiliy N.; Ricci, Vito; Modi, Niraj; Cacciotto, Pierpaolo; Kleinekathoefer, Ulrich; Ruggerone, Paolo; Vargiu, Attilio V.; Baylay, Alison J.; Smith, Helen E.; Brandon, Yvonne; Galloway, David; Piddock, Laura J. V.
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:3511-3516, MAR 17 2015
abstract, full text, DOI:10.1073/pnas.1419939112

Kinoshita, Mikitaka; Okada, Tetsuji
Structural conservation among the rhodopsin-like and other G protein-coupled receptors
SCIENTIFIC REPORTS, 5 Art. No. 9176, MAR 17 2015
abstract, full text, DOI:10.1038/srep09176

Bruno, Agostino; Scrima, Mario; Novellino, Ettore; D'Errico, Gerardino; D'Ursi, Anna Maria; Limongelli, Vittorio
The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)
SCIENTIFIC REPORTS, 5 Art. No. 9200, MAR 17 2015
abstract, full text, DOI:10.1038/srep09200

Mizuguchi, Tomoko; Ishizuka, Ryosuke; Matubayasi, Nobuyuki
Effect of diffuseness of micelle boundary on the solute distribution upon solubilization
CHEMICAL PHYSICS LETTERS, 624:19-23, MAR 16 2015
abstract, full text, DOI:10.1016/j.cplett.2015.02.001

Hameau, Aurelien; Fruchon, Severine; Bijani, Christian; Barducci, Alessandro; Blanzat, Muriel; Poupot, Remy; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cedric-Olivier
Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles
JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 53:761-774, MAR 15 2015
abstract, full text, DOI:10.1002/pola.27501

Hanasaki, Itsuo; Nagura, Ryo; Kawano, Satoyuki
Coarse-grained picture of Brownian motion in water: Role of size and interaction distance range on the nature of randomness
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 104301, MAR 14 2015
abstract, full text, DOI:10.1063/1.4913748

Megow, Joerg; Roehr, Merle I. S.; Busch, Marcel Schmidt am; Renger, Thomas; Mitric, Roland; Kirstein, Stefan; Rabe, Juergen P.; May, Volkhard
Site-dependence of van der Waals interaction explains exciton spectra of double-walled tubular J-aggregates
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6741-6747, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05945j

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue
Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6995-7001, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05909c

Hu, Yunfei; Wu, Yujie; Li, Qianwen; Zhang, Wenbo; Jin, Changwen
Solution Structure of Yeast Rpn9 INSIGHTS INTO PROTEASOME LID ASSEMBLY
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:6878-6889, MAR 13 2015
abstract, full text, DOI:10.1074/jbc.M114.626762

Islam, Shahidul M.; Roux, Benoit
Simulating the Distance Distribution between Spin-Labels Attached to Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3901-3911, MAR 12 2015
abstract, full text, DOI:10.1021/jp510745d

Lee, Cheng-Kuang; Pao, Chun-Wei; Smit, Berend
PSII-LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3999-4008, MAR 12 2015
abstract, full text, DOI:10.1021/jp511277c

Dubiez, Etienne; Aleksandrov, Alexey; Lazennec-Schurdevin, Christine; Mechulam, Yves; Schmitt, Emmanuelle
Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2
NUCLEIC ACIDS RESEARCH, 43:2946-2957, MAR 11 2015
abstract, full text, DOI:10.1093/nar/gkv053

Serratos, Iris N.; Castellanos, Pilar; Pastor, Nina; Millan-Pacheco, Cesar; Rembao, Daniel; Perez-Montfort, Ruy; Cabrera, Nallely; Reyes-Espinosa, Francisco; Diaz-Garrido, Paulina; Lopez-Macay, Ambar; Martinez-Flores, Karina; Lopez-Reyes, Alberto; Sanchez-Garcia, Aurora; Cuevas, Elvis; Santamaria, Abel
Modeling the Interaction between Quinolinate and the Receptor for Advanced Glycation End Products (RAGE): Relevance for Early Neuropathological Processes
PLOS ONE, 10 Art. No. UNSP e0120221, MAR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0120221

Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He
Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase
BIOCHEMISTRY, 54:1841-1848, MAR 10 2015
abstract, full text, DOI:10.1021/bi5015612

Leone, Vanessa; Pogoryelov, Denys; Meier, Thomas; Faraldo-Gomez, Jose D.
On the principle of ion selectivity in Na+/H+-coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E1057-E1066, MAR 10 2015
abstract, full text, DOI:10.1073/pnas.1421202112

Lee, Hui Sun; Qi, Yifei; Im, Wonpil
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study
SCIENTIFIC REPORTS, 5 Art. No. 8926, MAR 9 2015
abstract, full text, DOI:10.1038/srep08926

Carr, Matthew; MacPhee, Cait E.
Membrainy: a 'smart', unified membrane analysis tool
SOURCE CODE FOR BIOLOGY AND MEDICINE, 10 Art. No. 3, MAR 7 2015
abstract, full text, DOI:10.1186/s13029-015-0033-7

Mendoza-Martinez, Cesar; Galindo-Sevilla, Norma; Correa-Basurto, Jose; Manuel Ugalde-Saldivar, Victor; Georgina Rodriguez-Delgado, Rosa; Hernandez-Pineda, Jessica; Padierna-Mota, Cecilia; Flores-Alamo, Marcos; Hernandez-Luis, Francisco
Antileishmanial activity of quinazoline derivatives: Synthesis, docking screens, molecular dynamic simulations and electrochemical studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 92:314-331, MAR 6 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.12.051

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji
Origin of 1/f noise in hydration dynamics on lipid membrane surfaces
SCIENTIFIC REPORTS, 5 Art. No. 8876, MAR 6 2015
abstract, full text, DOI:10.1038/srep08876

Weng, Jingwei; Yang, Yanhong; Wang, Wenning
Lipid Regulated Conformational Dynamics of the Longin SNARE Protein Ykt6 Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 119:1554-1562, MAR 5 2015
abstract, full text, DOI:10.1021/jp5075708

Guzman, Irisbel; Ghaemi, Zhaleh; Baranger, Anne; Luthey-Schulten, Zaida; Gruebele, Martin
Native Conformational Dynamics of the Spliceosomal U1A Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3651-3661, MAR 5 2015
abstract, full text, DOI:10.1021/jp511760m

Zenn, Roland K.; Abad, Enrique; Kaestner, Johannes
Influence of the Environment on the Oxidative Deamination of p-Substituted Benzylamines in Monoamine Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3678-3686, MAR 5 2015
abstract, full text, DOI:10.1021/jp512470a

Nierzwicki, Lukasz; Czub, Jacek
Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:784-790, MAR 5 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00197

Miyashita, Naoyuki; Re, Suyong; Sugita, Yuji
REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:325-332, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24785

Yoshii, Noriyuki; Andoh, Yoshimichi; Fujimoto, Kazushi; Kojima, Hidekazu; Yamada, Atsushi; Okazaki, Susumu
MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:342-348, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24841

Ma, Wen; Schulten, Klaus
Mechanism of Substrate Trans location by a Ring-Shaped ATPase Motor at Millisecond Resolution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3031-3040, MAR 4 2015
abstract, full text, TCBG publications, DOI:10.1021/ja512605w

Yu, Tang-Qing; Lapelosa, Mauro; Vanden-Eijnden, Eric; Abrams, Cameron F.
Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3041-3050, MAR 4 2015
abstract, full text, DOI:10.1021/ja512484q

Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang
HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation
SCIENTIFIC REPORTS, 5 Art. No. 8741, MAR 4 2015
abstract, full text, DOI:10.1038/srep08741

Yao, Huili; Rui, Huan; Kumar, Ritesh; Eshelman, Kate; Lovell, Scott; Battaile, Kevin P.; Im, Wonpil; Rivera, Mario
Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic
BIOCHEMISTRY, 54:1611-1627, MAR 3 2015
abstract, full text, DOI:10.1021/bi501255r

Fetics, Susan K.; Guterres, Hugo; Kearney, Bradley M.; Buhrman, Greg; Ma, Buyong; Nussinov, Ruth; Mattos, Carla
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
STRUCTURE, 23:505-516, MAR 3 2015
abstract, full text, DOI:10.1016/j.str.2014.12.017

Vashisth, Harish
Theoretical and Computational Studies of Peptides and Receptors of the Insulin Family
MEMBRANES, 5:48-83, MAR 2015
abstract, full text, DOI:10.3390/membranes5010048

Pankavich, Stephen; Ortoleva, Peter
A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization
COMPUTATION, 3:29-57, MAR 2015
abstract, full text, DOI:10.3390/computation3010029

Merzhievskii, L. A.
Deformation models under intense dynamic loading (Review)
COMBUSTION EXPLOSION AND SHOCK WAVES, 51:269-283, MAR 2015
abstract, full text, DOI:10.1134/S0010508215020100

Ganesan, Prabhakar; Kim, Jong Goo; Lee, Jae Hyuk; Kim, Jeongho; Ihee, Hyotcherl
Implicit vs. Explicit Solvent Models for Calculating X-ray Solution Scattering Curves
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 36:955-962, MAR 2015
abstract, full text, DOI:10.1002/bkcs.10178

Yuan, Li; Nerngchamnong, Nisachol; Cao, Liang; Hamoudi, Hicham; del Barco, Enrique; Roemer, Max; Sriramula, Ravi K.; Thompson, Damien; Nijhuis, Christian A.
Controlling the direction of rectification in a molecular diode
NATURE COMMUNICATIONS, 6 Art. No. 6324, MAR 2015
abstract, full text, DOI:10.1038/ncomms7324

Schiro, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Haertlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins
NATURE COMMUNICATIONS, 6 Art. No. 6490, MAR 2015
abstract, full text, DOI:10.1038/ncomms7490

Miguel, Amanda; Hsin, Jen; Liu, Tianyun; Tang, Grace; Altman, Russ B.; Huang, Kerwyn Casey
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004117, MAR 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004117

Duran-Lara, Esteban F.; Avila-Salas, Fabian; Galaz, Sebastian; John, Amalraj; Marican, Adolfo; Gutierrez, Margarita; Nachtigall, Fabiane M.; Gonzalez-Nilo, Fernando D.; Santos, Leonardo S.
Nano-Detoxification of Organophosphate Agents by PAMAM Derivatives
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:580-591, MAR 2015
abstract, full text, DOI:10.5935/0103-5053.20150013

Wu, Di
Proline puckering parameters for collagen structure simulations
AIP ADVANCES, 5 Art. No. 037124, MAR 2015
abstract, full text, DOI:10.1063/1.4915295

Chen, Qi; Cheng, Xiaolin; Wei, Dongqing; Xu, Qin
Molecular Dynamics Simulation Studies of the Wild Type and E92Q/N155H Mutant of Elvitegravir-resistance HIV-1 Integrase
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 7:36-42, MAR 2015
abstract, full text, DOI:10.1007/s12539-014-0235-8

Izanloo, C.
Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study
CANADIAN JOURNAL OF CHEMISTRY, 93:348-361, MAR 2015
abstract, full text, DOI:10.1139/cjc-2014-0371

Feng, Zhiwei; Pearce, Larry V.; Xu, Xiaomeng; Yang, Xiaole; Yang, Peng; Blumberg, Peter M.; Xie, Xiang-Qun
Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:572-588, MAR 2015
abstract, full text, DOI:10.1021/ci5007189

Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolf; Overk, Cassia; Gonzalez, Tania; Trejo, Margarita; Spencer, Brian; Kosberg, Kori; Masliah, Eliezer
Molecular Determinants of alpha-Synuclein Mutants' Oligomerization and Membrane Interactions
ACS CHEMICAL NEUROSCIENCE, 6:403-416, MAR 2015
abstract, full text, DOI:10.1021/cn500332w

Tofoleanu, Florentina; Brooks, Bernard R.; Buchete, Nicolae-Viorel
Modulation of Alzheimer's A beta Protofilament-Membrane Interactions by Lipid Headgroups
ACS CHEMICAL NEUROSCIENCE, 6:446-455, MAR 2015
abstract, full text, DOI:10.1021/cn500277f

Pietra, Francesco
From the Sequence to the Conformation of the Unabridged Transmembrane Domains TM1 and TM2 of the cASIC1a Ion Channel - A Parallel Tempering Approach
CHEMISTRY & BIODIVERSITY, 12:350-357, MAR 2015
abstract, full text, DOI:10.1002/cbdv.201400298

Pothapragada, Seetha; Zhang, Peng; Sheriff, Jawaad; Livelli, Mark; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
A phenomenological particle-based platelet model for simulating filopodia formation during early activation
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, 31 Art. No. e02702, MAR 2015
abstract, full text, DOI:10.1002/cnm.2702

Ko, Jeong-Ahn; Kwon, Tae Woo; Ambrosia, Matthew; Ha, Man Yeong
Study of the wetting characteristics of water droplet on a heterogeneous pillared surface
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1243-1256, MAR 2015
abstract, full text, DOI:10.1007/s12206-015-0238-3

Chen, Liao Y.
Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin
BIOPHYSICAL CHEMISTRY, 198:14-21, MAR 2015
abstract, full text, DOI:10.1016/j.bpc.2015.01.004

Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
A robust all-atom model for LCAT generated by homology modeling
JOURNAL OF LIPID RESEARCH, 56:620-634, MAR 2015
abstract, full text, DOI:10.1194/jlr.M056382

Tovstun, S. A.; Ivanchikhina, A. V.; Nikolenko, L. M.; Nevidimov, A. V.; Brichkin, S. B.; Razumov, V. F.
J-aggregation of a thiacarbocyanine dye in reverse microemulsions
HIGH ENERGY CHEMISTRY, 49:111-116, MAR 2015
abstract, full text, DOI:10.1134/S0018143915020113

Lindert, Steffen; McCammon, J. Andrew
Improved cryoEM-Guided Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1337-1346, MAR 2015
abstract, full text, DOI:10.1021/ct500995d

Miller, John H., Jr.; Villagrau, Martha Y. Suarez; Mark, Sladjana; Briggs, James M.
Normal and impaired charge transport in biological systems
PHYSICA B-CONDENSED MATTER, 460:119-125, MAR 1 2015
abstract, full text, DOI:10.1016/j.physb.2014.11.052

Nicolas, Aurelie; Raguenes-Nicol, Celine; Ben Yaou, Rabah; Ameziane-Le Hir, Sarah; Cheron, Angelique; Vie, Veronique; Claustres, Mireille; Leturcq, France; Delalande, Olivier; Hubert, Jean-Francois; Tuffery-Giraud, Sylvie; Giudice, Emmanuel; Le Rumeur, Elisabeth
Becker muscular dystrophy severity is linked to the structure of dystrophin
HUMAN MOLECULAR GENETICS, 24:1267-1279, MAR 1 2015
abstract, full text, DOI:10.1093/hmg/ddu537

Mondal, Manas; Choudhury, Devapriya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay
Role of indirect readout mechanism in TATA box binding protein-DNA interaction
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:283-295, MAR 2015
abstract, full text, DOI:10.1007/s10822-014-9828-x

Marek, Ale; Shaffer, Christopher J.; Pepin, Robert; Slovakova, Kristina; Laszlo, Kenneth J.; Bush, Matthew F.; Turecek, Frantiek
Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 26:415-431, MAR 2015
abstract, full text, DOI:10.1007/s13361-014-1047-0

Cheatham, Thomas E., I.I.I.; Roe, Daniel R.
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
COMPUTING IN SCIENCE & ENGINEERING, 17:30-39, MAR-APR 2015
abstract, full text

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue
Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 40, MAR 2015
abstract, full text, DOI:10.1007/s00894-015-2588-2

Paudyal, Samridhdi; Alfonso-Prieto, Mercedes; Carnevale, Vincenzo; Redhu, Shiv K.; Klein, Michael L.; Nicholson, Allen W.
Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:459-472, MAR 2015
abstract, full text, DOI:10.1002/prot.24751

Baker, Christopher M.
Polarizable force fields for molecular dynamics simulations of biomolecules
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5:241-254, MAR-APR 2015
abstract, full text, DOI:10.1002/wcms.1215

Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny
A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma
JOURNAL OF COMPUTATIONAL PHYSICS, 284:668-686, MAR 1 2015
abstract, full text, DOI:10.1016/j.jcp.2015.01.004

Ai, Haixin; Zheng, Fangliang; Deng, Fangbo; Zhu, Chunyu; Gu, Ying; Zhang, Li; Li, Xuejiao; Chang, Alan K.; Zhao, Jian; Zhu, Junfeng; Liu, Hongsheng
Structure-Based Virtual Screening for Potential Inhibitors of Influenza A Virus RNA Polymerase PA Subunit
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 21:149-156, MAR 2015
abstract, full text, DOI:10.1007/s10989-014-9442-8

Mohan, Rohith R.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
A theoretical view of the C3d:CR2 binding controversy
MOLECULAR IMMUNOLOGY, 64:112-122, MAR 2015
abstract, full text, DOI:10.1016/j.molimm.2014.11.006

Mahboobi, Seyed Hanif; Javanpour, Alex A.; Mofrad, Mohammad R. K.
The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
PLOS ONE, 10 Art. No. e0112969, FEB 27 2015
abstract, full text, DOI:10.1371/journal.pone.0112969

Shinobu, Ai; Agmon, Noam
The Hole in the Barrel: Water Exchange at the GFP Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3464-3478, FEB 26 2015
abstract, full text, DOI:10.1021/jp5127255

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting
Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 137:701-710, FEB 25 2015
abstract, full text, DOI:10.1016/j.saa.2014.08.126

Johnson, Quentin R.; Lindsay, Richard J.; Nellas, Ricky B.; Fernandez, Elias J.; Shen, Tongye
Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue-Residue Contacts
BIOCHEMISTRY, 54:1534-1541, FEB 24 2015
abstract, full text, DOI:10.1021/bi501152d

Francisca Aguayo, M.; Carlos Caceres, Juan; Fuentealba, Matias; Munoz, Rodrigo; Stange, Claudia; Cabrera, Ricardo; Handford, Michael
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling
FRONTIERS IN PLANT SCIENCE, 6 Art. No. 91, FEB 23 2015
abstract, full text, DOI:10.3389/fpls.2015.00091

Singh, Rajesh; Ahalawat, Navjeet; Murarka, Rajesh K.
Activation of Corticotropin-Releasing Factor 1 Receptor: Insights from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2806-2817, FEB 19 2015
abstract, full text, DOI:10.1021/jp509814n

Mirjalili, Vahid; Feig, Michael
Interactions of Amino Acid Side-Chain Analogs within Membrane Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2877-2885, FEB 19 2015
abstract, full text, DOI:10.1021/jp511712u

Korchowiec, Beata; Korchowiec, Jacek; Gorczyca, Marcelina; de Vains, Jean-Bernard Regnouf; Rogalska, Ewa
Molecular Organization of Nalidixate Conjugated Calixarenes in Bacterial Model Membranes Probed by Molecular Dynamics Simulation and Langmuir Mono layer Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2990-3000, FEB 19 2015
abstract, full text, DOI:10.1021/jp567151r

Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Modeling Nanosized Single Molecule Objects: Dendronized Polymers Adsorbed onto Mica
JOURNAL OF PHYSICAL CHEMISTRY C, 119:3746-3753, FEB 19 2015
abstract, full text, DOI:10.1021/jp510586r

Farimani, A. Barati; Heiranian, M.; Aluru, N. R.
Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:650-657, FEB 19 2015
abstract, full text, DOI:10.1021/jz5025417

Plaschka, C.; Lariviere, L.; Wenzeck, L.; Seizl, M.; Hemann, M.; Tegunov, D.; Petrotchenko, E. V.; Borchers, C. H.; Baumeister, W.; Herzog, F.; Villa, E.; Cramer, P.
Architecture of the RNA polymerase II-Mediator core initiation complex
NATURE, 518:376-380, FEB 19 2015
abstract, full text, DOI:10.1038/nature14229

Huggins, David J.
Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations
BIOPHYSICAL JOURNAL, 108:928-936, FEB 17 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.035

Sharma, Vivek; Enkavi, Giray; Vattulainen, Ilpo; Rog, Tomasz; Wikstrom, Marten
Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2040-2045, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1409543112

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.
An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2204-2209, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1423754112

Cronin, Melissa; Coolbaugh, Michael J.; Nellis, David; Zhu, Jianwei; Wood, David W.; Nussinov, Ruth; Ma, Buyong
Dynamics differentiate between active and inactive inteins
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 91:51-62, FEB 16 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.07.094

Aguayo, Daniel; Pacheco, Nicolas; Morales, Eduardo H.; Collao, Bernardo; Luraschi, Roberto; Cabezas, Carolina; Calderon, Paulina; Gonzalez-Nilo, Fernando; Gil, Fernando; Calderon, Ivan L.; Saavedra, Claudia P.
Hydrogen peroxide and hypochlorous acid influx through the major S. Typhimurium porin OmpD is affected by substitution of key residues of the channel
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 568:38-45, FEB 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.01.005

Hatano, Hiroko; Shaw, Jacqueline; Marquardt, Kaitlin; Zhang, Zhiyong; Gauthier, Laurent; Chanteux, Stephanie; Rossi, Benjamin; Li, Demin; Mitchell, Julie; Kollnberger, Simon
The D0 Ig-like Domain Plays a Central Role in the Stronger Binding of KIR3DL2 to B27 Free H Chain Dimers
JOURNAL OF IMMUNOLOGY, 194:1591-1601, FEB 15 2015
abstract, full text, DOI:10.4049/jimmunol.1402214

Lu, Shouqin; Chen, Shenbao; Mao, Debin; Zhang, Yan; Long, Mian
Contribution of the CR Domain to P-Selectin Lectin Domain Allostery by Regulating the Orientation of the EGF Domain
PLOS ONE, 10 Art. No. e0118083, FEB 12 2015
abstract, full text, DOI:10.1371/journal.pone.0118083

Houari, Ymene; Chibani, Siwar; Jacquemin, Denis; Laurent, Adele D.
TD-DFT Assessment of the Excited State Intramolecular Proton Transfer in Hydroxyphenylbenzimidazole (HBI) Dyes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2180-2192, FEB 12 2015
abstract, full text, DOI:10.1021/jp505036d

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei
Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins
PLOS ONE, 10 Art. No. e0117506, FEB 11 2015
abstract, full text, DOI:10.1371/journal.pone.0117506

Banerjee, Shouvik; Wilson, James; Shim, Jiwook; Shankla, Manish; Corbin, Elise A.; Aksimentiev, Aleksei; Bashir, Rashid
Slowing DNA Transport Using Graphene-DNA Interactions
ADVANCED FUNCTIONAL MATERIALS, 25:936-946, FEB 11 2015
abstract, full text, DOI:10.1002/adfm.201403719

Diaz, Natalia; Suarez, Dimas
Extensive Simulations of the Full-Length Matrix Metalloproteinase-2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide
BIOCHEMISTRY, 54:1243-1258, FEB 10 2015
abstract, full text, DOI:10.1021/bi501014w

Mouchlis, Varnavas D.; Bucher, Denis; McCammon, J. Andrew; Dennis, Edward A.
Membranes serve as allosteric activators of phospholipase A(2), enabling it to extract, bind, and hydrolyze phospholipid substrates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E516-E525, FEB 10 2015
abstract, full text, DOI:10.1073/pnas.1424651112

Goldau, Thomas; Murayama, Keiji; Brieke, Clara; Steinwand, Sabrina; Mondal, Padmabati; Biswas, Mithun; Burghardt, Irene; Wachtveitl, Josef; Asanuma, Hiroyuki; Heckel, Alexander
Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C-Nucleoside
CHEMISTRY-A EUROPEAN JOURNAL, 21:2845-2854, FEB 9 2015
abstract, full text, DOI:10.1002/chem.201405840

Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy
Microscopic dynamics of water around unfolded structures of barstar at room temperature
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 055102, FEB 7 2015
abstract, full text, DOI:10.1063/1.4907007

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.
Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 054701, FEB 7 2015
abstract, full text, DOI:10.1063/1.4906877

Burger, Pieter B.; Williams, Marni; Sprenger, Janina; Reeksting, Shaun B.; Botha, Mariette; Mueller, Ingrid B.; Joubert, Fourie; Birkholtz, Lyn-Marie; Louw, Abraham I.
A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail
MALARIA JOURNAL, 14 Art. No. 54, FEB 5 2015
abstract, full text, DOI:10.1186/s12936-015-0572-z

Akyuz, Nurunisa; Georgieva, Elka R.; Zhou, Zhou; Stolzenberg, Sebastian; Cuendet, Michel A.; Khelashvili, George; Altman, Roger B.; Terry, Daniel S.; Freed, Jack H.; Weinstein, Harel; Boudker, Olga; Blanchard, Scott C.
Transport domain unlocking sets the uptake rate of an aspartate transporter
NATURE, 518:68-+, FEB 5 2015
abstract, full text, DOI:10.1038/nature14158

Calero, C.; Marti, J.; Guardia, E.
H-1 Nuclear Spin Relaxation of Liquid Water from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1966-1973, FEB 5 2015
abstract, full text, DOI:10.1021/jp510013q

Luan, Binquan; Tien Huynh; Zhou, Ruhong
Nanopore-Based Sensors for Ligand Receptor Lead Optimization
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:331-337, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025614

Martin, Daniel R.; Matyushov, Dmitry V.
Dipolar Nanodomains in Protein Hydration Shells
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:407-412, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025433

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei
BROMOC Suite: Monte Carlo/Brownian Dynamics Suite for Studies of Ion Permeation and DNA transport in Biological and Artificial Pores with Effective Potentials
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:264-271, FEB 5 2015
abstract, full text, DOI:10.1002/jcc.23799

Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos
Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics
SCIENTIFIC REPORTS, 5 Art. No. 8247, FEB 4 2015
abstract, full text, DOI:10.1038/srep08247

Jahangiri, Soran; Legris-Falardeau, Valery; Peslherbe, Gilles H.
Computational investigation of the hydration of alkyl diammonium cations in water clusters
CHEMICAL PHYSICS LETTERS, 621:85-90, FEB 4 2015
abstract, full text, DOI:10.1016/j.cplett.2014.12.045

Eddy, Matthew T.; Andreas, Loren; Teijido, Oscar; Su, Yongchao; Clark, Lindsay; Noskov, Sergei Y.; Wagner, Gerhard; Rostovtseva, Tatiana K.; Griffin, Robert G.
Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage-Dependent Anion Channel Gating in Two-Dimensional Lipid Crystalline Bilayers
BIOCHEMISTRY, 54:994-1005, FEB 3 2015
abstract, full text, DOI:10.1021/bi501260r

Mastrangelo, Eloise; Vachette, Patrice; Cossu, Federica; Malvezzi, Francesca; Bolognesi, Martino; Milani, Mario
The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution
BIOPHYSICAL JOURNAL, 108:714-723, FEB 3 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3471

Hackwon, Do; Kim, Soo Jin; Lee, Chang Woo; Kim, Han-Woo; Park, Hyun Ho; Kim, Ho Min; Park, Hyun; Park, HaJeung; Lee, Jun Hyuck
Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes
SCIENTIFIC REPORTS, 5 Art. No. 8196, FEB 3 2015
abstract, full text, DOI:10.1038/srep08196

Bertran, Oscar; del Valle, Luis J.; Revilla-Lopez, Guillermo; Rivas, Manuel; Chaves, Gustavo; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite
CHEMISTRY-A EUROPEAN JOURNAL, 21:2537-2546, FEB 2 2015
abstract, full text, DOI:10.1002/chem.201405428

Park, Yeonju; Seo, Yongil; Chae, Boknam; Pyo, Dongjin; Chung, Hoeil; Hwang, Hyonseok; Jung, Young Mee
Understanding the Structural Differences between Spherical and Rod-Shaped Human Insulin Nanoparticles Produced by Supercritical Fluids Precipitation
CHEMPHYSCHEM, 16:476-482, FEB 2 2015
abstract, full text, DOI:10.1002/cphc.201402504

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Zhang, Jinglai
Investigation of alanine mutations affecting insulin-like growth factor (IGF) I binding to IGF binding proteins
GROWTH FACTORS, 33:40-49, FEB 2015
abstract, full text, DOI:10.3109/08977194.2014.964868

Li Wenzhao; Meng Wei; Tian Pu
Impact of Stable Protein-protein Interaction on Protein Conformational Space
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:149-155, FEB 2015
abstract, full text, DOI:10.1007/s40242-015-3402-5

Fibriansah, Guntur; Tan, Joanne L.; Smith, Scott A.; de Alwis, Ruklanthi; Ng, Thiam-Seng; Kostyuchenko, Victor A.; Jadi, Ramesh S.; Kukkaro, Petra; de Silva, Aravinda M.; Crowe, James E.; Lok, Shee-Mei
A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins
NATURE COMMUNICATIONS, 6 Art. No. 6341, FEB 2015
abstract, full text, DOI:10.1038/ncomms7341

Barakat, Khaled H.; Anwar-Mohamed, Anwar; Tuszynski, Jack A.; Robins, Morris J.; Tyrrell, D. Lorne; Houghton, Michael
A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:362-373, FEB 2015
abstract, full text, DOI:10.1021/ci400631n

Sandberg, Robert B.; Banchelli, Martina; Guardiani, Carlo; Menichetti, Stefano; Caminati, Gabriella; Procacci, Piero
Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:423-435, FEB 2015
abstract, full text, DOI:10.1021/ct500964e

Hardy, David J.; Wu, Zhe; Phillips, James C.; Stone, John E.; Skeel, Robert D.; Schulten, Klaus
Multilevel Summation Method for Electrostatic Force Evaluation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:766-779, FEB 2015
abstract, full text, TCBG publications, DOI:10.1021/ct5009075

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suarez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.
WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:800-809, FEB 2015
abstract, full text, DOI:10.1021/ct5010615

Sieradzan, Adam K.; Krupa, Pawel; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary
Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:817-831, FEB 2015
abstract, full text, DOI:10.1021/ct500736a

Modi, Niraj; Barcena-Uribarri, Ivan; Bains, Manjeet; Benz, Roland; Hancock, Robert E. W.; Kleinekathoefer, Ulrich
Tuning the Affinity of Anion Binding Sites in Porin Channels with Negatively Charged Residues: Molecular Details for OprP
ACS CHEMICAL BIOLOGY, 10:441-451, FEB 2015
abstract, full text, DOI:10.1021/cb500399j

Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud
Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55:13-24, FEB 2015
abstract, full text, DOI:10.1016/j.jmgm.2014.10.011

Li, Chen-Yu; Hemmig, Elise A.; Kong, Jinglin; Yoo, Jejoong; Hernandez-Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei
Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
ACS NANO, 9:1420-1433, FEB 2015
abstract, full text, DOI:10.1021/nn505825z

Li Jun-Wei; Xiao Shao-Ying; Xie Xiao-Xiao; Yu Hui; Zhang Hai-Lin; Zhan Yong; An Hai-Long
Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein
CHINESE PHYSICS LETTERS, 32 Art. No. 028702, FEB 2015
abstract, full text, DOI:10.1088/0256-307X/32/2/028702

Madsen, J. J.; Persson, E.; Olsen, O. H.
Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 13:262-267, FEB 2015
abstract, full text, DOI:10.1111/jth.12791

Yu, Xiaofeng; Cojocaru, Vlad; Mustafa, Ghulam; Salo-Ahen, Outi M. H.; Lepesheva, Galina I.; Wade, Rebecca C.
Dynamics of CYP51: implications for function and inhibitor design
JOURNAL OF MOLECULAR RECOGNITION, 28:59-73, FEB 2015
abstract, full text, DOI:10.1002/jmr.2412

Noto, Rosina; Santangelo, Maria Grazia; Levantino, Matteo; Cupane, Antonio; Mangione, Maria Rosalia; Parisi, Daniele; Ricagno, Stefano; Bolognesi, Martino; Manno, Mauro; Martorana, Vincenzo
Functional and dysfunctional conformers of human neuroserpin characterized by optical spectroscopies and Molecular Dynamics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1854:110-117, FEB 2015
abstract, full text, DOI:10.1016/j.bbapap.2014.10.002

Moreau, Adrien; Gosselin-Badaroudine, Pascal; Delemotte, Lucie; Klein, Michael L.; Chahine, Mohamed
Gating pore currents are defects in common with two Na(v)1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy
JOURNAL OF GENERAL PHYSIOLOGY, 145:93-106, FEB 2015
abstract, full text, DOI:10.1085/jgp.201411304

Davis, Adam S.; Federici, Thais; Ray, William C.; Boulis, Nicholas M.; O'Connor, Deirdre; Clark, K. Reed; Bartlett, Jeffrey S.
Rational Design and Engineering of a Modified Adeno-Associated Virus (AAV1)-Based Vector System for Enhanced Retrograde Gene Delivery
NEUROSURGERY, 76:216-225, FEB 2015
abstract, full text, DOI:10.1227/NEU.0000000000000589

Zhang, Rui; Bhattacharjee, Anirban; Field, Martin J.; Salahub, Dennis R.
Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:268-281, FEB 2015
abstract, full text, DOI:10.1002/prot.24732

Langley, David R.; Kimura, S. Roy; Sivaprakasam, Prasanna; Zhou, Nannan; Dicker, Ira; McAuliffe, Brian; Wang, Tao; Kadow, John F.; Meanwell, Nicholas A.; Krystal, Mark
Homology models of the HIV-1 attachment inhibitor BMS-626529 bound to gp120 suggest a unique mechanism of action
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:331-350, FEB 2015
abstract, full text, DOI:10.1002/prot.24726

Kolsek, Katra; Gobec, Martina; Rascan, Irena Minaric; Dolenc, Marija Sollner
Screening of bisphenol A, triclosan and paraben analogues as modulators of the glucocorticoid and androgen receptor activities
TOXICOLOGY IN VITRO, 29:8-15, FEB 2015
abstract, full text, DOI:10.1016/j.tiv.2014.08.009

Zhang, Chongqian; Du, Chunmiao; Feng, Zhiwei; Zhu, Jingyu; Li, Youyong
Hologram Quantitative Structure Activity Relationship, Docking, and Molecular Dynamics Studies of Inhibitors for CXCR4
CHEMICAL BIOLOGY & DRUG DESIGN, 85:119-136, FEB 2015
abstract, full text, DOI:10.1111/cbdd.12377

Hamed, Elham; Ma, Dan; Keten, Sinan
Multiple PEG Chains Attached onto the Surface of a Helix Bundle: Conformations and Implications
ACS BIOMATERIALS-SCIENCE & ENGINEERING, 1:79-84, FEB 2015
abstract, full text, DOI:10.1021/ab500088b

Wang, Beibei; Opron, Kristopher; Burton, Zachary F.; Cukier, Robert I.; Feig, Michael
Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details
NUCLEIC ACIDS RESEARCH, 43:1133-1146, JAN 30 2015
abstract, full text, DOI:10.1093/nar/gku1370

Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele
The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility
JOURNAL OF MOLECULAR BIOLOGY, 427:478-490, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.09.026

Zheng, Fan; Jewell, Heather; Fitzpatrick, Jeremy; Zhang, Jian; Mierke, Dale F.; Grigoryan, Gevorg
Computational Design of Selective Peptides to Discriminate between Similar PDZ Domains in an Oncogenic Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:491-510, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.10.014

Darre, Leonardo; Furini, Simone; Domene, Carmen
Permeation and Dynamics of an Open-Activated TRPV1 Channel
JOURNAL OF MOLECULAR BIOLOGY, 427:537-549, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.016

Freudenthal, Bret D.; Beard, William A.; Perera, Lalith; Shock, David D.; Kim, Taejin; Schlick, Tamar; Wilson, Samuel H.
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide
NATURE, 517:635-U261, JAN 29 2015
abstract, full text, DOI:10.1038/nature13886

Li, Jun; Deng, Mingsen; Voronine, Dmitri V.; Mukamel, Shaul; Jiang, Jun
Two-Dimensional Near Ultraviolet (2DNUV) Spectroscopic Probe of Structural-Dependent Exciton Dynamics in a Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1314-1322, JAN 29 2015
abstract, full text, DOI:10.1021/jp509314y

Meng, Yilin; Lin, Yen-lin; Roux, Benoit
Computational Study of the "DFG-Flip" Conformational Transition in c-Abl and c-Src Tyrosine Kinases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1443-1456, JAN 29 2015
abstract, full text, DOI:10.1021/jp511792a

Samoylova, Olga N.; Calixte, Emvia I.; Shuford, Kevin L.
Molecular Dynamics Simulations of Ion Transport in Carbon Nanotube Channels
JOURNAL OF PHYSICAL CHEMISTRY C, 119:1659-1666, JAN 29 2015
abstract, full text, DOI:10.1021/jp5103669

Luedemann, Gesa; Solov'yov, Ilia A.; Kubar, Tomas; Elstner, Marcus
Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:1147-1156, JAN 28 2015
abstract, full text, DOI:10.1021/ja510550g

Chakraborty, Srirupa; Zheng, Wenjun
Decrypting the Structural, Dynamic, and Energetic Basis of a Monomeric Kinesin Interacting with a Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation
BIOCHEMISTRY, 54:859-869, JAN 27 2015
abstract, full text, DOI:10.1021/bi501056h

Francois-Heude, Marc; Mendez-Ardoy, Alejandro; Cendret, Virginie; Lafite, Pierre; Daniellou, Richard; Ortiz Mellet, Carmen; Garcia Fernandez, Jose M.; Moreau, Vincent; Djedaini-Pilard, Florence
Synthesis of High-Mannose Oligosaccharide Analogues through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins?
CHEMISTRY-A EUROPEAN JOURNAL, 21:1978-1991, JAN 26 2015
abstract, full text, DOI:10.1002/chem.201405481

Poblete, Horacio; Oyarzun, Ingrid; Olivero, Pablo; Comer, Jeffrey; Zuniga, Matias; Sepulveda, Ronnina V.; Baez-Nieto, David; Gonzalez Leon, Carlos; Gonzalez-Nilo, Fernando; Latorre, Ramon
Molecular Determinants of Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P-2) Binding to Transient Receptor Potential V1 (TRPV1) Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:2086-2098, JAN 23 2015
abstract, full text, DOI:10.1074/jbc.M114.613620

Patel, Dhilon S.; He, Xibing; MacKerell, Alexander D., Jr.
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
JOURNAL OF PHYSICAL CHEMISTRY B, 119:637-652, JAN 22 2015
abstract, full text, DOI:10.1021/jp412696m

Krzeminska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Swiderek, Katarzyna
Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT
JOURNAL OF PHYSICAL CHEMISTRY B, 119:917-927, JAN 22 2015
abstract, full text, DOI:10.1021/jp506119h

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.
Multi-Conformer Ensemble Docking to Difficult Protein Targets
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1026-1034, JAN 22 2015
abstract, full text, DOI:10.1021/jp506511p

Craft, John W., Jr.; Shen, Tsai-wei; Brier, Lindsey M.; Briggs, James M.
Biophysical Characteristics of Cholera Toxin and Escherichia coli Heat-Labile Enterotoxin Structure and Chemistry Lead to Differential Toxicity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1048-1061, JAN 22 2015
abstract, full text, DOI:10.1021/jp506509c

Comer, Jeffrey; Gumbart, James C.; Henin, Jerome; Lelievre, Tony; Pohorille, Andrew; Chipot, Christophe
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1129-1151, JAN 22 2015
abstract, full text, DOI:10.1021/jp506633n

Gianti, Eleonora; Carnevale, Vincenzo; DeGrado, William F.; Klein, Michael L.; Fiorin, Giacomo
Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1173-1183, JAN 22 2015
abstract, full text, DOI:10.1021/jp506807y

Gleed, Mitchell L.; Busath, David D.
Why Bound Amantadine Fails to Inhibit Proton Conductance According to Simulations of the Drug-Resistant Influenza A M2 (S31N)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1225-1231, JAN 22 2015
abstract, full text, DOI:10.1021/jp508545d

Holden, Jeffrey K.; Kang, Soosung; Hollingsworth, Scott A.; Li, Huiying; Lim, Nathan; Chen, Steven; Huang, He; Xue, Fengtian; Tang, Wei; Silverman, Richard B.; Poulos, Thomas L.
Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 58:994-1004, JAN 22 2015
abstract, full text, DOI:10.1021/jm501723p

Schur, Florian K. M.; Hagen, Wim J. H.; Rumlova, Michaela; Ruml, Tomas; Mueller, Barbara; Kraeusslich, Hans-Georg; Briggs, John A. G.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 angstrom resolution
NATURE, 517:505-508, JAN 22 2015
abstract, full text, DOI:10.1038/nature13838

Gun'ko, Vladimir M.; Nasiri, Rasoul; Sazhin, Sergei S.
Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034502, JAN 21 2015
abstract, full text, DOI:10.1063/1A905496

Harrach, Michael F.; Klameth, Felix; Drossel, Barbara; Vogel, Michael
Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034703, JAN 21 2015
abstract, full text, DOI:10.1063/1.4905557

Lindert, Steffen; Cheng, Yuanhua; Kekenes-Huskey, Peter; Regnier, Michael; McCammon, J. Andrew
Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation Elucidated by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 108:395-407, JAN 20 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3461

Chamberlin, Adam; Qiu, Feng; Wang, Yibo; Noskov, Sergei Y.; Larsson, H. Peter
Mapping the Gating and Permeation Pathways in the Voltage-Gated Proton Channel Hv1
JOURNAL OF MOLECULAR BIOLOGY, 427:131-145, JAN 16 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.018

Yan, Si; Zhang, Huilan; Hou, Guangjin; Ahmed, Shubbir; Williams, John C.; Polenova, Tatyana
Internal Dynamics of Dynactin CAP-Gly Is Regulated by Microtubules and Plus End Tracking Protein EB1
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:1607-1622, JAN 16 2015
abstract, full text, DOI:10.1074/jbc.M114.603118

Barragan, Angela M.; Crofts, Antony R.; Schulten, Klaus; Solov'yov, Ilia A.
Identification of Ubiquinol Binding Motifs at the Q(o)-Site of the Cytochrome bc(1) Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 119:433-447, JAN 15 2015
abstract, full text, TCBG publications, DOI:10.1021/jp510022w

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:482-490, JAN 15 2015
abstract, full text, DOI:10.1021/jp511485n

Mejri, Alia; Vardanega, Delphine; Tangour, Bahoueddine; Gharbi, Tijani; Picaud, Fabien
Encapsulation into Carbon Nanotubes and Release of Anticancer Cisplatin Drug Molecule
JOURNAL OF PHYSICAL CHEMISTRY B, 119:604-611, JAN 15 2015
abstract, full text, DOI:10.1021/jp5102384

Li, Chunyu; Strachan, Alejandro
Molecular Scale Simulations on Thermoset Polymers: A Review
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 53:103-122, JAN 15 2015
abstract, full text, DOI:10.1002/polb.23489

Tao, Jinhui; Battle, Keith C.; Pan, Haihua; Salter, E. Alan; Chien, Yung-Ching; Wierzbicki, Andrzej; De Yoreo, James J.
Energetic basis for the molecular-scale organization of bone
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:326-331, JAN 13 2015
abstract, full text, DOI:10.1073/pnas.1404481112

He Jia; Feng Xizeng; Shao Xueguang; Cai Wensheng
Adsorption Behavior of Hydrophobin Proteins on Surface of Mica
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:110-115, JAN 10 2015
abstract, full text, DOI:10.7503/cjcu20140808

Baul, Upayan; Vemparala, Satyavani
Ion hydration and associated defects in hydrogen bond network of water: Observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl2
PHYSICAL REVIEW E, 91 Art. No. 012114, JAN 8 2015
abstract, full text, DOI:10.1103/PhysRevE.91.012114

Cui, Di; Ou, Shu-Ching; Patel, Sandeep
Protein Denaturants at Aqueous-Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 119:164-178, JAN 8 2015
abstract, full text, DOI:10.1021/jp507203g

Polak, Andraz; Velikonja, Aljaz; Kramar, Peter; Tarek, Mounir; Miklavcic, Damijan
Electroporation Threshold of POPC Lipid Bilayers with Incorporated Polyoxyethylene Glycol (C12E8)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:192-200, JAN 8 2015
abstract, full text, DOI:10.1021/jp509789m

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 015101, JAN 7 2015
abstract, full text, DOI:10.1063/1.4904896

Kim, Hanseong; Zou, Taisong; Modi, Chintan; Doerner, Katerina; Grunkemeyer, Timothy J.; Chen, Liqing; Fromme, Raimund; Matz, Mikhail V.; Ozkan, S. Banu; Wachter, Rebekka M.
A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins
STRUCTURE, 23:34-43, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.011

Baker, Joseph L.; Courtemanche, Naomi; Parton, Daniel L.; McCullagh, Martin; Pollard, Thomas D.; Voth, Gregory A.
Electrostatic Interactions between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation
STRUCTURE, 23:68-79, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.10.014

Dai, Jian; Zhou, Huan-Xiang
Reduced Curvature of Ligand-Binding Domain Free-Energy Surface Underlies Partial Agonism at NMDA Receptors
STRUCTURE, 23:228-236, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.012

Huang, Wei; Ravikumar, Krishnakumar M.; Chance, Mark R.; Yang, Sichun
Quantitative Mapping of Protein Structure by Hydroxyl Radical Footprinting-Mediated Structural Mass Spectrometry: A Protection Factor Analysis
BIOPHYSICAL JOURNAL, 108:107-115, JAN 6 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.013

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir
PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6
SCIENTIFIC REPORTS, 5 Art. No. 7474, JAN 6 2015
abstract, full text, DOI:10.1038/srep07474

Xu, Ji; Li, Xiaoxia; Hou, Chaofeng; Wang, Limin; Zhou, Guangzheng; Ge, Wei; Li, Jinghai
Engineering molecular dynamics simulation in chemical engineering
CHEMICAL ENGINEERING SCIENCE, 121:200-216, JAN 6 2015
abstract, full text, DOI:10.1016/j.ces.2014.09.051

Rovigatti, Lorenzo; Sulc, Petr; Reguly, Istvan Z.; Romano, Flavio
A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1-8, JAN 5 2015
abstract, full text, DOI:10.1002/jcc.23763

Zomot, Elia; Gur, Mert; Bahar, Ivet
Microseconds Simulations Reveal a New Sodium-binding Site and the Mechanism of Sodium-coupled Substrate Uptake by LeuT
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:544-555, JAN 2 2015
abstract, full text, DOI:10.1074/jbc.M114.617555

Bujalowski, Paul J.; Nicholls, Paul; Barral, Jose M.; Oberhauser, Andres F.
Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone
FEBS LETTERS, 589:123-130, JAN 2 2015
abstract, full text, DOI:10.1016/j.febslet.2014.11.034

Sellers, Michael S.; Lisal, Martin; Brennan, John K.
Exponential-six potential scaling for the calculation of free energies in molecular simulations
MOLECULAR PHYSICS, 113:45-54, JAN 2 2015
abstract, full text, DOI:10.1080/00268976.2014.942405

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping
Exploring signal transduction in heteromultimeric protein based on energy dissipation model
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:134-146, JAN 2 2015
abstract, full text, DOI:10.1080/07391102.2013.855145

Fu, Yi; Chen, Zhiguo; Zhao, Ji
MOLECULAR DYNAMICS SIMULATION TO ELUCIDATE THE THERMOSTABILITY OF B DOMAIN IN CGTASE
THEORETICAL BIOLOGY FORUM, 108:57-73, 2015
abstract, full text

Sotomayor, Marcos
Computational Exploration of Single-Protein Mechanics by Steered Molecular Dynamics
MECHANICS OF HEARING: PROTEIN TO PERCEPTION, 1703 Art. No. 030001, 2015
abstract, full text, DOI:10.1063/1.4939316

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.; Corey, David P.
Towards Force Spectroscopy of Single Tip-Link Bonds
MECHANICS OF HEARING: PROTEIN TO PERCEPTION, 1703 Art. No. 030002, 2015
abstract, full text, DOI:10.1063/1.4939317

Bussi, Giovanni; Branduardi, Davide
Free-Energy Calculations with Metadynamics: Theory and Practice
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:1-49, 2015
full text

Shi, Yue; Ren, Pengyu; Schnieders, Michael; Piquemal, Jean-Philip
Polarizable Force Fields for Biomolecular Modeling
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:51-86, 2015
full text

Towse, Clare-Louise; Daggett, Valerie
Modeling Protein Folding Pathways
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:87-135, 2015
full text

Blackburn, Elizabeth A.; Wear, Martin A.; Landre, Vivian; Narayan, Vikram; Ning, Jia; Erman, Burak; Ball, Kathryn L.; Walkinshaw, Malcolm D.
Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90
BIOSCIENCE REPORTS, 35 Art. No. e00258, 2015
abstract, full text, DOI:10.1042/BSR20150124

Zmejev, D.N.; Klimov, A.V.; Levchenko, N.N.; Okunev, A.S.; Stempkovsky, A.L.
Emulation on Hardware and Software of the Parallel Computing Streaming System "Buran"
Informatsionnye tekhnologii, 21:757-763, 2015
abstract, full text

Abdizadeh, Haleh; Guven, Gokce; Atilgan, Ali Rana; Atilgan, Canan
Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 30:867-873, 2015
abstract, full text, DOI:10.3109/14756366.2014.979345

Hernandez, Monica L.; Dreher, Matthieu; Barrios, Carlos J.; Raffin, Bruno
Asynchronous in Situ Processing with Gromacs: Taking Advantage of GPUs
HIGH PERFORMANCE COMPUTING, CARLA 2015, 565:89-106, 2015
abstract, full text, DOI:10.1007/978-3-319-26928-3_7

Culka, Martin; Milichovsky, Jan; Jerabek, Petr; Stiborova, Marie; Martinek, Vaclav
Ferrous and ferric state of cytochromes P450 in intact Escherichia coli cells: a possible role of cytochrome P450-flavodoxin interactions
NEUROENDOCRINOLOGY LETTERS, 36:29-37, 2015
abstract, full text

Badu, Shyam; Melnik, Roderick; Prabhakar, Sanjay
RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications
PHYSICS OF LIQUID MATTER: MODERN PROBLEMS, 171:337-355, 2015
abstract, full text, DOI:10.1007/978-3-319-20875-6_13

Mak, Michael; Kim, Taeyoon; Zaman, Muhammad H.; Kamm, Roger D.
Multiscale mechanobiology: computational models for integrating molecules to multicellular systems
INTEGRATIVE BIOLOGY, 7:1093-1108, 2015
abstract, full text, DOI:10.1039/c5ib00043b

Truong, Tiffany; Shams, Hengameh; Mofrad, Mohammad R. K.
Mechanisms of integrin and filamin binding and their interplay with talin during early focal adhesion formation
INTEGRATIVE BIOLOGY, 7:1285-1296, 2015
abstract, full text, DOI:10.1039/c5ib00133a

Grigoriev, F. V.; Sulimov, A. V.; Kochikov, I. V.; Kondakova, O. A.; Sulimov, V. B.; Tikhonravov, A. V.
Supercomputer modeling of the ion beam sputtering process: full-atomistic level
OPTICAL SYSTEMS DESIGN 2015: ADVANCES IN OPTICAL THIN FILMS V, 9627 Art. No. 962708, 2015
abstract, full text, DOI:10.1117/12.2190938

Simonovsky, Eyal; Kozlowski, Henryk; Miller, Yifat
Termini capping of metal-poly-His peptide complexes induces the formation of alpha-helix
RSC ADVANCES, 5:104551-104555, 2015
abstract, full text, DOI:10.1039/c5ra15385a

Liubysh, O. O.; Vlasiuk, A. V.; Perepelytsya, S. M.
STRUCTURIZATION OF COUNTERIONS AROUND DNA DOUBLE HELIX: A MOLECULAR DYNAMICS STUDY
UKRAINIAN JOURNAL OF PHYSICS, 60:433-442, 2015
abstract, full text

Mannoor, Madhusoodanan; Kang, Sangmo; Suh, Yong Kweon
Molecular Dynamics Simulation of Aggregates in the Dodecane/span80 System and Their Behaviour in an Electric Field
ADVANCES IN CONDENSED MATTER PHYSICS, Art. No. 739458, 2015
abstract, full text, DOI:10.1155/2015/739458

Velichko, Elena; Zezina, Tatyana; Cheremiskina, Anastasia; Tsybin, Oleg
Nano Communication Device with Embedded Molecular Films: Effect of Electromagnetic Field and Dipole Moment Dynamics
INTERNET OF THINGS, SMART SPACES, AND NEXT GENERATION NETWORKS AND SYSTEMS, 9247:765-771, 2015
abstract, full text, DOI:10.1007/978-3-319-23126-6_71

Mertz, Blake; Feng, Jun; Corcoran, Conor; Neeley, Brandon
Explaining the mobility of retinal in activated rhodopsin and opsin
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 14:1952-1964, 2015
abstract, full text, DOI:10.1039/c5pp00173k

Gao, Lu; Liu, Wenhao; Lee, One-Sun; Dmochowski, Ivan J.; Saven, Jeffery G.
Xe affinities of water-soluble cryptophanes and the role of confined water
CHEMICAL SCIENCE, 6:7238-7248, 2015
abstract, full text, DOI:10.1039/c5sc02401c

Nandy, Bidisha; Saurabh, Suman; Sahoo, Anil Kumar; Dixit, Narendra M.; Maiti, Prabal K.
The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex
NANOSCALE, 7:18628-18641, 2015
abstract, full text, DOI:10.1039/c5nr04632g

Spata, Vincent A.; Matsika, Spiridoula
Photophysical deactivation pathways in adenine oligonucleotides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:31073-31083, 2015
abstract, full text, DOI:10.1039/c5cp04254b

Cordeiro, Jhonatam; Desai, Salil
lPROCESS PARAMETER STUDIES OF MOLECULAR DYNAMICS MODELS TO CONTROL SUBSTRATE WETTABILITY
PROCEEDINGS OF THE ASME 10TH INTERNATIONAL MANUFACTURING SCIENCE AND ENGINEERING CONFERENCE, 2015, VOL 1, Art. No. V001T02A025, 2015
abstract, full text

Fu, Haohao; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much?
RSC ADVANCES, 5:95682-95689, 2015
abstract, full text, DOI:10.1039/c5ra17472d

Majhi, Amit Kumar; Kanchi, Subbarao; Venkataraman, V.; Ayappa, K. G.; Maiti, Prabal K.
Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations
SOFT MATTER, 11:8632-8640, 2015
abstract, full text, DOI:10.1039/c5sm02029h

Cozza, Giorgio; Venerando, Andrea; Sarno, Stefania; Pinna, Lorenzo A.
The Selectivity of CK2 Inhibitor Quinalizarin: A Reevaluation
BIOMED RESEARCH INTERNATIONAL, Art. No. 734127, 2015
abstract, full text, DOI:10.1155/2015/734127

Teo, Ruijie D.; Dong, Sijia S.; Gross, Zeev; Gray, Harry B.; Goddard, William A., I.I.I.
Computational predictions of corroles as a class of Hsp90 inhibitors
MOLECULAR BIOSYSTEMS, 11:2907-2914, 2015
abstract, full text, DOI:10.1039/c5mb00352k

Duan, Mei Lin; Liu, Lin; Du, Juan; Yao, Xiao Jun
pH effects on the structural dynamics of cutinase from Trichoderma reesei: insights from molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 11:3149-3155, 2015
abstract, full text, DOI:10.1039/c5mb00467e

Galano-Frutos, Juan J.; Carmen Moron, M.; Sancho, Javier
The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:28635-28646, 2015
abstract, full text, DOI:10.1039/c5cp04504e

Yagi, Kiyoshi; Li, Pai-Chi; Shirota, Koichiro; Kobayashi, Toshihide; Sugita, Yuji
A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:29113-29123, 2015
abstract, full text, DOI:10.1039/c5cp04131g

Gong, Huichao; Zhang, Sai; Wang, Jiangdian; Gong, Haipeng; Zeng, Jianyang
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data
RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 2015), 9029:108-121, 2015
abstract, full text, DOI:10.1007/978-3-319-16706-0_13

Merzhievskii, L.A.
Deformation Models under Intense Dynamic Loading (Review)
Fizika goreniya i vzryva, 51:144-160, 2015
abstract, full text

Forsythe, Jay G.; Petrov, Anton S.; Walker, Chelsea A.; Allen, Samuel J.; Pellissier, Jarrod S.; Bush, Matthew F.; Hud, Nicholas V.; Fernandez, Facundo M.
Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry
ANALYST, 14:6853-6861, 2015
abstract, full text, DOI:10.1039/c5an00946d

Palermo, Mattia Felice; Muccioli, Luca; Zannoni, Claudio
Molecular organization in freely suspended nano-thick 8CB smectic films. An atomistic simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:26149-26159, 2015
abstract, full text, DOI:10.1039/c5cp04213e

Autzen, Henriette Elisabeth; Siuda, Iwona; Sonntag, Yonathan; Nissen, Poul; Moller, Jesper Vuust; Thogersen, Lea
Regulation of the Ca2+-ATPase by cholesterol: A specific or non-specific effect?
MOLECULAR MEMBRANE BIOLOGY, 32:75-87, 2015
abstract, full text, DOI:10.3109/09687688.2015.1073382

Duan, Guangxin; Kang, Seung-gu; Tian, Xin; Garate, Jose Antonio; Zhao, Lin; Ge, Cuicui; Zhou, Ruhong
Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane
NANOSCALE, 7:15214-15224, 2015
abstract, full text, DOI:10.1039/c5nr01839k

Kubiak-Ossowska, Karina; Cwieka, Monika; Kaczynska, Agnieszka; Jachimska, Barbara; Mulheran, Paul A.
Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:24070-24077, 2015
abstract, full text, DOI:10.1039/c5cp03910j

Kucuk, Sami Emre; Biktagirov, Timur; Sezer, Deniz
Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:24874-24884, 2015
abstract, full text, DOI:10.1039/c5cp04405g

Do, Hainam; Troisi, Alessandro
Developing accurate molecular mechanics force fields for conjugated molecular systems
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25123-25132, 2015
abstract, full text, DOI:10.1039/c5cp04328j

Jiang, Yafei; Tan, Hongwei; Zheng, Jimin; Li, Xichen; Chen, Guangju; Jia, Zongchao
Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25228-25234, 2015
abstract, full text, DOI:10.1039/c5cp03342j

Wang, Xiaoqing; Ritschel, Gerhard; Wuester, Sebastian; Eisfeld, Alexander
Open quantum system parameters for light harvesting complexes from molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25629-25641, 2015
abstract, full text, DOI:10.1039/c5cp03891j

Das, Amit; Sikdar, Samapan; Ghosh, Mahua; Chakrabarti, J.
Conformational thermodynamics of biomolecular complexes: The histogram-based method
STATPHYS-KOLKATA VIII, 638 Art. No. 012013, 2015
abstract, full text, DOI:10.1088/1742-6596/638/1/012013

Yi, Changhong; Wambo, Thierry O.
Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:23074-23080, 2015
abstract, full text, DOI:10.1039/c5cp02312b

Chinnasamy, Sathishkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan
Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study
RSC ADVANCES, 5:70566-70576, 2015
abstract, full text, DOI:10.1039/c5ra14693c

Pablo Mendez, Juan; Carlos Zenteno, Juan; Coronel, Agustin; Antonio Soriano-Ursua, Marvin; Yazmin Valencia-Villalvazo, Elith; Soderlund, Daniela; Mauricio Coral-Vazquez, Ramon; Canto, Patricia
Triallelic digenic mutation in the prokineticin 2 and GNRH receptor genes in two brothers with normosmic congenital hypogonadotropic hypogonadism
ENDOCRINE RESEARCH, 40:166-171, 2015
abstract, full text, DOI:10.3109/07435800.2014.982327

Russell, B. A.; Kubiak-Ossowska, K.; Mulheran, P. A.; Birch, D. J. S.; Chen, Y.
Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:21935-21941, 2015
abstract, full text, DOI:10.1039/c5cp02380g

Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas
Mass partitioning effects in diffusion transport
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:20630-20635, 2015
abstract, full text, DOI:10.1039/c5cp02720a

Bhunia, Shome S.; Singh, Supriya; Saxena, Shruti; Saxena, Anil K.
Pharmacophore Modeling, Docking and Molecular Dynamics Studies on Caspase-3 Activators Binding at beta-Tubulin Site
CURRENT COMPUTER-AIDED DRUG DESIGN, 11:72-83, 2015
abstract, full text

Bellani, S.; Porro, M.; Caddeo, C.; Saba, M. I.; Miranda, P. B.; Mattoni, A.; Lanzani, G.; Antognazza, M. R.
The study of polythiophene/water interfaces by sum-frequency generation spectroscopy and molecular dynamics simulations
JOURNAL OF MATERIALS CHEMISTRY B, 3:6429-6438, 2015
abstract, full text, DOI:10.1039/c5tb00388a

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical Analysis of the Binding of Potential Inhibitors to Protein Kinases MK2 and MK3
MEDICINAL CHEMISTRY, 11:573-579, 2015
abstract, full text

Espinoza-Fonseca, L. Michel; Alamo, Lorenzo; Pinto, Antonio; Thomas, David D.; Padron, Raul
Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition
MOLECULAR BIOSYSTEMS, 11:2167-2179, 2015
abstract, full text, DOI:10.1039/c5mb00162e

Alamo, Lorenzo; Li, Xiaochuan (Edward); Espinoza-Fonseca, L. Michel; Pinto, Antonio; Thomas, David D.; Lehman, William; Padron, Raul
Tarantula myosin free head regulatory light chain phosphorylation stiffens N-terminal extension, releasing it and blocking its docking back
MOLECULAR BIOSYSTEMS, 11:2180-2189, 2015
abstract, full text, DOI:10.1039/c5mb00163c

Wang, Yanli; Yao, Chenjie; Li, Chenchen; Ding, Lin; Liu, Jian; Dong, Peng; Fang, Haiping; Lei, Zhendong; Shi, Guosheng; Wu, Minghong
Excess titanium dioxide nanoparticles on the cell surface induce cytotoxicity by hindering ion exchange and disrupting exocytosis processes
NANOSCALE, 7:13105-13115, 2015
abstract, full text, DOI:10.1039/c5nr03269e

Alberga, Domenico; Perrier, Aurelie; Ciofini, Ilaria; Mangiatordi, Giuseppe Felice; Lattanzi, Gianluca; Adamo, Carlo
Morphological and charge transport properties of amorphous and crystalline P3HT and PBTTT: insights from theory
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:18742-18750, 2015
abstract, full text, DOI:10.1039/c5cp02769a

Camarada, M. B.; Marquez-Miranda, V.; Araya-Duran, I.; Yevenes, A.; Gonzalez-Nilo, F.
PAMAM G4 dendrimers as inhibitors of the iron storage properties of human L-chain ferritin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:19001-19011, 2015
abstract, full text, DOI:10.1039/c5cp02594j

Rhinehardt, Kristen L.; Mohan, Ram V.; Srinivas, Goundla
Computational Modeling of Peptide-Aptamer Binding
COMPUTATIONAL PEPTIDOLOGY, 1268:313-333, 2015
abstract, full text, DOI:10.1007/978-1-4939-2285-7_14

Shen, Jia-Wei; Tang, Ting; Wei, Xiao-Hong; Zheng, Wei; Sun, Tian-Yang; Zhang, Zhisen; Liang, Lijun; Wang, Qi
On the loading mechanism of ssDNA into carbon nanotubes
RSC ADVANCES, 5:56896-56903, 2015
abstract, full text, DOI:10.1039/c5ra01941a

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
What causes tumbling of altro-alpha-CD derivatives? Insight from computer simulations
RSC ADVANCES, 5:57309-57317, 2015
abstract, full text, DOI:10.1039/c5ra05642j

Bouvier, Benjamin; Cezard, Christine; Sonnet, Pascal
Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:18022-18034, 2015
abstract, full text, DOI:10.1039/c5cp02939b

Michino, Mayako; Shi, Lei
Computational Approaches in the Structure-Function Studies of Dopamine Receptors
DOPAMINE RECEPTOR TECHNOLOGIES, 96:31-42, 2015
abstract, full text, DOI:10.1007/978-1-4939-2196-6_3

Pothula, Karunakar Reddy; Kleinekathoefer, Ulrich
Theoretical analysis of ion conductance and gating transitions in the OpdK (OccK1) channel
ANALYST, 140:4855-4864, 2015
abstract, full text, DOI:10.1039/c5an00036j

Espinoza-Fonseca, L. Michel; Kelekar, Ameeta
High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 11:1850-1856, 2015
abstract, full text, DOI:10.1039/c5mb00170f

Tse, A.; Verkhivker, G. M.
Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects
MOLECULAR BIOSYSTEMS, 11:2082-2095, 2015
abstract, full text, DOI:10.1039/c5mb00246j

Lu, Yan; Salsbury, Freddie R., Jr.
Recapturing the Correlated Motions of Protein Using Coarse-Grained Models
PROTEIN AND PEPTIDE LETTERS, 22:654-659, 2015
abstract, full text

Kraszewski, Sebastian; Drabik, Dominik; Langner, Marek; Ramseyer, Christophe; Kembubpha, Sineenat; Yasothornsrikul, Sukkid
A molecular dynamics study of catestatin docked on nicotinic acetylcholine receptors to identify amino acids potentially involved in the binding of chromogranin A fragments
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:17454-17460, 2015
abstract, full text, DOI:10.1039/c4cp02491e

Skelton, A. A.; Agrawal, N.; Fried, J. R.
Quantum mechanical calculations of the interactions between diazacrowns and the sodium cation: an insight into Na+ complexation in diazacrown-based synthetic ion channels
RSC ADVANCES, 5:55033-55047, 2015
abstract, full text, DOI:10.1039/c4ra14000a

Penna, M. J.; Mijajlovic, M.; Tamerler, C.; Biggs, M. J.
Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface
SOFT MATTER, 11:5192-5203, 2015
abstract, full text, DOI:10.1039/c5sm00123d

Guo, Song; Xu, Liang; Xu, Kejing; Zhao, Jianzhang; Kucukoz, Betul; Karatay, Ahmet; Yaglioglu, Halime Gul; Hayvali, Mustafa; Elmali, Ayhan
Bodipy-C-60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer
CHEMICAL SCIENCE, 6:3724-3737, 2015
abstract, full text, DOI:10.1039/c4sc03865g

Perez-Fuentes, Leonor; Drummond, Carlos; Faraudo, Jordi; Bastos-Gonzalez, Delfi
Anions make the difference: insights from the interaction of big cations and anions with poly(N-isopropylacrylamide) chains and microgels
SOFT MATTER, 11:5077-5086, 2015
abstract, full text, DOI:10.1039/c5sm00750j

Sabbadin, Davide; Ciancetta, Antonella; Deganutti, Giuseppe; Cuzzolin, Alberto; Moro, Stefano
Exploring the recognition pathway at the human A(2A) adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations
MEDCHEMCOMM, 6:1081-1085, 2015
abstract, full text, DOI:10.1039/c5md00016e

Badu, Shyam; Melnik, Roderick; Prabhakar, Sanjay
Studying Properties of RNA Nanotubes via Molecular Dynamics
NANOSENSORS, BIOSENSORS, AND INFO-TECH SENSORS AND SYSTEMS 2015, 9434 Art. No. 94340E, 2015
abstract, full text, DOI:10.1117/12.2087444

Maity, Sibaprasad; Zanuy, David; Razvag, Yair; Das, Priyadip; Aleman, Carlos; Reches, Meital
Elucidating the mechanism of interaction between peptides and inorganic surfaces
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:15305-15315, 2015
abstract, full text, DOI:10.1039/c5cp00088b

Pall, Szilard; Abraham, Mark James; Kutzner, Carsten; Hess, Berk; Lindahl, Erik
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
SOLVING SOFTWARE CHALLENGES FOR EXASCALE, 8759:3-27, 2015
abstract, full text, DOI:10.1007/978-3-319-15976-8_1

Dixit, Purushottam D.
Detecting temperature fluctuations at equilibrium
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:13000-13005, 2015
abstract, full text, DOI:10.1039/c5cp01423a

Bansode, Sneha B.; Batkulwar, Kedar B.; Warkad, Shrikant D.; Jana, Asis K.; Sengupta, Neelanjana; Kulkarni, Mahesh J.
Tolbutamide induces conformational change and promotes albumin glycation
RSC ADVANCES, 5:40070-40075, 2015
abstract, full text, DOI:10.1039/c5ra03839a

Menon, Sneha; Sengupta, Neelanjana
Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrPC: insights from atomistic simulations
MOLECULAR BIOSYSTEMS, 11:1443-1453, 2015
abstract, full text, DOI:10.1039/c4mb00689e

Kucukkal, Tugba G.; Alexov, Emil
Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 746157, 2015
abstract, full text, DOI:10.1155/2015/746157

Verma, Saroj; Prabhakar, Yenamandra S.
Target Based Drug Design - A Reality in Virtual Sphere
CURRENT MEDICINAL CHEMISTRY, 22:1603-1630, 2015
abstract, full text

Ding, Yun-Qiao; Chen, Cheng-Lung; Li, Tian-Duo; Cheng, Jin-Yong; Zhang, Hua-Yong
Effects of Chromium-olation Length on Crosslinking Effects Investigated by Molecular Dynamics Simulation
SOFT MATERIALS, 13:24-31, 2015
abstract, full text, DOI:10.1080/1539445X.2014.998342

Bochicchio, Brigida; Pepe, Antonietta; Crudele, Maria; Belloy, Nicolas; Baud, Stephanie; Dauchez, Manuel
Tuning self-assembly in elastin-derived peptides
Soft Matter, 11:3385-3395, 2015
abstract, full text, DOI:10.1039/c5sm00072f

Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M
DRUG DESIGN DEVELOPMENT AND THERAPY, 9:1897-1912, 2015
abstract, full text, DOI:10.2147/DDDT.S77020

Kelly, Catherine M.; Muzard, Julien; Brooks, Bernard R.; Lee, Gil U.; Buchete, Nicolae-Viorel
Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:9634-9643, 2015
abstract, full text, DOI:10.1039/c4cp05307a

Vitiello, Giuseppe; Falanga, Annarita; Alcides Petruk, Ariel; Merlino, Antonello; Fragneto, Giovanna; Paduano, Luigi; Galdiero, Stefania; D'Errico, Gerardino
Fusion of raft-like lipid bilayers operated by a membranotropic domain of the HSV-type I glycoprotein gH occurs through a cholesterol-dependent mechanism
SOFT MATTER, 11:3003-3016, 2015
abstract, full text, DOI:10.1039/c4sm02769h

Mintzer, Mary Rose; Troxler, Thomas; Gai, Feng
p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:7881-7887, 2015
abstract, full text, DOI:10.1039/c5cp00050e

Basu, Ipsita; Mukhopadhyay, Chaitali
Effect of Temperature on the Phase Behaviour of Fully Saturated DAPC Lipid Bilayer: A Comparative Molecular Dynamics Simulation Study
BIOCHEMICAL ROLES OF EUKARYOTIC CELL SURFACE MACROMOLECULES, 842:263-277, 2015
full text

Abroshan, Hadi; Kim, Hyung J.
On the structural stability of ionic liquid-IRMOF composites: a computational study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6248-6254, 2015
abstract, full text, DOI:10.1039/c4cp02428a

Kucuk, Sami Emre; Neugebauer, Petr; Prisner, Thomas F.; Sezer, Deniz
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6618-6628, 2015
abstract, full text, DOI:10.1039/c4cp05832a

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Removal of heavy metals from water through armchair carbon and boron nitride nanotubes: a computer simulation study
RSC ADVANCES, 5:25097-25104, 2015
abstract, full text, DOI:10.1039/c4ra17048b

Insaidoo, Francis K.; Rauscher, Michael A.; Smithline, Shepard J.; Kaarsholm, Niels C.; Feuston, Bradley P.; Ortigosa, Allison D.; Linden, Thomas O.; Roush, David J.
Targeted Purification Development Enabled by Computational Biophysical Modeling
BIOTECHNOLOGY PROGRESS, 31:154-164, JAN-FEB 2015
abstract, full text, DOI:10.1002/btpr.2023

Duarte Junior, Francisco Ferreira; de Lima Neto, Quirino Alves; Rando, Fabiana dos Santos; Bassalobre de Freitas, Douglas Vinicius; Pattaro Junior, Jose Renato; Polizelli, Lorena Gomes; Ferreira Munhoz, Roxelle Ethienne; Vicente Seixas, Flavio Augusto; Fernandez, Maria Aparecida
Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome
MOLECULAR BIOSYSTEMS, 11:801-808, 2015
abstract, full text, DOI:10.1039/c4mb00595c

Li, Hui; Chen, Qi; Schoenbeck, Christian; Han, Bao-Hang
Sugar-functionalized water-soluble pillar[5] arene and its host-guest interaction with fullerene
RSC ADVANCES, 5:19041-19047, 2015
abstract, full text, DOI:10.1039/c4ra07523d

Alishahi, Marzieh; Kamali, Reza; Abouali, Omid
Molecular Dynamics Study of Electric Double Layer in Nanochannel
RUSSIAN JOURNAL OF ELECTROCHEMISTRY, 51:49-55, JAN 2015
abstract, full text, DOI:10.1134/S1023193515010024

Gonnet, Pedro
EFFICIENT AND SCALABLE ALGORITHMS FOR SMOOTHED PARTICLE HYDRODYNAMICS ON HYBRID SHARED/DISTRIBUTED-MEMORY ARCHITECTURES
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 37:C95-C121, 2015
abstract, full text, DOI:10.1137/140964266

Kumar, Amit; Sechi, Leonardo A.; Caboni, Pierluigi; Marrosu, Maria Giovanna; Atzori, Luigi; Pieroni, Enrico
Dynamical insights into the differential characteristics of Mycobacterium avium subsp paratuberculosis peptide binding to HLA-DRB1 proteins associated with multiple sclerosis
NEW JOURNAL OF CHEMISTRY, 39:1355-1366, 2015
abstract, full text, DOI:10.1039/c4nj01903b

Grimes, Leanne; Young, Mark T.
Purinergic P2X Receptors: Structural and Functional Features Depicted by X-Ray and Molecular Modelling Studies
CURRENT MEDICINAL CHEMISTRY, 22:783-798, 2015
abstract, full text

Dean, Kevin M.; Lubbeck, Jennifer L.; Davis, Lloyd M.; Regmi, Chola K.; Chapagain, Prem P.; Gerstman, Bernard S.; Jimenez, Ralph; Palmer, Amy E.
Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching
INTEGRATIVE BIOLOGY, 7:263-273, 2015
abstract, full text, DOI:10.1039/c4ib00251b

Wessel, Jennifer; Chu, Audrey Y.; Willems, Sara M.; Wang, Shuai; Yaghootkar, Hanieh; Brody, Jennifer A.; Dauriz, Marco; Hivert, Marie-France; Raghavan, Sridharan; Lipovich, Leonard; Hidalgo, Bertha; Fox, Keolu; Huffman, Jennifer E.; An, Ping; Lu, Yingchang; Rasmussen-Torvik, Laura J.; Grarup, Niels; Ehm, Margaret G.; Li, Li; Baldridge, Abigail S.; Stancakova, Alena; Abrol, Ravinder; Besse, Celine; Boland, Anne; Bork-Jensen, Jette; Fornage, Myriam; Freitag, Daniel F.; Garcia, Melissa E.; Guo, Xiuqing; Hara, Kazuo; Isaacs, Aaron; Jakobsdottir, Johanna; Lange, Leslie A.; Layton, Jill C.; Li, Man; Zhao, Jing Hua; Meidtner, Karina; Morrison, Alanna C.; Nalls, Mike A.; Peters, Marjolein J.; Sabater-Lleal, Maria; Schurmann, Claudia; Silveira, Angela; Smith, Albert V.; Southam, Lorraine; Stoiber, Marcus H.; Strawbridge, Rona J.; Taylor, Kent D.; Varga, Tibor V.; Allin, Kristine H.; Amin, Najaf; Aponte, Jennifer L.; Aung, Tin; Barbieri, Caterina; Bihlmeyer, Nathan A.; Boehnke, Michael; Bombieri, Cristina; Bowden, Donald W.; Burns, Sean M.; Chen, Yuning; Chen, Yii-Deri; Cheng, Ching-Yu; Correa, Adolfo; Czajkowski, Jacek; Dehghan, Abbas; Ehret, Georg B.; Eiriksdottir, Gudny; Escher, Stefan A.; Farmaki, Aliki-Eleni; Franberg, Mattias; Gambaro, Giovanni; Giulianini, Franco; Goddard, William A., I.I.I.; Goel, Anuj; Gottesman, Omri; Grove, Megan L.; Gustafsson, Stefan; Hai, Yang; Hallmans, Goeran; Heo, Jiyoung; Hoffmann, Per; Ikram, Mohammad K.; Jensen, Richard A.; Jorgensen, Marit E.; Jorgensen, Torben; Karaleftheri, Maria; Khor, Chiea C.; Kirkpatrick, Andrea; Kraja, Aldi T.; Kuusisto, Johanna; Lange, Ethan M.; Lee, I. T.; Lee, Wen-Jane; Leong, Aaron; Liao, Jiemin; Liu, Chunyu; Liu, Yongmei; Lindgren, Cecilia M.; Linneberg, Allan; Malerba, Giovanni; Mamakou, Vasiliki; Marouli, Eirini; Maruthur, Nisa M.; Matchan, Angela; McKean-Cowdin, Roberta; McLeod, Olga; Metcalf, Ginger A.; Mohlke, Karen L.; Muzny, Donna M.; Ntalla, Ioanna; Palmer, Nicholette D.; Pasko, Dorota; Peter, Andreas; Rayner, Nigel W.; Renstroem, Frida; Rice, Ken; Sala, Cinzia F.; Sennblad, Bengt; Serafetinidis, Ioannis; Smith, Jennifer A.; Soranzo, Nicole; Speliotes, Elizabeth K.; Stahl, Eli A.; Stirrups, Kathleen; Tentolouris, Nikos; Thanopoulou, Anastasia; Torres, Mina; Traglia, Michela; Tsafantakis, Emmanouil; Javad, Sundas; Yanek, Lisa R.; Zengini, Eleni; Becker, Diane M.; Bis, Joshua C.; Brown, James B.; Cupples, L. Adrienne; Hansen, Torben; Ingelsson, Erik; Karter, Andrew J.; Lorenzo, Carlos; Mathias, Rasika A.; Norris, Jill M.; Peloso, Gina M.; Sheu, Wayne H. -H.; Toniolo, Daniela; Vaidya, Dhananjay; Varma, Rohit; Wagenknecht, Lynne E.; Boeing, Heiner; Bottinger, Erwin P.; Dedoussis, George; Deloukas, Panos; Ferrannini, Ele; Franco, Oscar H.; Franks, Paul W.; Gibbs, Richard A.; Gudnason, Vilmundur; Hamsten, Anders; Harris, Tamara B.; Hattersley, Andrew T.; Hayward, Caroline; Hofman, Albert; Jansson, Jan-Hakan; Langenberg, Claudia; Launer, Lenore J.; Levy, Daniel; Oostra, Ben A.; O'Donnell, Christopher J.; O'Rahilly, Stephen; Padmanabhan, Sandosh; Pankow, James S.; Polasek, Ozren; Province, Michael A.; Rich, Stephen S.; Ridker, Paul M.; Rudan, Igor; Schulze, Matthias B.; Smith, Blair H.; Uitterlinden, Andre G.; Walker, Mark; Watkins, Hugh; Wong, Tien Y.; Zeggini, Eleftheria; Laakso, Markku; Borecki, Ingrid B.; Chasman, Daniel I.; Pedersen, Oluf; Psaty, Bruce M.; Tai, E. Shyong; van Duijn, Cornelia M.; Wareham, Nicholas J.; Waterworth, Dawn M.; Boerwinkle, Eric; Kao, W. H. Linda; Florez, Jose C.; Loos, Ruth J. F.; Wilson, James G.; Frayling, Timothy M.; Siscovick, David S.; Dupuis, Josee; Rotter, Jerome I.; Meigs, James B.; Scott, Robert A.; Goodarzi, Mark O.; Sharp, Stephen J.; Forouhi, Nita G.; Kerrison, Nicola D.; Lucarelli, Debora M. E.; Sims, Matt; Barroso, Ines; McCarthy, Mark I.; Arriola, Larraitz; Balkau, Beverley; Barricarte, Aurelio; Gonzalez, Carlos; Grioni, Sara; Kaaks, Rudolf; Key, Timothy J.; Navarro, Carmen; Nilsson, Peter M.; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quiros, J. Ramon; Rolandsson, Olov; Sacerdote, Carlotta; Sanchez, Maria-Jose; Slimani, Nadia; Tjonneland, Anne; Tumino, Rosario; van der A, Daphne L.; van der Schouw, Yvonne T.; Riboli, Elio
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
NATURE COMMUNICATIONS, 6 Art. No. 5897, JAN 2015
abstract, full text, DOI:10.1038/ncomms6897

Luan, Binquan; Tien Huynh; Zhao, Lin; Zhou, Ruhong
Potential Toxicity of Graphene to Cell Functions via Disrupting Protein-Protein Interactions
ACS NANO, 9:663-669, JAN 2015
abstract, full text, DOI:10.1021/nn506011j

Cheng, Bo; Wu, Shaogui; Liu, Shixin; Rodriguez-Aliaga, Piere; Yu, Jin; Cui, Shuxun
Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases
NANOSCALE, 7:2970-2977, 2015
abstract, full text, DOI:10.1039/c4nr07140a

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M.; Singh, Satish K.; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R.; Sek, David; Allen, Martin J.
Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobic versus electrostatic inter-molecular interactions
MABS, 7:212-230, JAN-FEB 2015
abstract, full text, DOI:10.4161/19420862.2014.985504

Danishuddin, Mohd; Khan, Asad U.
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
METHODS, 71:135-145, JAN 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.019

Rakos, Balazs
Modeling of dipole-dipole-coupled, electric field-driven, protein-based computing architectures
INTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, 43:60-72, JAN 2015
abstract, full text, DOI:10.1002/cta.1924

Ferrarotti, Marco Jacopo; Bottaro, Sandro; Perez-Villa, Andrea; Bussi, Giovanni
Accurate Multiple Time Step in Biased Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:139-146, JAN 2015
abstract, full text, DOI:10.1021/ct5007086

Cordova-Mateo, Esther; Bertran, Oscar; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Internal organization of macromonomers and dendronized polymers based on thiophene dendrons
SOFT MATTER, 11:1116-1126, 2015
abstract, full text, DOI:10.1039/c4sm02523g

Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.
In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:162-172, JAN 2015
abstract, full text, DOI:10.1107/S1399004714026777

Schulz, Robert; Vargiu, Attilio V.; Ruggerone, Paolo; Kleinekathoefer, Ulrich
Computational Study of Correlated Domain Motions in the AcrB Efflux Transporter
BIOMED RESEARCH INTERNATIONAL, Art. No. 487298, 2015
abstract, full text, DOI:10.1155/2015/487298

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea
The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning
Nature Communications, 6 Art. No. 6155, JAN 2015
abstract, full text, DOI:10.1038/ncomms7155

Lu Shi-Jing; Zhou Xin
Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function
COMMUNICATIONS IN THEORETICAL PHYSICS, 63:10-18, JAN 2015
abstract, full text

Rocca, Roberta; Moraca, Federica; Costa, Giosue; Alcaro, Stefano; Distinto, Simona; Maccioni, Elias; Ortuso, Francesco; Artese, Anna; Parrotta, Lucia
Structure-Based Virtual Screening of Novel Natural Alkaloid Derivatives as Potential Binders of h-telo and c-myc DNA G-Quadruplex Conformations
MOLECULES, 20:206-223, JAN 2015
abstract, full text, DOI:10.3390/molecules20010206

Wineman-Fisher, Vered; Atsmon-Raz, Yoav; Miller, Yifat
Orientations of Residues along the beta-Arch of Self-Assembled Amylin Fibril-Like Structures Lead to Polymorphism
BIOMACROMOLECULES, 16:156-165, JAN 2015
abstract, full text, DOI:10.1021/bm501326y

Rovira, Xavier; Malhaire, Fanny; Scholler, Pauline; Rodrigo, Jordi; Gonzalez-Bulnes, Patricia; Llebaria, Amadeu; Pin, Jean-Philippe; Giraldo, Jesus; Goudet, Cyril
Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors
FASEB JOURNAL, 29:116-130, JAN 2015
abstract, full text, DOI:10.1096/fj.14-257287

Gerbier, Romain; Leroux, Vincent; Couvineau, Pierre; Alvear-Perez, Rodrigo; Maigret, Bernard; Llorens-Cortes, Catherine; Iturrioz, Xavier
New structural insights into the apelin receptor: identification of key residues for apelin binding
FASEB JOURNAL, 29:314-322, JAN 2015
abstract, full text, DOI:10.1096/fj.14-256339

Katti, Dinesh R.; Sharma, Anurag; Ambre, Avinash H.; Katti, Kalpana S.
Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 46:207-217, JAN 1 2015
abstract, full text, DOI:10.1016/j.msec.2014.07.057

Fraiberg, Milana; Afanzar, Oshri; Cassidy, C. Keith; Gabashvili, Alexandra; Schulten, Klaus; Levin, Yishai; Eisenbach, Michael
CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli
MOLECULAR MICROBIOLOGY, 95:231-244, JAN 2015
abstract, full text, TCBG publications, DOI:10.1111/mmi.12858

Wu, Wenyun; Yue, Jingying; Li, Dongqi; Lin, Xiaoyang; Zhu, Fangqiang; Yin, Xue; Zhu, Jun; Dai, Xingcan; Liu, Peng; Wei, Yang; Wang, Jiaping; Yang, Haitao; Zhang, Lina; Li, Qunqing; Fan, Shoushan; Jiang, Kaili
Interface dipole enhancement effect and enhanced Rayleigh scattering
NANO RESEARCH, 8:303-319, JAN 2015
abstract, full text, DOI:10.1007/s12274-014-0687-5

Xu, Lei; Li, Youyong; Li, Dan; Xu, Peng; Tian, Sheng; Sun, Huiyong; Liu, Hui; Hou, Tingjun
Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3370-3382, 2015
abstract, full text, DOI:10.1039/c4cp05095a

Villarreal, Oscar D.; Chen, Liao Y.; Whetten, Robert L.; Yacaman, Miguel J.
Ligand-modulated interactions between charged monolayer-protected Au-144(SR)(60) gold nanoparticles in physiological saline
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3680-3688, 2015
abstract, full text, DOI:10.1039/c4cp05137h

Gupta, Kushol; Selinsky, Barry S.
Bacterial and algal orthologs of prostaglandin H-2 synthase: novel insights into the evolution of an integral membrane protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:83-94, JAN 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.09.011

Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepulveda, Romina V.; Aguayo, Daniel; Gonzalez-Nilo, Fernando; Gonzalez, Carlos; Latorre, Ramon
Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel
JOURNAL OF GENERAL PHYSIOLOGY, 145:61-74, JAN 2015
abstract, full text, DOI:10.1085/jgp.201411194

Rodriguez-Rodriguez, C.; Telpoukhovskaia, M. A.; Ali-Torres, J.; Rodriguez-Santiago, L.; Manso, Y.; Bailey, G. A.; Hidalgo, J.; Sodupe, M.; Orvig, C.
Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models
METALLOMICS, 7:78-87, 2015
abstract, full text, DOI:10.1039/c4mt00167b

Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio
Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field
JOURNAL OF NON-CRYSTALLINE SOLIDS, 407:494-501, JAN 1 2015
abstract, full text, DOI:10.1016/j.jnoncrysol.2014.07.005

Ruiz, Luis; Wu, Yuanqiao; Keten, Sinan
Tailoring the water structure and transport in nanotubes with tunable interiors
NANOSCALE, 7:121-132, 2015
abstract, full text, DOI:10.1039/c4nr05407e

Leman, Julia Koehler; Ulmschneider, Martin B.; Gray, Jeffrey J.
Computational modeling of membrane proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1-24, JAN 2015
abstract, full text, DOI:10.1002/prot.24703

Ng, Yao Zong; Kannan, Srinivasaraghavan; Lane, David P.; Fuentes, Gloria; Verma, Chandra S.
mAb806 binding to epidermal growth factor receptor: a computational study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:153-168, JAN 2015
abstract, full text, DOI:10.1002/prot.24714

Sule, Nitesh V.; Ugrinov, Angel; Mallik, Sanku; Srivastava, D. K.
Bridging of a substrate between cyclodextrin and an enzyme's active site pocket triggers a unique mode of inhibition
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:141-149, JAN 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.10.016

Choi, Bumjoon; Yoon, Gwonchan; Lee, Sang Woo; Eom, Kilho
Mechanical deformation mechanisms and properties of amyloid fibrils
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1379-1389, 2015
abstract, full text, DOI:10.1039/c4cp03804e

Nierzwicki, L.; Wieczor, M.; Censi, V.; Baginski, M.; Calucci, L.; Samaritani, S.; Czub, J.; Forte, C.
Interaction of cisplatin and two potential antitumoral platinum(II) complexes with a model lipid membrane: a combined NMR and MD study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1458-1468, 2015
abstract, full text, DOI:10.1039/c4cp04360j

Agosta, Lorenzo; Zollo, Giuseppe; Arcangeli, Caterina; Buonocore, Francesco; Gala, Fabrizio; Celino, Massimo
Water driven adsorption of amino acids on the (101) anatase TiO2 surface: an ab initio study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1556-1561, 2015
abstract, full text, DOI:10.1039/c4cp03056g

Culleton, Bridget A.; Lall, Patrick; Kinsella, Gemma K.; Doyle, Sean; McCaffrey, John; Fitzpatrick, David A.; Burnell, Ann M.
A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus
CELL STRESS & CHAPERONES, 20:121-137, JAN 2015
abstract, full text, DOI:10.1007/s12192-014-0531-6

Wang, Feng; Wan, Hua; Hu, Jian-ping; Chang, Shan
Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C
MOLECULAR BIOSYSTEMS, 11:223-231, JAN 2015
abstract, full text, DOI:10.1039/c4mb00383g

Carmona, Christopher; Langan, Paul; Smith, Jeremy C.; Petridis, Loukas
Why genetic modification of lignin leads to low-recalcitrance biomass
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:358-364, 2015
abstract, full text, DOI:10.1039/c4cp05004e

Sun, Yeping; Liu, Qian
Differential structural dynamics and antigenicity of two similar influenza H5N1 virus HA-specific HLA-A*0201-restricted CLT epitopes
RSC ADVANCES, 5:2318-2327, 2015
abstract, full text, DOI:10.1039/c4ra08874c

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; Ho, Chian-Sing; Khadka, Nawal; Katsaras, John
Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations
SOFT MATTER, 11:130-138, 2015
abstract, full text, DOI:10.1039/c4sm02227k

Jana, Asis K.; Sengupta, Neelanjana
A beta self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response
SOFT MATTER, 11:269-279, 2015
abstract, full text, DOI:10.1039/c4sm01845a

Palese, Luigi Leonardo
Random Matrix Theory in molecular dynamics analysis
BIOPHYSICAL CHEMISTRY, 196:1-9, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.007

Kelly, Catherine M.; Northey, Thomas; Ryan, Kate; Brooks, Bernard R.; Kholkin, Andrei L.; Rodriguez, Brian J.; Buchete, Nicolae-Viorel
Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field
BIOPHYSICAL CHEMISTRY, 196:16-24, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.009

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael
On the hydration of subnanometric antifouling organosilane adlayers: A molecular dynamics simulation
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 437:197-204, JAN 1 2015
abstract, full text, DOI:10.1016/j.jcis.2014.09.025

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical Modelling of Potential Chk1 Inhibitors
LETTERS IN DRUG DESIGN & DISCOVERY, 12:60-65, 2015
abstract, full text

Bal, Naresh C.; Jena, Nivedita; Chakravarty, Harapriya; Kumar, Amit; Chi, Mei; Balaraju, Tuniki; Rawale, Sharad V.; Rawale, Jayashree S.; Sharon, Ashoke; Periasamy, Muthu
The C-Terminal Calcium-Sensitive Disordered Motifs Regulate Isoform-Specific Polymerization Characteristics of Calsequestrin
BIOPOLYMERS, 103:15-22, JAN 2015
abstract, full text, DOI:10.1002/bip.22534

Lindahl, Erik
Molecular Dynamics Simulations
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:3-26, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_1

Biggin, Philip C.; Bond, Peter J.
Molecular Dynamics Simulations of Membrane Proteins
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:91-108, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_5

Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.
Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:253-287, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_12

Sorensen, Jesper; Demir, Oezlem; Swift, Robert V.; Feher, Victoria A.; Amaro, Rommie E.
Molecular Docking to Flexible Targets
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:445-469, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_20

Fossepre, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P.
On the Modularity of the Intrinsic Flexibility of the mu Opioid Receptor: A Computational Study
PLOS ONE, 9 Art. No. e115856, DEC 30 2014
abstract, full text, DOI:10.1371/journal.pone.0115856

Fichna, Jakub Piotr; Karolczak, Justyna; Potulska-Chromik, Anna; Miszta, Przemyslaw; Berdynski, Mariusz; Sikorska, Agata; Filipek, Slawomir; Redowicz, Maria Jolanta; Kaminska, Anna; Zekanowski, Cezary
Two Desmin Gene Mutations Associated with Myofibrillar Myopathies in Polish Families
PLOS ONE, 9 Art. No. UNSP e115470, DEC 26 2014
abstract, full text, DOI:10.1371/journal.pone.0115470

Spata, Vincent A.; Matsika, Spiridoula
Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 118:12021-12030, DEC 25 2014
abstract, full text, DOI:10.1021/jp507520c

Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M.; Li, Bo; McCammon, J. Andrew
Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14827-14832, DEC 25 2014
abstract, full text, DOI:10.1021/jp511702w

Raczynski, Przemyslaw; Gorny, Krzysztof; Samios, Jannis; Gburski, Zygmunt
Interaction Between Silicon-Carbide Nanotube and Cholesterol Domain. A Molecular Dynamics Simulation Study.
JOURNAL OF PHYSICAL CHEMISTRY C, 118:30115-30119, DEC 25 2014
abstract, full text, DOI:10.1021/jp505532f

Basu, Ipsita; Multhopadhyay, Chaitali
Insights into Binding of Cholera Toxin to GM1 Containing Membrane
LANGMUIR, 30:15244-15252, DEC 23 2014
abstract, full text, DOI:10.1021/la5036618

Karatasos, Kostas
Graphene/Hyperbranched Polymer Nanocomposites: Insight from Molecular Dynamics Simulations
MACROMOLECULES, 47:8833-8845, DEC 23 2014
abstract, full text, DOI:10.1021/ma502123a

Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji
Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:4343-4348, DEC 18 2014
abstract, full text, DOI:10.1021/jz502299m

Pujato, Mario; Kieken, Fabien; Skiles, Amanda A.; Tapinos, Nikos; Fiser, Andras
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes
NUCLEIC ACIDS RESEARCH, 42:13500-13512, DEC 16 2014
abstract, full text, DOI:10.1093/nar/gku1228

Marinelli, Fabrizio; Almagor, Lior; Hiller, Reuben; Giladi, Moshe; Khananshvili, Daniel; Faraldo-Gomez, Jose D.
Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E5354-E5362, DEC 16 2014
abstract, full text, DOI:10.1073/pnas.1415751111

Fuerst, Oliver; Nichols, Colin G.; Lamoureux, Guillaume; D'Avanzo, Nazzareno
Identification of a Cholesterol-Binding Pocket in Inward Rectifier K+ (Kir) Channels
BIOPHYSICAL JOURNAL, 107:2786-2796, DEC 16 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.066

Lopez-Emparan, Ada; Quezada-Martinez, Daniela; Zuniga-Bustos, Matias; Cifuentes, Victor; Iniguez-Luy, Federico; Laura Federico, Maria
Functional Analysis of the Brassica napus L. Phytoene Synthase (PSY) Gene Family
PLOS ONE, 9 Art. No. e114878, DEC 15 2014
abstract, full text, DOI:10.1371/journal.pone.0114878

Sinko, Robert; Keten, Sinan
Effect of moisture on the traction-separation behavior of cellulose nanocrystal interfaces
APPLIED PHYSICS LETTERS, 105 Art. No. 243702, DEC 15 2014
abstract, full text, DOI:10.1063/1.4904708

Naddaf, Lamis; Sayyed-Ahmad, Abdallah
Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 564:12-19, DEC 15 2014
abstract, full text, DOI:10.1016/j.abb.2014.08.016

Huang, Zhehao; Yao, Yuan; Han, Lu; Che, Shunai
Control of Chiral Nanostructures by Self-Assembly of Designed Amphiphilic Peptides and Silica Biomineralization
CHEMISTRY-A EUROPEAN JOURNAL, 20:17068-17076, DEC 15 2014
abstract, full text, DOI:10.1002/chem.201403498

Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Ni Qin; Anh, Vo
Fractal and complex network analyses of protein molecular dynamics
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 416:21-32, DEC 15 2014
abstract, full text, DOI:10.1016/j.physa.2014.08.047

Duboue-Dijon, Elise; Laage, Damien
Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D529, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902822

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery
Multibody correlations in the hydrophobic solvation of glycine peptides
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D525, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901886

Martinez, Anna Victoria; Malolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.
Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides A beta(16-22) and Sup35(7-13) in AOT reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D530, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902550

Sharp, Kim A.
The remarkable hydration of the antifreeze protein Maxi: A computational study
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D510, DEC 14 2014
abstract, full text, DOI:10.1063/1.4896693

Sinha, Sudipta Kumar; Jana, Madhurima; Chakraborty, Kausik; Bandyopadhyay, Sanjoy
In silico studies of the properties of water hydrating a small protein
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D502, DEC 14 2014
abstract, full text, DOI:10.1063/1.4895533

Sode, Olaseni; Voth, Gregory A.
Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D527, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902236

Vaitheeswaran, S.; Thirumalai, D.
Entropy and enthalpy of interaction between amino acid side chains in nanopores
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D523, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901204

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.
Ionic strength independence of charge distributions in solvation of biomolecules
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D503, DEC 14 2014
abstract, full text, DOI:10.1063/1.4895522

Wilson, Michael A.; Thuy Hien Nguyen; Pohorille, Andrew
Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D519, DEC 14 2014
abstract, full text, DOI:10.1063/1.4900879

Morishita, Masayo; Mevius, Damiaan; di Luccio, Eric
In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L
BMC STRUCTURAL BIOLOGY, 14 Art. No. 25, DEC 12 2014
abstract, full text, DOI:10.1186/s12900-014-0025-x

Migliori, Amy D.; Smith, Douglas E.; Arya, Gaurav
Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor
JOURNAL OF MOLECULAR BIOLOGY, 426:4002-4017, DEC 12 2014
abstract, full text, DOI:10.1016/j.jmb.2014.09.023

Nategholeslam, Mostafa; Gray, C. G.; Tomberli, Bruno
Implementation of the Forward-Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14203-14214, DEC 11 2014
abstract, full text, DOI:10.1021/jp504942t

Weng, Lindong; Elliott, Gloria D.
Polymerization Effect of Electrolytes on Hydrogen-Bonding Cryoprotectants: Ion-Dipole Interactions between Metal Ions and Glycerol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14546-14554, DEC 11 2014
abstract, full text, DOI:10.1021/jp5105533

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.
Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
PLOS ONE, 9 Art. No. e113119, DEC 11 2014
abstract, full text, DOI:10.1371/journal.pone.0113119

Dwyer, Patrick J.; Vander Valk, Rory J.; Caltaldo, Vito; Dennanicz, David; Keite, Stephen P.
All-Atom CHARMM Force Field and Bulk Properties of Perfluorozinc Phthalocyanines
JOURNAL OF PHYSICAL CHEMISTRY A, 118:11583-11590, DEC 11 2014
abstract, full text, DOI:10.1021/jp506601e

Segrest, Jere P.; Jones, Martin K.; Shao, Baohai; Heinecke, Jay W.
An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations
BIOCHEMISTRY, 53:7625-7640, DEC 9 2014
abstract, full text, DOI:10.1021/bi501111j

Souza, Caio S.; Amaral, Cristiano; Treptow, Werner
Electric fingerprint of voltage sensor domains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:17510-17515, DEC 9 2014
abstract, full text, DOI:10.1073/pnas.1413971111

Jayaram, B.; Dhingra, Priyanka; Mishra, Avinash; Kaushik, Rahul; Mukherjee, Goutam; Singh, Ankita; Shekhar, Shashank
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
BMC BIOINFORMATICS, 15 Art. No. S7, DEC 8 2014
abstract, full text, DOI:10.1186/1471-2105-15-S16-S7

Semino, Rocio; Zaldivar, Gervasio; Calvo, Ernesto J.; Laria, Daniel
Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 214509, DEC 7 2014
abstract, full text, DOI:10.1063/1.4902837

Starzyk, Joanna; Gruszecki, Marcin; Tutaj, Krzysztof; Luchowski, Rafal; Szlazak, Radoslaw; Wasko, Piotr; Grudzinski, Wojciech; Czub, Jacek; Gruszecki, Wieslaw I.
Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13821-13832, DEC 4 2014
abstract, full text, DOI:10.1021/jp510245n

Shi, Wei; Hong, Lei; Damodaran, Krishnan; Nulwala, Hunaid B.; Luebke, David R.
Molecular Simulation and Experimental Study of CO2 Absorption in Ionic Liquid Reverse Micelle
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13870-13881, DEC 4 2014
abstract, full text, DOI:10.1021/jp509282h

Sahillioglu, Ali Can; Sumbul, Fidan; Ozoren, Nesrin; Haliloglu, Turkan
Structural and Dynamics Aspects of ASC Speck Assembly
STRUCTURE, 22:1722-1734, DEC 2 2014
abstract, full text, DOI:10.1016/j.str.2014.09.011

Liu, Ming S.; Wang, Die; Morimoto, Hiroyuki; Yim, Howard C. H.; Irving, Aaron T.; Williams, Bryan R. G.; Sadler, Anthony J.
Molecular dynamics reveal a novel kinase-substrate interface that regulates protein translation
JOURNAL OF MOLECULAR CELL BIOLOGY, 6:473-485, DEC 2014
abstract, full text, DOI:10.1093/jmcb/mju044

Dorn, Marcio; Barbachan e Silva, Mariel; Buriol, Luciana S.; Lamb, Luis C.
Three-dimensional protein structure prediction: Methods and computational strategies
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 53:251-276, DEC 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.10.001

Peters, Gunther H.; Werge, Mikkel; Elf-Lind, Maria Northved; Madsen, Jesper J.; Velardez, Gustavo F.; Westh, Peter
Interaction of neurotransmitters with a phospholipid bilayer: A molecular dynamics study
CHEMISTRY AND PHYSICS OF LIPIDS, 184:7-17, DEC 2014
abstract, full text, DOI:10.1016/j.chemphyslip.2014.08.003

Schoeler, Constantin; Malinowska, Klara H.; Bernardi, Rafael C.; Milles, Lukas F.; Jobst, Markus A.; Durner, Ellis; Ott, Wolfgang; Fried, Daniel B.; Bayer, Edward A.; Schulten, Klaus; Gaub, Hermann E.; Nash, Michael A.
Ultrastable cellulosome-adhesion complex tightens under load
NATURE COMMUNICATIONS, 5 Art. No. 5635, DEC 2014
abstract, full text, TCBG publications, DOI:10.1038/ncomms6635

Kalimeri, Maria; Girard, Eric; Madern, Dominique; Sterpone, Fabio
Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase
PLOS ONE, 9 Art. No. e113895, DEC 1 2014
abstract, full text, DOI:10.1371/journal.pone.0113895

Li, Tianxia; Yang, Dejun; Zhong, Shijun; Thomas, Joseph M.; Xue, Fengtian; Liu, Jingnan; Kong, Lingbo; Voulalas, Pamela; Hassan, Hazem E.; Park, Jae-Sung; MacKerell, Alexander D., Jr.; Smith, Wanli W.
Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models
HUMAN MOLECULAR GENETICS, 23:6212-6222, DEC 1 2014
abstract, full text, DOI:10.1093/hmg/ddu341

Mahdavi, Somayeh; Kuyucak, Serdar
Systematic Study of Binding of mu-Conotoxins to the Sodium Channel Na(V)1.4
TOXINS, 6:3454-3470, DEC 2014
abstract, full text, DOI:10.3390/toxins6123454

du Bourg, Lila Bouessel; Ortiz, Aurelie U.; Boutin, Anne; Coudert, Francois-Xavier
Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs
APL MATERIALS, 2 Art. No. 124110, DEC 2014
abstract, full text, DOI:10.1063/1.4904818

Ma, Buyong; Kolb, Stephanie; Diprima, Michael; Karna, Molleshree; Tosato, Giovanna; Yang, Qiqi; Huang, Qiang; Nussinov, Ruth
Investigation of the interactions between the EphB2 receptor and SNEW peptide variants
GROWTH FACTORS, 32:236-246, DEC 2014
abstract, full text, DOI:10.3109/08977194.2014.985786

Elward, Jennifer M.; Irudayanathan, Flaviyan Jerome; Nangia, Shikha; Chakraborty, Arindam
Optical Signature of Formation of Protein Corona in the Firefly Luciferase-CdSe Quantum Dot Complex
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5224-5228, DEC 2014
abstract, full text, DOI:10.1021/ct500681m

Comer, Jeffrey; Phillips, James C.; Schulten, Klaus; Chipot, Christophe
Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5276-5285, DEC 2014
abstract, full text, TCBG publications, DOI:10.1021/ct500874p

Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.
CW dipolar broadening EPR spectroscopy and mechanically aligned bilayers used to measure distance and relative orientation between two TOAC spin labels on an antimicrobial peptide
JOURNAL OF MAGNETIC RESONANCE, 249:72-79, DEC 2014
abstract, full text, DOI:10.1016/j.jmr.2014.09.020

Delacour, Herve; Lushchekina, Sofya; Mabboux, Isabelle; Ceppa, Franck; Masson, Patrick; Schopfer, Lawrence M.; Lockridge, Oksana
Characterization of a novel butyrylcholinesterase point mutation (p.Ala34Val), "silent" with mivacurium
BIOCHEMICAL PHARMACOLOGY, 92:476-483, DEC 1 2014
abstract, full text, DOI:10.1016/j.bcp.2014.09.014

Pietra, Francesco
Molecular Dynamics Simulation of Dioxygen Pathways through Mini Singlet Oxygen Generator (miniSOG), a Genetically Encoded Marker and Killer Protein
CHEMISTRY & BIODIVERSITY, 11:1883-1891, DEC 2014
abstract, full text, DOI:10.1002/cbdv.201400125

Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1964-1972, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.09.006

Woelke, Anna Lena; Galstyan, Gegham; Knapp, Ernst-Walter
Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pK(A) and conformation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1998-2003, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.08.003

Ungvarsky, Jan; Plsikova, Jana; Janovec, Ladislav; Koval, Jan; Mikes, Jaromir; Mikesova, Lucia; Harvanova, Denisa; Fedorocko, Peter; Kristian, Pavol; Kasparkova, Jana; Brabec, Viktor; Vojtickova, Maria; Sabolova, Danica; Stramova, Zuzana; Rosocha, Jan; Imrich, Jan; Kozurkova, Maria
Novel trisubstituted acridines as human telomeric quadruplex binding ligands
BIOORGANIC CHEMISTRY, 57:13-29, DEC 2014
abstract, full text, DOI:10.1016/j.bioorg.2014.07.010

Bagatin, Mariane Cristovao; Suniga Tozatti, Camila Santos; Abiko, Layara Akemi; dos Santos Yamazaki, Diego Alberto; Alves Silva, Priscila Rebeca; Perego, Leonardo Martins; Audi, Elisabeth Aparecida; Vicente Seixas, Flavio Augusto; Basso, Ernani Abicht; Gauze, Gisele de Freitas
Molecular Docking and Panicolytic Effect of 8-Prenylnaringenin in the Elevated T-Maze
CHEMICAL & PHARMACEUTICAL BULLETIN, 62:1231-1237, DEC 2014
abstract, full text

Hundt, Nikolas; Preller, Matthias; Swolski, Olga; Ang, Angella M.; Mannherz, Hans G.; Manstein, Dietmar J.; Mueller, Mirco
Molecular mechanisms of disease-related human beta-actin mutations p.R183W and p.E364K
FEBS JOURNAL, 281:5279-5291, DEC 2014
abstract, full text, DOI:10.1111/febs.13068

Kim, Soo-Kyung; Goddard, William A., I.I.I.
Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1175-1190, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9793-4

Virginia Saavedra-Velez, Margarita; Correa-Basurto, Jose; Matus, Myrna H.; Gasca-Perez, Eloy; Bello, Martiniano; Cuevas-Hernandez, Roberto; Virginia Garcia-Rodriguez, Rosa; Trujillo-Ferrara, Jose; Rafael Ramos-Morales, Fernando
Seeking potential anticonvulsant agents that target GABA(A) receptors using experimental and theoretical procedures
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1217-1232, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9798-z

Lipovsek, Marcela; Fierro, Angelica; Perez, Edwin G.; Boffi, Juan C.; Millar, Neil S.; Fuchs, Paul A.; Katz, Eleonora; Belen Elgoyhen, Ana
Tracking the Molecular Evolution of Calcium Permeability in a Nicotinic Acetylcholine Receptor
MOLECULAR BIOLOGY AND EVOLUTION, 31:3250-3265, DEC 2014
abstract, full text, DOI:10.1093/molbev/msu258

Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa
Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844:2059-2067, DEC 2014
abstract, full text, DOI:10.1016/j.bbapap.2014.09.004

Strohalmova-Bohmova, Karolina; Spiwok, Vojtech; Lepsik, Martin; Hadravova, Romana; Krizova, Ivana; Ulbrich, Pavel; Pichova, Iva; Bednarova, Lucie; Ruml, Tomas; Rumlova, Michaela
Role of Mason-Pfizer Monkey Virus CA-NC Spacer Peptide-Like Domain in Assembly of Immature Particles
JOURNAL OF VIROLOGY, 88:14148-14160, DEC 2014
abstract, full text, DOI:10.1128/JVI.02286-14

Persson, Egon; Madsen, Jesper J.; Olsen, Ole H.
The length of the linker between the epidermal growth factor-like domains in factor VIIa is critical for a productive interaction with tissue factor
PROTEIN SCIENCE, 23:1717-1727, DEC 2014
abstract, full text, DOI:10.1002/pro.2553

Cui, Di; Ou, Shuching; Patel, Sandeep
Protein-Spanning Water Networks and Implications for Prediction of Protein-Protein Interactions Mediated through Hydrophobic Effects
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:3312-3326, DEC 2014
abstract, full text, DOI:10.1002/prot.24683

Li, Qing; Scholl, Zackary N.; Marszalek, Piotr E.
Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 53:13429-13433, DEC 1 2014
abstract, full text, DOI:10.1002/anie.201407211

Pinto da Silva, Luis; Esteves da Silva, Joaquim C. G.
A Theoretical Analysis of the Potential Role of pi-pi Stacking Interactions in the Photoprotolytic Cycle of Firefly Luciferin
CHEMPHYSCHEM, 15:3761-3767, DEC 1 2014
abstract, full text, DOI:10.1002/cphc.201402558

Pillai, Jitesh K.; Venkadesh, Sarkarai; Ajees, A. Abdul; Rosen, Barry P.; Bhattacharjee, Hiranmoy
Mutations in the ArsA ATPase that restore interaction with the ArsD metallochaperone
BIOMETALS, 27:1263-1275, DEC 2014
abstract, full text, DOI:10.1007/s10534-014-9788-6

Grizel, Anastasia; Popinako, Anna; Kasimova, Marina A.; Stevens, Louisa; Karlova, Maria; Moisenovich, Mikhail M.; Sokolova, Olga S.
Domain Structure and Conformational Changes in rat K(V)2.1 ion Channel
JOURNAL OF NEUROIMMUNE PHARMACOLOGY, 9:727-739, DEC 2014
abstract, full text, DOI:10.1007/s11481-014-9565-x

Boynton, P.; Balatsky, A. V.; Schuller, I. K.; Di Ventra, M.
Improving sequencing by tunneling with multiplexing and cross-correlations
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:794-800, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0571-2

Belkin, Maxim; Chao, Shu-Han; Giannetti, Gino; Aksimentiev, Aleksei
Modeling thermophoretic effects in solid-state nanopores
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:826-838, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0594-8

Polak, Andraz; Tarek, Mounir; Tomsic, Matija; Valant, Janez; Ulrih, Natasa Poklar; Jamnik, Andrej; Kramar, Peter; Miklavcic, Damijan
Electroporation of archaeal lipid membranes using MD simulations
BIOELECTROCHEMISTRY, 100:18-26, DEC 2014
abstract, full text, DOI:10.1016/j.bioelechem.2013.12.006

Olavarria, K.; De Ingeniis, J.; Zielinski, D. C.; Fuentealba, M.; Munoz, R.; McCloskey, D.; Feist, A. M.; Cabrera, R.
Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli
MICROBIOLOGY-SGM, 160:2780-2793, DEC 2014
abstract, full text, DOI:10.1099/mic.0.082180-0

Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Nicchia, Grazia Paola; Frigeri, Antonio; Pisani, Francesco; Benfenati, Valentina; Mangiatordi, Giuseppe Felice
A new gating site in human aquaporin-4: Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3052-3060, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.015

Vermaas, Josh V.; Tajkhorshid, Emad
Conformational heterogeneity of alpha-synuclein in membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3107-3117, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.012

Deleu, Magali; Crowet, Jean-Marc; Nasir, Mehmet N.; Lins, Laurence
Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3171-3190, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.023

Schillinger, Anne-Sophie; Grauffel, Cedric; Khan, Hanif Muhammad; Halskau, Oyvind; Reuter, Nathalie
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3191-3202, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.09.003

Benavidez, Tomas E.; Torrente, Daniel; Marucho, Marcelo; Garcia, Carlos D.
Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:164-170, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.08.012

Adamczyk, Zbigniew; Jamrozy, Krzysztof; Batys, Piotr; Michna, Aneta
Influence of ionic strength on poly(diallyldimethylammonium chloride) macromolecule conformations in electrolyte solutions
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:182-190, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.07.037

Abdul-Ridha, Alaa; Lane, J. Robert; Mistry, Shailesh N.; Lopez, Laura; Sexton, Patrick M.; Scammells, Peter J.; Christopoulos, Arthur; Canals, Meritxell
Mechanistic Insights into Allosteric Structure-Function Relationships at the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:33701-33711, NOV 28 2014
abstract, full text, DOI:10.1074/jbc.M114.604967

Chatterjee, Prathit; Bagchi, Sayan; Sengupta, Neelanjana
The non-uniform early structural response of globular proteins to cold denaturing conditions: A case study with Yfh1
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 205103, NOV 28 2014
abstract, full text, DOI:10.1063/1.4901897

Budnjo, Adnan; Narawane, Shailesh; Grauffel, Cedric; Schillinger, Anne-Sophie; Fossen, Torgils; Reuter, Nathalie; Haug, Bengt Erik
Reversible Ketomethylene-Based Inhibitors of Human Neutrophil Proteinase 3
JOURNAL OF MEDICINAL CHEMISTRY, 57:9396-9408, NOV 27 2014
abstract, full text, DOI:10.1021/jm500782s

Khrenova, Maria G.; Savitsky, Alexander P.; Topol, Igor A.; Nemukhin, Alexander V.
Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13505-13512, NOV 27 2014
abstract, full text, DOI:10.1021/jp5088702

Baker, Michelle K.; Abrams, Cameron F.
Dynamics of Lipids, Cholesterol, and Transmembrane alpha-Helices from Microsecond Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13590-13600, NOV 27 2014
abstract, full text, DOI:10.1021/jp507027t

James, Kevin A.; Verkhivker, Gennady M.
Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions
PLOS ONE, 9 Art. No. e113488, NOV 26 2014
abstract, full text, DOI:10.1371/journal.pone.0113488

Laine, Jennifer M.; Amat, Miguel; Morgan, Brittany R.; Royer, William E., Jr.; Massi, Francesca
Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin
BIOCHEMISTRY, 53:7199-7210, NOV 25 2014
abstract, full text, DOI:10.1021/bi500591s

Bera, Manindra; Kotamarthi, Hema Chandra; Dutta, Subarna; Ray, Angana; Ghosh, Saptaparni; Bhattacharyya, Dhananjay; Ainavarapu, Sri Rama Koti; Sengupta, Kaushik
Characterization of Unfolding Mechanism of Human Lamin A Ig Fold by Single-Molecule Force Spectroscopy-Implications in EDMD
BIOCHEMISTRY, 53:7247-7258, NOV 25 2014
abstract, full text, DOI:10.1021/bi500726f

Lim, San Sui; Yang, Wei; Krishnarjuna, Bankala; Sivaraman, Komagal Kannan; Chandrashekaran, Indu R.; Kass, Itamar; MacRaild, Christopher A.; Devine, Shane M.; Debono, Cael O.; Anders, Robin F.; Scanlon, Martin J.; Scammells, Peter J.; Norton, Raymond S.; McGowan, Sheena
Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO
BIOCHEMISTRY, 53:7310-7320, NOV 25 2014
abstract, full text, DOI:10.1021/bi5012089

Zhang, Li; Liu, Zhipei; Ren, Tao; Wu, Pan; Shen, Jia-Wei; Zhang, Wei; Wang, Xinping
Understanding the Structure of Hydrophobic Surfactants at the Air/Water Interface from Molecular Level
LANGMUIR, 30:13815-13822, NOV 25 2014
abstract, full text, DOI:10.1021/la5030586

Yang, J.; Singharoy, A.; Sereda, Yu. V.; Ortoleva, P. J.
Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin
CHEMICAL PHYSICS LETTERS, 616:154-160, NOV 25 2014
abstract, full text, DOI:10.1016/j.cplett.2014.10.020

Shang, Zhiguo; Zhou, Kaifeng; Xu, Chen; Csencsits, Roseann; Cochran, Jared C.; Sindelar, Charles V.
High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation
ELIFE, 3 Art. No. e04686, NOV 21 2014
abstract, full text, DOI:10.7554/eLife.04686

Perlinska, Agata; Grynberg, Marcin
Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin
PEERJ, 2 Art. No. UNSP e679, NOV 20 2014
abstract, full text, DOI:10.7717/peerj.679

Furini, Simone; Domene, Carmen
DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13059-13065, NOV 20 2014
abstract, full text, DOI:10.1021/jp505885j

Aranda, Juan; Zinovjev, Kirill; Roca, Maite; Tunon, Inaki
Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16227-16239, NOV 19 2014
abstract, full text, DOI:10.1021/ja5077124

Kastner, Kevin W.; Shoue, Douglas A.; Estiu, Guillermina L.; Wolford, Julia; Fuerst, Megan F.; Markley, Lowell D.; Izaguirre, Jesus A.; McDowell, Mary Ann
Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach
MALARIA JOURNAL, 13 Art. No. 434, NOV 18 2014
abstract, full text, DOI:10.1186/1475-2875-13-434

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni
Smooth DNA Transport through a Narrowed Pore Geometry
BIOPHYSICAL JOURNAL, 107:2381-2393, NOV 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.017

Sayer, James R.; Wallden, Karin; Pesnot, Thomas; Campbell, Frederick; Gane, Paul J.; Simone, Michela; Koss, Hans; Buelens, Floris; Boyle, Timothy P.; Selwood, David L.; Waksman, Gabriel; Tabor, Alethea B.
2-and 3-substituted imidazo[1,2-a]pyrazines as inhibitors of bacterial type IV secretion
BIOORGANIC & MEDICINAL CHEMISTRY, 22:6459-6470, NOV 15 2014
abstract, full text, DOI:10.1016/j.bmc.2014.09.036

Padhi, Siladitya; Burri, Raghunadha Reddy; Jameel, Shahid; Priyakumar, U. Deva
Atomistic Detailed Mechanism and Weak Cation-Conducting Activity of HIV-1 Vpu Revealed by Free Energy Calculations
PLOS ONE, 9 Art. No. e112983, NOV 13 2014
abstract, full text, DOI:10.1371/journal.pone.0112983

Wei, Chenyu; Pohorille, Andrew
Flip-Flop of Oleic Acid in a Phospholipid Membrane: Rate and Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12919-12926, NOV 13 2014
abstract, full text, DOI:10.1021/jp508163e

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.; Khelashvili, George; Weinstein, Harel
A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16044-16054, NOV 12 2014
abstract, full text, DOI:10.1021/ja508394x

Asthana, Shailendra; Shukla, Saumya; Ruggerone, Paolo; Vargiu, Attilio V.
Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
BIOCHEMISTRY, 53:6941-6953, NOV 11 2014
abstract, full text, DOI:10.1021/bi500490z

Andreasen, Maria; Skeby, Katrine Kirkeby; Zhang, Shuai; Nielsen, Erik Holm; Klausen, Lasse Hyldgaard; Frahm, Heidi; Christiansen, Gunna; Skrydstrup, Troels; Dong, Mingdong; Schiott, Birgit; Otzen, Daniel
The Importance of Being Capped: Terminal Capping of an Amyloidogenic Peptide Affects Fibrillation Propensity and Fibril Morphology
BIOCHEMISTRY, 53:6968-6980, NOV 11 2014
abstract, full text, DOI:10.1021/bi500674u

Krishnan, Subramanian; Liu, Fan; Abrol, Ravinder; Hodges, Jacqueline; Goddard, William A., I.I.I.; Prasadarao, Nemani V.
The Interaction of N-Glycans in Fc gamma Receptor I alpha-Chain with Escherichia coli K1 Outer Membrane Protein A for Entry into Macrophages EXPERIMENTAL AND COMPUTATIONAL ANALYSIS
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30937-30949, NOV 7 2014
abstract, full text, DOI:10.1074/jbc.M114.599407

Panecka, Joanna; Mura, Cameron; Trylska, Joanna
Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study
PLOS ONE, 9 Art. No. e111811, NOV 7 2014
abstract, full text, DOI:10.1371/journal.pone.0111811

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus
Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores
NANOTECHNOLOGY, 25 Art. No. 445105, NOV 7 2014
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/25/44/445105

Dong, Hao; Fiorin, Giacomo; DeGrado, William F.; Klein, Michael L.
Proton Release from the Histidine-Tetrad in the M2 Channel of the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12644-12651, NOV 6 2014
abstract, full text, DOI:10.1021/jp5102225

Craddock, Travis John Adrian; Friesen, Douglas; Mane, Jonathan; Hameroff, Stuart; Tuszynski, Jack A.
The feasibility of coherent energy transfer in microtubules
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 11 Art. No. UNSP 20140677, NOV 6 2014
abstract, full text, DOI:10.1098/rsif.2014.0677

Chen, Rong; Gryn'ova, Ganna; Wu, Yingliang; Coote, Michelle L.; Chung, Shin-Ho
Mechanisms and Energetics of Potassium Channel Block by Local Anesthetics and Antifungal Agents
BIOCHEMISTRY, 53:6786-6792, NOV 4 2014
abstract, full text, DOI:10.1021/bi5009408

Petukh, Marharyta; Wu, Bohua; Stefl, Shannon; Smith, Nick; Hyde-Volpe, David; Wang, Li; Alexov, Emil
Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2
PLOS ONE, 9 Art. No. e111604, NOV 4 2014
abstract, full text, DOI:10.1371/journal.pone.0111604

Arcario, Mark J.; Tajkhorshid, Emad
Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3
BIOPHYSICAL JOURNAL, 107:2059-2069, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.022

Blanchard, Andrew E.; Arcario, Mark J.; Schulten, Klaus; Tajkhorshid, Emad
A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin
BIOPHYSICAL JOURNAL, 107:2112-2121, NOV 4 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.09.013

Woelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-Walter
Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilus
BIOPHYSICAL JOURNAL, 107:2177-2184, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.010

Anwar-Mohamed, Anwar; Barakat, Khaled H.; Bhat, Rakesh; Noskov, Sergei Y.; Tyrrell, D. Lorne; Tuszynski, Jack A.; Houghton, Michael
A human ether-a-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
TOXICOLOGY LETTERS, 230:382-392, NOV 4 2014
abstract, full text, DOI:10.1016/j.toxlet.2014.08.007

Stewart, Matthew B.; Gray, Stephen R.; Vasiljevic, Todor; Orbell, John D.
The role of poly-M and poly-GM sequences in the metal-mediated assembly of alginate gels
CARBOHYDRATE POLYMERS, 112:486-493, NOV 4 2014
abstract, full text, DOI:10.1016/j.carbpol.2014.06.001

Klose, Daniel; Voskoboynikova, Natalia; Orban-Glass, Ioan; Rickert, Christian; Engelhard, Martin; Klare, Johann P.; Steinhoff, Heinz-Juergen
Light-induced switching of HAMP domain conformation and dynamics revealed by time-resolved EPR spectroscopy
FEBS LETTERS, 588:3970-3976, NOV 3 2014
abstract, full text, DOI:10.1016/j.febslet.2014.09.012

Neuhaeuser, Benjamin; Dynowski, Marek; Ludewig, Uwe
Switching substrate specificity of AMT/MEP/Rh proteins
CHANNELS, 8:496-502, NOV-DEC 2014
abstract, full text, DOI:10.4161/19336950.2014.967618

Carvalho, Alexandra T. P.; Barrozo, Alexandre; Doron, Dvir; Kilshtain, Alexandra Vardi; Major, Dan Thomas; Kamerlin, Shina Caroline Lynn
Challenges in computational studies of enzyme structure, function and dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 54:62-79, NOV 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.09.003

Kalinic, Marko; Zloh, Mire; Eric, Slavica
Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1109-1128, NOV 2014
abstract, full text, DOI:10.1007/s10822-014-9788-1

Matthies, Doreen; Zhou, Wenchang; Klyszejko, Adriana L.; Anselmi, Claudio; Yildiz, Oezkan; Brandt, Karsten; Mueller, Volker; Faraldo-Goemez, Jose D.; Meier, Thomas
High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase
NATURE COMMUNICATIONS, 5 Art. No. 5286, NOV 2014
abstract, full text, DOI:10.1038/ncomms6286

Zhang, Xiaoming; Niu, DongDong; Carbonell, Alberto; Wang, Airong; Lee, Angel; Tun, Vinnary; Wang, Zonghua; Carrington, James C.; Chang, Chia-en A.; Jin, Hailing
ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis
NATURE COMMUNICATIONS, 5 Art. No. 5468, NOV 2014
abstract, full text, DOI:10.1038/ncomms6468

Cocaign, Angelique; Kubiak, Xavier; Xu, Ximing; Garnier, Guillaume; de la Sierra-Gallay, Ines Li; Linh Chi-Bui; Dairou, Julien; Busi, Florent; Abuhammad, Areej; Haouz, Ahmed; Dupret, Jean-Marie; Herrmann, Jean-Louis; Rodrigues-Lima, Fernando
Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:3066-3079, NOV 2014
abstract, full text, DOI:10.1107/S1399004714021282

Sathaye, Sameer; Zhang, Huixi; Sonmez, Cem; Schneider, Joel P.; MacDermaid, Christopher M.; Von Bargen, Christopher D.; Saven, Jeffery G.; Pochan, Darrin J.
Engineering Complementary Hydrophobic Interactions to Control beta-Hairpin Peptide Self-Assembly, Network Branching, and Hydrogel Properties
BIOMACROMOLECULES, 15:3891-3900, NOV 2014
abstract, full text, DOI:10.1021/bm500874t

Apellaniz, Beatriz; Rujas, Edurne; Carravilla, Pablo; Requejo-Isidro, Jose; Huarte, Nerea; Domene, Carmen; Nieva, Jose L.
Cholesterol-Dependent Membrane Fusion Induced by the gp41 Membrane-Proximal External Region-Transmembrane Domain Connection Suggests a Mechanism for Broad HIV-1 Neutralization
JOURNAL OF VIROLOGY, 88:13367-13377, NOV 2014
abstract, full text, DOI:10.1128/JVI.02151-14

Adams, David R.; Yuan, Hongjie; Holyoak, Todd; Arajs, Katrina H.; Hakimi, Parvin; Markello, Thomas C.; Wolfe, Lynne A.; Vilboux, Thierry; Burton, Barbara K.; Fajardo, Karin Fuentes; Grahame, George; Holloman, Conisha; Sincan, Murat; Smith, Ann C. M.; Wells, Gordon A.; Huang, Yan; Vega, Hugo; Snyder, James P.; Golas, Gretchen A.; Tifft, Cynthia J.; Boerkoel, Cornelius F.; Hanson, Richard W.; Traynelis, Stephen F.; Kerr, Douglas S.; Gahl, William A.
Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith-Magenis Syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity
MOLECULAR GENETICS AND METABOLISM, 113:161-170, NOV 2014
abstract, full text, DOI:10.1016/j.ymgme.2014.04.001

Gillet, Natacha; Levy, Bernard; Moliner, Vicent; Demachy, Isabelle; de la Lande, Aurelien
Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5036-5046, NOV 2014
abstract, full text, DOI:10.1021/ct500173y

Durrant, Jacob D.; Votapka, Lane; Sorensen, Jesper; Amaro, Rommie E.
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5047-5056, NOV 2014
abstract, full text, DOI:10.1021/ct500381c

Bhattacharya, Supriyo; Lee, Sangbae; Grisshammer, Reinhard; Tate, Christopher G.; Vaidehi, Nagarajan
Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5149-5160, NOV 2014
abstract, full text, DOI:10.1021/ct500616v

Ho, Junming; Newcomer, Michael B.; Ragain, Christina M.; Gascon, Jose A.; Batista, Enrique R.; Loria, J. Patrick; Batista, Victor S.
MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5125-5135, NOV 2014
abstract, full text, DOI:10.1021/ct500571k

Arenas-Salinas, Mauricio; Townsend, Philip D.; Brito, Christian; Marquez, Valeria; Marabolli, Vanessa; Gonzalez-Nilo, Fernando; Matias, Cata; Watt, Richard K.; Lopez-Castro, Juan D.; Dominguez-Vera, Jose; Pohl, Ehmke; Yevenes, Alejandro
The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family
BIOCHIMIE, 106:39-47, NOV 2014
abstract, full text, DOI:10.1016/j.biochi.2014.07.019

Badu, S. R.; Melnik, R.; Paliy, M.; Prabhakar, S.; Sebetci, A.; Shapiro, B. A.
Modeling of RNA nanotubes using molecular dynamics simulation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 43:555-564, NOV 2014
abstract, full text, DOI:10.1007/s00249-014-0985-6

Wu, Sangwook; Lee, Chang Jun; Pedersen, Lee G.
Analysis on long-range residue-residue communication using molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2896-2901, NOV 2014
abstract, full text, DOI:10.1002/prot.24629

Mori, Yoshiharu; Okumura, Hisashi
Molecular dynamics of the structural changes of helical peptides induced by pressure
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2970-2981, NOV 2014
abstract, full text, DOI:10.1002/prot.24654

Faller, Christina E.; Guvench, Olgun
Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:3079-3089, NOV 2014
abstract, full text, DOI:10.1002/prot.24668

Xi, Yi-Bo; Zhao, Wei-Jie; Zuo, Xiao-Tong; Tjondro, Harry Christianto; Li, Jing; Dai, An-Bang; Wang, Sha; Yan, Yong-Bin
Cataract-causing mutation R233H affects the stabilities of beta B1-and beta A3/beta B1-crystallins with different pH-dependence
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842:2216-2229, NOV 2014
abstract, full text, DOI:10.1016/j.bbadis.2014.07.022

ben Bdira, Fredj; Gonzalez, Esperanza; Pluta, Paula; Lain, Ana; Sanz-Parra, Arantza; Manuel Falcon-Perez, Juan; Millet, Oscar
Tuning intracellular homeostasis of human uroporphyrinogen III synthase by enzyme engineering at a single hotspot of congenital erythropoietic porphyria
HUMAN MOLECULAR GENETICS, 23:5805-5813, NOV 1 2014
abstract, full text, DOI:10.1093/hmg/ddu298

Leiva, Angel; Fuentes, Irma; Bossel, Esteban; Urzua, Marcela; Mendez, Maximiliano; Pino, Maximiliano; Radic, Deodato; Marquez, Valeria; Gonzalez-Nilo, Fernando D.
Block Copolymers in the Synthesis of Gold Nanoparticles. Two New Approaches: Copolymer Aggregates as Reductants and Stabilizers and Simultaneous Formation of Copolymer Aggregates and Gold Nanoparticles
JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 52:3069-3079, NOV 1 2014
abstract, full text, DOI:10.1002/pola.27354

Cardone, Giovanni; Duda, Robert L.; Cheng, Naiqian; You, Lili; Conway, James F.; Hendrix, Roger W.; Steven, Alasdair C.
Metastable Intermediates as Stepping Stones on the Maturation Pathways of Viral Capsids
MBIO, 5 Art. No. e02067-14, NOV-DEC 2014
abstract, full text, DOI:10.1128/mBio.02067-14

Liu, Sen; Liu, Song; Wang, Yanlin; Liao, Zhaojiang
The P2/P2 ' sites affect the substrate cleavage of TNF-alpha converting enzyme (TACE)
MOLECULAR IMMUNOLOGY, 62:122-128, NOV 2014
abstract, full text, DOI:10.1016/j.molimm.2014.05.017

Tang, Yu-Hang; Karniadakis, George Em
Accelerating dissipative particle dynamics simulations on GPUs: Algorithms, numerics and applications
COMPUTER PHYSICS COMMUNICATIONS, 185:2809-2822, NOV 2014
abstract, full text, DOI:10.1016/j.cpc.2014.06.015

Pisani, Francesco; Mola, Maria Grazia; Simone, Laura; Rosito, Stefania; Alberga, Domenico; Mangiatordi, Giuseppe Felice; Lattanzi, Gianluca; Nicolotti, Orazio; Frigeri, Antonio; Svelto, Maria; Nicchia, Grazia Paola
Identification of a Point Mutation Impairing the Binding between Aquaporin-4 and Neuromyelitis Optica Autoantibodies
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30578-30589, OCT 31 2014
abstract, full text, DOI:10.1074/jbc.M114.582221

Wang, Connie Y.; Miller, Thomas F., I.I.I.
Allosteric Response and Substrate Sensitivity in Peptide Binding of the Signal Recognition Particle
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30868-30879, OCT 31 2014
abstract, full text, DOI:10.1074/jbc.M114.584912

Shi, Jipei; Wang, Jianping
Interaction between Metal Cation and Unnatural Peptide Backbone Mediated by Polarized Water Molecules: Study of Infrared Spectroscopy and Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12336-12347, OCT 30 2014
abstract, full text, DOI:10.1021/jp504615f

von Rudorff, Guido Falk; Watermann, Tobias; Sebastiani, Daniel
Perfluoroalkane Force Field for Lipid Membrane Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12531-12540, OCT 30 2014
abstract, full text, DOI:10.1021/jp507464m

Caddeo, Claudia; Fazzi, Daniele; Caironi, Mario; Mattoni, Alessandro
Atomistic Simulations of P(NDI2OD-T2) Morphologies: From Single Chain to Condensed Phases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12556-12565, OCT 30 2014
abstract, full text, DOI:10.1021/jp5085789

Orlando, Marta; Lignani, Gabriele; Maragliano, Luca; Fassio, Anna; Onofri, Franco; Baldelli, Pietro; Giovedi, Silvia; Benfenati, Fabio
Functional Role of ATP Binding to Synapsin I In Synaptic Vesicle Trafficking and Release Dynamics
JOURNAL OF NEUROSCIENCE, 34:14752-14768, OCT 29 2014
abstract, full text, DOI:10.1523/JNEUROSCI.1093-14.2014

Jerabek, Petr; Florian, Jan; Stiborova, Marie; Martinek, Vaclav
Flexible Docking-Based Molecular Dynamics/Steered Molecular Dynamics Calculations of Protein-Protein Contacts in a Complex of Cytochrome P450 1A2 with Cytochronne b(5)
BIOCHEMISTRY, 53:6695-6705, OCT 28 2014
abstract, full text, DOI:10.1021/bi500814t

Li, Junwei; Xie, Xiaoxiao; Liu, Jun; Yu, Hui; Zhang, Suhua; Zhan, Yong; Zhang, Hailin; Logothetis, Diomedes E.; An, Hailong
Lack of Negatively Charged Residues at the External Mouth of Kir2.2 Channels Enable the Voltage-Dependent Block by External Mg2+
PLOS ONE, 9 Art. No. e111372, OCT 28 2014
abstract, full text, DOI:10.1371/journal.pone.0111372

Shi, Guosheng; Shen, Yue; Liu, Jian; Wang, Chunlei; Wang, Ying; Song, Bo; Hu, Jun; Fang, Haiping
Molecular-scale Hydrophilicity Induced by Solute: Molecular-thick Charged Pancakes of Aqueous Salt Solution on Hydrophobic Carbon-based Surfaces
SCIENTIFIC REPORTS, 4 Art. No. 6793, OCT 28 2014
abstract, full text, DOI:10.1038/srep06793

Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:15396-15401, OCT 28 2014
abstract, full text, DOI:10.1073/pnas.1407768111

Ozcan, Nergiz; Mares, Jiri; Sundholm, Dage; Vaara, Juha
Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:22309-22320, OCT 28 2014
abstract, full text, DOI:10.1039/c4cp02894e

Dong, Sheng; Wei, Tian-Di; Chen, Xiu-Lan; Li, Chun-Yang; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Pang, Xiu-Hua; Zhou, Bai-Cheng; Zhang, Yu-Zhong
Molecular Insight into the Role of the N-terminal Extension in the Maturation, Substrate Recognition, and Catalysis of a Bacterial Alginate Lyase from Polysaccharide Lyase Family 18
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:29558-29569, OCT 24 2014
abstract, full text, DOI:10.1074/jbc.M114.584573

Handschuh, Karen; Feenstra, Jennifer; Koss, Matthew; Ferretti, Elisabetta; Risolino, Maurizio; Zewdu, Rediet; Sahai, Michelle A.; Benazet, Jean-Denis; Peng, Xiao P.; Depew, Michael J.; Quintana, Laura; Sharpe, James; Wang, Baolin; Alcorn, Heather; Rivi, Roberta; Butcher, Stephen; Manak, J. Robert; Vaccari, Thomas; Weinstein, Harel; Anderson, Kathryn V.; Lacy, Elizabeth; Selleri, Licia
ESCRT-II/Vps25 Constrains Digit Number by Endosome-Mediated Selective Modulation of FGF-SHH Signaling
CELL REPORTS, 9:674-687, OCT 23 2014
abstract, full text, DOI:10.1016/j.celrep.2014.09.019

Boyken, Scott E.; Chopra, Nikita; Xie, Nan; Joseph, Raji E.; Wales, Thomas E.; Fulton, D. Bruce; Engen, John R.; Jernigan, Robert L.; Andreotti, Amy H.
A Conserved Isoleucine Maintains the Inactive State of Bruton's Tyrosine Kinase
JOURNAL OF MOLECULAR BIOLOGY, 426:3656-3669, OCT 23 2014
abstract, full text, DOI:10.1016/j.jmb.2014.08.018

Wang, Kaituo; Sitsel, Oleg; Meloni, Gabriele; Autzen, Henriette Elisabeth; Andersson, Magnus; Klymchuk, Tetyana; Nielsen, Anna Marie; Rees, Douglas C.; Nissen, Poul; Gourdon, Pontus
Structure and mechanism of Zn2+-transporting P-type ATPases
NATURE, 514:518-+, OCT 23 2014
abstract, full text, DOI:10.1038/nature13618

Arcario, Mark J.; Mayne, Christopher G.; Tajkhorshid, Emad
Atomistic Models of General Anesthetics for Use in in Silico Biological Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12075-12086, OCT 23 2014
abstract, full text, DOI:10.1021/jp502716m

Furlan, Sara; La Penna, Giovanni; Appelhans, Dietmar; Cangiotti, Michela; Ottaviani, Maria Francesca; Danani, Andrea
Combined EPR and Molecular Modeling Study of PPI Dendrimers Interacting with Copper Ions: Effect of Generation and Maltose Decoration
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12098-12111, OCT 23 2014
abstract, full text, DOI:10.1021/jp505420s

Wang, Zunliang; Han, Xiaofeng; He, Nongyue; Chen, Zhan; Brooks, Charles L., I.I.I.
Environmental Effect on Surface Immobilized Biological Molecules
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12176-12185, OCT 23 2014
abstract, full text, DOI:10.1021/jp508550d

Lin, Yen-Lin; Meng, Yilin; Huang, Lei; Roux, Benoit
Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:14753-14762, OCT 22 2014
abstract, full text, DOI:10.1021/ja504146x

Han, Lei; Zhang, Yong-Jun; Zhang, Long; Cui, Xu; Yu, Jinpu; Zhang, Ziding; Liu, Ming S.
Operating Mechanism and Molecular Dynamics of Pheromone-Binding Protein ASP1 as Influenced by pH
PLOS ONE, 9 Art. No. e110565, OCT 22 2014
abstract, full text, DOI:10.1371/journal.pone.0110565

Elghobashi-Meinhardt, Nadia
Niemann-Pick Type C Disease: A QM/MM Study of Conformational Changes in Cholesterol in the NPC1(NTD) and NPC2 Binding Pockets
BIOCHEMISTRY, 53:6603-6614, OCT 21 2014
abstract, full text, DOI:10.1021/bi500548f

Golji, Javad; Mofrad, Mohammad R. K.
The Talin Dimer Structure Orientation Is Mechanically Regulated
BIOPHYSICAL JOURNAL, 107:1802-1809, OCT 21 2014
abstract, full text, DOI:10.1016/j.bpj.2014.08.038

Kern, Nathan R.; Lee, Hui Sun; Wu, Emilia L.; Park, Soohyung; Vanommeslaeghe, Kenno; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Jo, Sunhwan; Im, Wonpil
Lipid-Linked Oligosaccharides in Membranes Sample Conformations That Facilitate Binding to Oligosaccharyltransferase
BIOPHYSICAL JOURNAL, 107:1885-1895, OCT 21 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.007

Ahn, Young O.; Mahinthichaichan, Paween; Lee, Hyun Ju; Ouyang, Hanlin; Kaluka, Daniel; Yeh, Syun-Ru; Arjona, Davinia; Rousseau, Denis L.; Tajkhorshid, Emad; Adelroth, Pia; Gennis, Robert B.
Conformational coupling between the active site and residues within the K-C-channel of the Vibrio cholerae cbb(3)-type (C-family) oxygen reductase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E4419-E4428, OCT 21 2014
abstract, full text, DOI:10.1073/pnas.1411676111

Gkionis, K.; Obodo, J. T.; Cucinotta, C.; Sanvito, S.; Schwingenschloegl, U.
Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions
JOURNAL OF MATERIALS CHEMISTRY A, 2:16498-16506, OCT 21 2014
abstract, full text, DOI:10.1039/c4ta02760d

Tah, Bidisha; Pal, Prabir; Mishra, Sabyashachi; Talapatra, G. B.
Interaction of insulin with anionic phospholipid (DPPG) vesicles
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:21657-21663, OCT 21 2014
abstract, full text, DOI:10.1039/c4cp03028a

Mandal, Manoj; Mukhopadhyay, Chaitali
Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:21706-21716, OCT 21 2014
abstract, full text, DOI:10.1039/c4cp01657b

Schmidt, Thomas C.; Welker, Armin; Rieger, Max; Sahu, Prabhat K.; Sotriffer, Christoph A.; Schirmeister, Tanja; Engels, Bernd
Protocol for Rational Design of Covalently Interacting Inhibitors
CHEMPHYSCHEM, 15:3226-3235, OCT 20 2014
abstract, full text, DOI:10.1002/cphc.201402542

Cooper, April M.; Kaestner, Johannes
Averaging Techniques for Reaction Barriers in QM/MM Simulations
CHEMPHYSCHEM, 15:3264-3269, OCT 20 2014
abstract, full text, DOI:10.1002/cphc.201402382

Song, Minseok; Snyder, Mark A.; Mittal, Jeetain
Effect of molecular structure on fluid transport through carbon nanotubes
MOLECULAR PHYSICS, 112:2658-2664, OCT 18 2014
abstract, full text, DOI:10.1080/00268976.2014.903578

Androulaki, Eleni; Vergadou, Niki; Economou, Ioannis G.
Analysis of the heterogeneous dynamics of imidazolium-based [Tf2N-] ionic liquids using molecular simulation
MOLECULAR PHYSICS, 112:2694-2706, OCT 18 2014
abstract, full text, DOI:10.1080/00268976.2014.906670

Pappalardo, Matteo; Shachaf, Nir; Basile, Livia; Milardi, Danilo; Zeidan, Mouhammed; Raiyn, Jamal; Guccione, Salvatore; Rayan, Anwar
Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism
PLOS ONE, 9 Art. No. e109340, OCT 16 2014
abstract, full text, DOI:10.1371/journal.pone.0109340

Kang, Myungshim; Loverde, Sharon M.
Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11965-11972, OCT 16 2014
abstract, full text, DOI:10.1021/jp50476131

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep
Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Trans location into DMPC Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11973-11992, OCT 16 2014
abstract, full text, DOI:10.1021/jp504853t

He, Jia; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer
JOURNAL OF PHYSICAL CHEMISTRY C, 118:24173-24180, OCT 16 2014
abstract, full text, DOI:10.1021/jp507325j

Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan; Rui, Huan; Song, Kevin C.; Davila-Contreras, Eder M.; Qi, Yifei; Lee, Jumin; Monje-Galvan, Viviana; Venable, Richard M.; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1997-2004, OCT 15 2014
abstract, full text, DOI:10.1002/jcc.23702

Dick, Veronika V.; Klein, Peter
Molecular simulation of the hydrodynamics of water in contact with hydrophilized poly(vinylidene fluoride) surfaces
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 432:70-76, OCT 15 2014
abstract, full text, DOI:10.1016/j.jcis.2014.06.049

Xie, Dexuan
New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
JOURNAL OF COMPUTATIONAL PHYSICS, 275:294-309, OCT 15 2014
abstract, full text, DOI:10.1016/j.jcp.2014.07.012

Harris, Robert C.; Pettitt, B. Montgomery
Effects of geometry and chemistry on hydrophobic solvation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:14681-14686, OCT 14 2014
abstract, full text, DOI:10.1073/pnas.1406080111

Hong, Chunkit; Tieleman, D. Peter; Wang, Yi
Microsecond Molecular Dynamics Simulations of Lipid Mixing
LANGMUIR, 30:11993-12001, OCT 14 2014
abstract, full text, DOI:10.1021/la502363b

Hsu, Hao-jui; Sen, Soumyo; Pearson, Ryan M.; Uddin, Sayam; Kral, Petr; Hong, Seungpyo
Poly(ethylene glycol) Corona Chain Length Controls End-Group-Dependent Cell Interactions of Dendron Micelles
MACROMOLECULES, 47:6911-6918, OCT 14 2014
abstract, full text, DOI:10.1021/ma501258c

Pang, Xiaoyun; Fan, Jun; Zhang, Yan; Zhang, Kai; Gao, Bingquan; Ma, Jun; Li, Jian; Deng, Yuchen; Zhou, Qiangjun; Egelman, Edward H.; Hsu, Victor W.; Sun, Fei
A PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature
DEVELOPMENTAL CELL, 31:73-86, OCT 13 2014
abstract, full text, DOI:10.1016/j.devcel.2014.08.020

Yao, Qing; Lu, Qiuhe; Wan, Xiaobo; Song, Feng; Xu, Yue; Hu, Mo; Zamyatina, Alla; Liu, Xiaoyun; Huang, Niu; Zhu, Ping; Shao, Feng
A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family
ELIFE, 3 Art. No. 03714, OCT 13 2014
abstract, full text, DOI:10.7554/eLife.03714

Bellacchio, Emanuele; Palma, Alessia; Corrente, Stefania; Di Girolamo, Francesco; Kemp, E. Helen; Di Matteo, Gigliola; Comelli, Laura; Carsetti, Rita; Cascioli, Simona; Cancrini, Caterina; Fierabracci, Alessandra
The possible implication of the S250C variant of the autoimmune regulator protein in a patient with autoimmunity and immunodeficiency: in silico analysis suggests a molecular pathogenic mechanism for the variant
GENE, 549:286-294, OCT 10 2014
abstract, full text, DOI:10.1016/j.gene.2014.07.064

Jose, Jaya C.; Khatua, Prabir; Bansal, Nupur; Sengupta, Neelanjana; Bandyopadhyay, Sanjoy
Microscopic Hydration Properties of the A beta(1-42) Peptide Monomer and the Globular Protein Ubiquitin: A Comparative Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11591-11604, OCT 9 2014
abstract, full text, DOI:10.1021/jp505629q

Fu, Haohao; Liu, Yingzhe; Adria, Ferran; Shao, Xueguang; Cai, Wensheng; Chipot, Christophe
From Material Science to Avant-Garde Cuisine. The Art of Shaping Liquids into Spheres
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11747-11756, OCT 9 2014
abstract, full text, DOI:10.1021/jp508841p

Morrison, Lindsay J.; Wysocki, Vicki H.
Gas-Phase Helical Peptides Mimic Solution-Phase Behavior
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:14173-14183, OCT 8 2014
abstract, full text, DOI:10.1021/ja507298e

Qiu, Wanzhi; Skafidas, Efstratios
Detection of Protein Conformational Changes with Multilayer Graphene Nanopore Sensors
ACS APPLIED MATERIALS & INTERFACES, 6:16777-16781, OCT 8 2014
abstract, full text, DOI:10.1021/am5040279

Cheng, Yuanhua; Lindert, Steffen; Kekenes-Huskey, Peter; Rao, Vijay S.; Solaro, R. John; Rosevear, Paul R.; Amaro, Rommie; McCulloch, Andrew D.; McCammon, J. Andrew; Regnier, Michael
Computational Studies of the Effect of the S23D/S24D Troponin I Mutation on Cardiac Troponin Structural Dynamics
BIOPHYSICAL JOURNAL, 107:1675-1685, OCT 7 2014
abstract, full text, DOI:10.1016/j.bpj.2014.08.008

Yang, Li-Jun; Zhao, Wen-Hua; Liu, Qian
Detailed conformation dynamics and activation process of wild type c-Abl and T3151 mutant
JOURNAL OF MOLECULAR STRUCTURE, 1075:292-298, OCT 5 2014
abstract, full text, DOI:10.1016/j.molstruc.2014.06.087

Mena-Ulecia, Karel; Vergara-Jaque, Ariela; Poblete, Horacio; Tiznado, William; Caballero, Julio
Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA
PLOS ONE, 9 Art. No. e109639, OCT 2 2014
abstract, full text, DOI:10.1371/journal.pone.0109639

Church, Philip C.; Goscinski, Andrzej M.
A Survey of Cloud-Based Service Computing Solutions for Mammalian Genomics
IEEE Transactions on Services Computing, 7:726-740, OCT-DEC 2014
abstract, full text, DOI:10.1109/TSC.2014.2353645

Lefoulon, Cecile; Karnik, Rucha; Honsbein, Annegret; Gutla, Paul Vijay; Grefen, Christopher; Riedelsberger, Janin; Poblete, Tomas; Dreyer, Ingo; Gonzalez, Wendy; Blatt, Michael R.
Voltage-Sensor Transitions of the Inward-Rectifying K+ Channel KAT1 Indicate a Latching Mechanism Biased by Hydration within the Voltage Sensor
PLANT PHYSIOLOGY, 166:960-U776, OCT 2014
abstract, full text, DOI:10.1104/pp.114.244319

Vargiu, Attilio V.; Ruggerone, Paolo; Opperman, Timothy J.; Nguyen, Son T.; Nikaido, Hiroshi
Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 58:6224-6234, OCT 2014
abstract, full text, DOI:10.1128/AAC.03283-14

Lin, Ying-Wu; Shu, Xiao-Gang; Du, Ke-Jie; Nie, Chang-Ming; Wen, Ge-Bo
Computational insight into nitration of human myoglobin
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 52:60-65, OCT 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.09.004

Shankla, Manish; Aksimentiev, Aleksei
Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene
NATURE COMMUNICATIONS, 5 Art. No. 5171, OCT 2014
abstract, full text, DOI:10.1038/ncomms6171

Cheng, Mary Hongying; Bahar, Ivet
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003879, OCT 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003879

Gkeka, Paraskevi; Evangelidis, Thomas; Pavlaki, Maria; Lazani, Vasiliki; Christoforidis, Savvas; Agianian, Bogos; Cournia, Zoe
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003895, OCT 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003895

Garrido-Arandia, Maria; Gomez-Casado, Cristina; Diaz-Perales, Araceli; Pacios, Luis F.
Molecular Dynamics of Major Allergens from Alternaria, Birch Pollen and Peach
MOLECULAR INFORMATICS, 33:682-694, OCT 2014
abstract, full text, DOI:10.1002/minf.201400057

Kapoor, Abhijeet; Travesset, Alex
Mechanism of the Exchange Reaction in HRAS from Multiscale Modeling
PLOS ONE, 9 Art. No. e108846, OCT 1 2014
abstract, full text, DOI:10.1371/journal.pone.0108846

Geng Yi-Zhao; Ji Qing; Liu Shu-Xia; Yan Shi-Wei
Initial conformation of kinesin's neck linker
CHINESE PHYSICS B, 23 Art. No. 108701, OCT 2014
abstract, full text, DOI:10.1088/1674-1056/23/10/108701

McHarris, Danielle M.; Barr, Daniel A.
Truncated Variants of the GCN4 Transcription Activator Protein Bind DNA with Dramatically Different Dynamical Motifs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2869-2875, OCT 2014
abstract, full text, DOI:10.1021/ci500448e

Abdul-Wahid, Badi'; Feng, Haoyun; Rajan, Dinesh; Costaouec, Ronan; Darve, Eric; Thain, Douglas; Izaguirre, Jesus A.
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:3033-3043, OCT 2014
abstract, full text, DOI:10.1021/ci500321g

Wang, Qiuming; Liang, Guizhao; Zhang, Mingzhen; Zhao, Jun; Patel, Kunal; Yu, Xiang; Zhao, Chao; Ding, Binrong; Zhang, Ge; Zhou, Feimeng; Zheng, Jie
De Novo Design of Self-Assembled Hexapeptides as beta-Amyloid (A beta) Peptide Inhibitors
ACS CHEMICAL NEUROSCIENCE, 5:972-981, OCT 2014
abstract, full text, DOI:10.1021/cn500165s

Li, Nan K.; Quiroz, Felipe Garcia; Hall, Carol K.; Chilkoti, Ashutosh; Yingling, Yaroslava G.
Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide
BIOMACROMOLECULES, 15:3522-3530, OCT 2014
abstract, full text, DOI:10.1021/bm500658w

Sugihara, Minoru; Suwa, Makiko; Bondar, Ana-Nicoleta
Dynamics of bovine opsin bound to G-protein fragments
JOURNAL OF STRUCTURAL BIOLOGY, 188:79-86, OCT 2014
abstract, full text, DOI:10.1016/j.jsb.2014.08.001

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Separation of a heavy metal from water through a membrane containing boron nitride nanotubes: molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2468, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2468-1

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Ge, Zhongxue; Kang, Ying
Structural characteristics of liquid nitromethane at the nanoscale confinement in carbon nanotubes
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2459, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2459-2

Wood, Irene; Pickholz, Monica
Triptan partition in model membranes
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2463, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2463-6

Korb, Oliver; Finn, Paul W.; Jones, Gareth
The cloud and other new computational methods to improve molecular modelling
EXPERT OPINION ON DRUG DISCOVERY, 9:1121-1131, OCT 2014
abstract, full text, DOI:10.1517/17460441.2014941800

Bolintineanu, Dan S.; Volzing, Katherine; Vivcharuk, Victor; Sayyed-Ahmad, Abdallah; Srivastava, Poonam; Kaznessis, Yiannis N.
Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator
JOURNAL OF CHEMICAL AND ENGINEERING DATA, 59:3167-3176, OCT 2014
abstract, full text, DOI:10.1021/je500225x

Anisimov, Victor M.; Bauer, Gregory H.; Chadalavada, Kalyana; Olson, Ryan M.; Glenski, Joseph W.; Krarner, William T. C.; Apra, Edoardo; Kowalski, Karol
Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4307-4316, OCT 2014
abstract, full text, DOI:10.1021/ct500404c

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W.; Hasse, Hans; Vrabec, Jadran; Horsch, Martin
ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4455-4464, OCT 2014
abstract, full text, DOI:10.1021/ct500169q

Orsi, Mario; Ding, Wei; Palaiokostas, Michail
Direct Mixing of Atomistic Solutes and Coarse-Grained Water
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4684-4693, OCT 2014
abstract, full text, DOI:10.1021/ct500065k

Suarez, Dimas; Diaz, Natalia
Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4718-4729, OCT 2014
abstract, full text, DOI:10.1021/ct500700d

Thomas, James R.; Gedeon, Patrick C.; Madura, Jeffry D.
Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2289-2302, OCT 2014
abstract, full text, DOI:10.1002/prot.24588

Krueger, Susan; Shin, Jae-Ho; Curtis, Joseph E.; Rubinson, Kenneth A.; Kelman, Zvi
The solution structure of full-length dodecameric MCM by SANS and molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2364-2374, OCT 2014
abstract, full text, DOI:10.1002/prot.24598

Fang, Liang; Cho, Hyun Ju; Chan, Christina; Feig, Michael
Binding site multiplicity with fatty acid ligands: Implications for the regulation of PKR kinase autophosphorylation with palmitate
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2429-2442, OCT 2014
abstract, full text, DOI:10.1002/prot.24607

Selwa, Edithe; Tru Huynh; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Therese E.
Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2483-2496, OCT 2014
abstract, full text, DOI:10.1002/prot.24612

Najor, Matthew S.; Olsen, Kenneth W.; Graham, Daniel J.; de Freitas, Duarte Mota
Contribution of each Trp residue toward the intrinsic fluorescence of the G(i alpha 1) protein
PROTEIN SCIENCE, 23:1392-1402, OCT 2014
abstract, full text, DOI:10.1002/pro.2523

Valenzuela, Claudio; Ramos, Patricio; Carrasco, Cristian; Alejandra Moya-Leon, Maria; Herrera, Raul
Cloning and characterization of a xyloglucan endo-transglycosylase/hydrolase gene expressed in response to inclination in radiata pine seedlings
TREE GENETICS & GENOMES, 10:1305-1315, OCT 2014
abstract, full text, DOI:10.1007/s11295-014-0762-9

Barra, Pabla A.; Barraza, Luis F.; Jimenez, Veronica A.; Gavin, Jose A.; Alderete, Joel B.
Drug-dendrimer supramolecular complexation studied from molecular dynamics simulations and NMR spectroscopy
STRUCTURAL CHEMISTRY, 25:1443-1455, OCT 2014
abstract, full text, DOI:10.1007/s11224-014-0424-4

Omidvar, Ramin; Tafazzoli-Shadpour, Mohammad; Rostami, Mostafa; Abolfathi, Nabi
Cancer Mutation Alters Mechanical Stiffness of Epithelial Cadherin Domains: A Molecular Dynamics Study
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:2228-2236, OCT 2014
abstract, full text, DOI:10.1166/jctn.2014.3631

Zhuang, Xiaohong; Makover, Judah R.; Im, Wonpil; Klauda, Jeffery B.
A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:2520-2529, OCT 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.06.010

Lockhart, Christopher; Klimov, Dmitri K.
Binding of A beta peptide creates lipid density depression in DMPC bilayer
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:2678-2688, OCT 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.07.010

Breitwieser, Romain; Hu, Yu-Cheng; Chao, Yen Cheng; Li, Ren-Jie; Tzeng, Yi Ren; Li, Lain-Jong; Liou, Sz-Chian; Lin, Keng Ching; Chen, Chih Wei; Pai, Woei Wu
Flipping nanoscale ripples of free-standing graphene using a scanning tunneling microscope tip
CARBON, 77:236-243, OCT 2014
abstract, full text, DOI:10.1016/j.carbon.2014.05.026

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Fast and efficient optimization of Molecular Dynamics force fields for microporous materials: Bonded interactions via force matching
MICROPOROUS AND MESOPOROUS MATERIALS, 197:339-347, OCT 2014
abstract, full text, DOI:10.1016/j.micromeso.2014.06.023

Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto
Petascale molecular dynamics simulation using the fast multipole method on K computer
COMPUTER PHYSICS COMMUNICATIONS, 185:2575-2585, OCT 2014
abstract, full text, DOI:10.1016/j.cpc.2014.06.004

Iacovelli, Federico; Alves, Cassio; Falconi, Mattia; Oteri, Francesco; de Oliveira, Cristiano L. P.; Desideri, Alessandro
Influence of the Single-Strand Linker Composition on the Structural/Dynamical Properties of a Truncated Octahedral DNA Nano-Cage Family
BIOPOLYMERS, 101:992-999, OCT 2014
abstract, full text, DOI:10.1002/bip.22475

Ghosh, Saikat; Ghosh, Dhiman; Ranganathan, Srivastav; Anoop, A.; Kumar, Santosh P.; Jha, Narendra Nath; Padinhateeri, Ranjith; Maji, Samir K.
Investigating the Intrinsic Aggregation Potential of Evolutionarily Conserved Segments in p53
BIOCHEMISTRY, 53:5995-6010, SEP 30 2014
abstract, full text, DOI:10.1021/bi500825d

Zerbetto, Mirco; Piserchia, Andrea; Frezzato, Diego
Looking for Some Free Energy? Call JEFREE (...)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1865-1881, SEP 30 2014
abstract, full text, DOI:10.1002/jcc.23701

Walavalkar, Ninad M.; Cramer, Jason M.; Buchwald, William A.; Scarsdale, J. Neel; Williams, David C., Jr.
Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for (m)CpG/TpG mismatches
NUCLEIC ACIDS RESEARCH, 42:11218-11232, SEP 29 2014
abstract, full text, DOI:10.1093/nar/gku782

Samson, Andre L.; Knaupp, Anja S.; Kass, Itamar; Kleifeld, Oded; Marijanovic, Emilia M.; Hughes, Victoria A.; Lupton, Chris J.; Buckle, Ashley M.; Bottomley, Stephen P.; Medcalf, Robert L.
Oxidation of an Exposed Methionine Instigates the Aggregation of Glyceraldehyde-3-phosphate Dehydrogenase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:26922-26936, SEP 26 2014
abstract, full text, DOI:10.1074/jbc.M114.570275

Wolff, Philippe; Amal, Ismail; Olieric, Vincent; Chaloin, Olivier; Gygli, Gudrun; Ennifar, Eric; Lorber, Bernard; Guichard, Gilles; Wagner, Jerome; Dejaegere, Annick; Burnouf, Dominique Y.
Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins
JOURNAL OF MEDICINAL CHEMISTRY, 57:7565-7576, SEP 25 2014
abstract, full text, DOI:10.1021/jm500467a

Taranova, Maryna; Hirsh, Andrew D.; Perkins, Noel C.; Andricioaei, Ioan
Role of Microscopic Flexibility in Tightly Curved DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11028-11036, SEP 25 2014
abstract, full text, DOI:10.1021/jp503233u

Fitzpatrick, Jeremy M.; Pellegrini, Maria; Cushing, Patrick R.; Mierke, Dale F.
Small Molecule Inhibition of the Na+/H+ Exchange Regulatory Factor 1 and Parathyroid Hormone 1 Receptor Interaction
BIOCHEMISTRY, 53:5916-5922, SEP 23 2014
abstract, full text, DOI:10.1021/bi500368k

Paasche, Alexander; Zipper, Andreas; Schaefer, Simon; Ziebuhr, John; Schirmeister, Tanja; Engels, Bernd
Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease
BIOCHEMISTRY, 53:5930-5946, SEP 23 2014
abstract, full text, DOI:10.1021/bi400604t

Sun, Xiaotian; Feng, Zhiwei; Zhang, Liling; Hou, Tingjun; Li, Youyong
The Selective Interaction between Silica Nanoparticles and Enzymes from Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e107696, SEP 22 2014
abstract, full text, DOI:10.1371/journal.pone.0107696

Caboni, Pierluigi; Liori, Barbara; Kumar, Amit; Santoru, Maria Laura; Asthana, Shailendra; Pieroni, Enrico; Fais, Antonella; Era, Benedetta; Cacace, Enrico; Ruggiero, Valeria; Atzori, Luigi
Metabolomics Analysis and Modeling Suggest a Lysophosphocholines-PAF Receptor Interaction in Fibromyalgia
PLOS ONE, 9 Art. No. e107626, SEP 19 2014
abstract, full text, DOI:10.1371/journal.pone.0107626

Eicher, Thomas; Seeger, Markus A.; Anselmi, Claudio; Zhou, Wenchang; Brandstaetter, Lorenz; Verrey, Francois; Diederichs, Kay; Faraldo-Gomez, Jose D.; Pos, Klaas M.
Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
ELIFE, 3 Art. No. e03145, SEP 19 2014
abstract, full text, DOI:10.7554/eLife.03145

Aghtar, Mortaza; Struempfer, Johan; Olbrich, Carsten; Schulten, Klaus; Kleinekathoefer, Ulrich
Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:3131-3137, SEP 18 2014
abstract, full text, TCBG publications, DOI:10.1021/jz501351p

Perisic, Ognjen; Lu, Hui
On the Improvement of Free-Energy Calculation from Steered Molecular Dynamics Simulations Using Adaptive Stochastic Perturbation Protocols
PLOS ONE, 9 Art. No. e101810, SEP 18 2014
abstract, full text, DOI:10.1371/journal.pone.0101810

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald
Exploring Hamiltonian dielectric solvent molecular dynamics
CHEMICAL PHYSICS LETTERS, 612:20-24, SEP 18 2014
abstract, full text, DOI:10.1016/j.cplett.2014.07.070

Yu, Tao; Lee, One-Sun; Schatz, George C.
Molecular Dynamics Simulations and Electronic Excited State Properties of a Self-Assembled Peptide Amphiphile Nanofiber with Metalloporphyrin Arrays
JOURNAL OF PHYSICAL CHEMISTRY A, 118:8553-8562, SEP 18 2014
abstract, full text, DOI:10.1021/jp502459r

Sun, Xianqiang; Agren, Hans; Tu, Yaoquan
Functional Water Molecules in Rhodopsin Activation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10863-10873, SEP 18 2014
abstract, full text, DOI:10.1021/jp505180t

Tidemand, Kasper D.; Schonbeck, Christian; Holm, Rene; Westh, Peter; Peters, Gunther H.
Computational Investigation of Enthalpy-Entropy Compensation in Complexation of Glycoconjugated Bile Salts with beta-Cyclodextrin and Analogs
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10889-10897, SEP 18 2014
abstract, full text, DOI:10.1021/jp506716d

Tang, Zhiye; Zhang, Qiao; Yin, Yadong; Chang, Chia-en A.
Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study
JOURNAL OF PHYSICAL CHEMISTRY C, 118:21589-21598, SEP 18 2014
abstract, full text, DOI:10.1021/jp503319s

Chang, Leifu; Zhang, Ziguo; Yang, Jing; McLaughlin, Stephen H.; Barford, David
Molecular architecture and mechanism of the anaphase-promoting complex
NATURE, 513:388-+, SEP 18 2014
abstract, full text, DOI:10.1038/nature13543

Bai, Qifeng; Shao, Yonghua; Pan, Dabo; Zhang, Yang; Liu, Huanxiang; Yao, Xiaojun
Search for beta(2) Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e107837, SEP 17 2014
abstract, full text, DOI:10.1371/journal.pone.0107837

Cailliez, Fabien; Mueller, Pavel; Gallois, Michael; de la Lande, Aurelien
ATP Binding and Aspartate Protonation Enhance Photoinduced Electron Transfer in Plant Cryptochrome
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:12974-12986, SEP 17 2014
abstract, full text, DOI:10.1021/ja506084f

McCullagh, Martin; Saunders, Marissa G.; Voth, Gregory A.
Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:13053-13058, SEP 17 2014
abstract, full text, DOI:10.1021/ja507169f

Yang, Lee-Wei; Kitao, Akio; Huang, Bang-Chieh; Go, Nobuhiro
Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories
BIOPHYSICAL JOURNAL, 107:1415-1425, SEP 16 2014
abstract, full text, DOI:10.1016/j.bpj.2014.07.049

Guan, Xiangying; Lin, Ping; Knoll, Eric; Chakrabarti, Raj
Mechanism of Inhibition of the Human Sirtuin Enzyme SIRT3 by Nicotinamide: Computational and Experimental Studies
PLOS ONE, 9 Art. No. e107729, SEP 15 2014
abstract, full text, DOI:10.1371/journal.pone.0107729

Suresh, Gorle; Priyakumar, U. Deva
DNA-RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18148-18155, SEP 14 2014
abstract, full text, DOI:10.1039/c4cp02478h

Kim, J. I.; Lee, M.; Baek, I.; Yoon, G.; Na, S.
The mechanical response of hIAPP nanowires based on different bending direction simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18493-18500, SEP 14 2014
abstract, full text, DOI:10.1039/c4cp02494j

Jose, Jaya C.; Chatterjee, Prathit; Sengupta, Neelanjana
Cross Dimerization of Amyloid-beta and alpha Synuclein Proteins in Aqueous Environment: A Molecular Dynamics Simulations Study
PLOS ONE, 9 Art. No. e106883, SEP 11 2014
abstract, full text, DOI:10.1371/journal.pone.0106883

Liu, Zizhao; Du, Hongbo; Wickramasinghe, S. Ranil; Qian, Xianghong
Membrane Surface Engineering for Protein Separations: Experiments and Simulations
LANGMUIR, 30:10651-10660, SEP 9 2014
abstract, full text, DOI:10.1021/la5026119

Boiteux, Celine; Vorobyov, Igor; French, Robert J.; French, Christopher; Yarov-Yarovoy, Vladimir; Allen, Toby W.
Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:13057-13062, SEP 9 2014
abstract, full text, DOI:10.1073/pnas.1408710111

Cabello-Aguilar, S.; Abou Chaaya, A.; Picaud, F.; Bechelany, M.; Pochat-Bohatier, C.; Yesylevskyy, S.; Kraszewski, S.; Bechelany, M. C.; Rossignol, F.; Balanzat, E.; Janot, J. M.; Miele, P.; Dejardin, P.; Balme, S.
Experimental and simulation studies of unusual current blockade induced by translocation of small oxidized PEG through a single nanopore
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:17883-17892, SEP 7 2014
abstract, full text, DOI:10.1039/c4cp01954g

Backus, Keriann M.; Dolan, Michael A.; Barry, Conor S.; Joe, Maju; McPhie, Peter; Boshoff, Helena I. M.; Lowary, Todd L.; Davis, Benjamin G.; Barry, Clifton E., I.I.I.
The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:25041-25053, SEP 5 2014
abstract, full text, DOI:10.1074/jbc.M114.581579

Bravo-Rodriguez, Kenny; Ismail-Ali, Ahmed F.; Klopries, Stephan; Kushnir, Susanna; Ismail, Shehab; Fansa, Eyad K.; Wittinghofer, Alfred; Schulz, Frank; Sanchez-Garcia, Elsa
Predicted Incorporation of Non-native Substrates by a Polyketide Synthase Yields Bioactive Natural Product Derivatives
CHEMBIOCHEM, 15:1991-1997, SEP 5 2014
abstract, full text, DOI:10.1002/cbic.201402206

Laghaei, Rozita; Kowallis, William; Evans, Deborah G.; Coalson, Rob D.
Calculation of Iron Transport through Human H-chain Ferritin
JOURNAL OF PHYSICAL CHEMISTRY A, 118:7442-7453, SEP 4 2014
abstract, full text, DOI:10.1021/jp500198u

Chen, Houyang; Ruckenstein, Eli
Nanomembrane Containing a Nanopore in an Electrolyte Solution: A Molecular Dynamics Approach
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:2979-2982, SEP 4 2014
abstract, full text, DOI:10.1021/jz501502y

Han, Wei; Schulten, Klaus
Fibril Elongation by A beta(17-42): Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:12450-12460, SEP 3 2014
abstract, full text, TCBG publications, DOI:10.1021/ja507002p

Merino, Felipe; Ng, Calista Keow Leng; Veerapandian, Veeramohan; Schoeler, Hans Robert; Jauch, Ralf; Cojocaru, Vlad
Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation
STRUCTURE, 22:1274-1286, SEP 2 2014
abstract, full text, DOI:10.1016/j.str.2014.06.014

Langan, Paul; Sangha, Amandeep K.; Wymore, Troy; Parks, Jerry M.; Yang, Zamin Koo; Hanson, B. Leif; Fisher, Zoe; Mason, Sax A.; Blakeley, Matthew P.; Forsyth, V. Trevor; Glusker, Jenny P.; Carrell, Horace L.; Smith, Jeremy C.; Keen, David A.; Graham, David E.; Kovalevsky, Andrey
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study
STRUCTURE, 22:1287-1300, SEP 2 2014
abstract, full text, DOI:10.1016/j.str.2014.07.002

Wu, Zhe; Schulten, Klaus
Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-induced Conformational Transition
BIOPHYSICAL JOURNAL, 107:1156-1166, SEP 2 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.07.041

Chen, Hong; Zhang, Mingzhen; Yang, Jintao; Zhao, Chao; Hu, Rundong; Chen, Qiang; Chang, Yung; Zheng, Jie
Synthesis and Characterization of Antifouling Poly(N-acryloylaminoethoxyethanol) with Ultralow Protein Adsorption and Cell Attachment
LANGMUIR, 30:10398-10409, SEP 2 2014
abstract, full text, DOI:10.1021/la502136q

Amarouch, Mohamed-Yassine; Kasimova, Marina A.; Tarek, Mounir; Abriel, Hugues
Functional interaction between S1 and S4 segments in voltage-gated sodium channels revealed by human channelopathies
CHANNELS, 8:414-420, SEP-OCT 2014
abstract, full text, DOI:10.4161/19336950.2014.958922

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Functionalized graphene as a nanostructured membrane for removal of copper and mercury from aqueous solution: A molecular dynamics simulation study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 53:112-117, SEP 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.07.013

Guo, W.; Liu, R.; Bhardwaj, G.; Yang, J. C.; Changou, C.; Ma, A.-.H.; Mazloom, A.; Chintapalli, S.; Xiao, K.; Xiao, W.; Kumaresan, P.; Sanchez, E.; Yeh, C.-.T.; Evans, C. P.; Patterson, R.; Lam, K. S.; Kung, H.-.J.
Targeting Btk/Etk of prostate cancer cells by a novel dual inhibitor
CELL DEATH & DISEASE, 5, SEP 2014
abstract, full text, DOI:10.1038/cddis.2014.343

Secrier, Maria; Schneider, Reinhard
Visualizing time-related data in biology, a review
BRIEFINGS IN BIOINFORMATICS, 15:771-782, SEP 2014
abstract, full text, DOI:10.1093/bib/bbt021

Yasaei, Poya; Kumar, Bijandra; Hantehzadeh, Reza; Kayyalha, Morteza; Baskin, Artem; Repnin, Nikita; Wang, Canhui; Klie, Robert F.; Chen, Yong P.; Kral, Petr; Salehi-Khojin, Amin
Chemical sensing with switchable transport channels in graphene grain boundaries
NATURE COMMUNICATIONS, 5 Art. No. 4911, SEP 2014
abstract, full text, DOI:10.1038/ncomms5911

Takahashi, Nobuaki; Hamada-Nakahara, Sayaka; Itoh, Yuzuru; Takemura, Kazuhiro; Shimada, Atsushi; Ueda, Yoshifumi; Kitamata, Manabu; Matsuoka, Rei; Hanawa-Suetsugu, Kyoko; Senju, Yosuke; Mori, Masayuki X.; Kiyonaka, Shigeki; Kohda, Daisuke; Kitao, Akio; Mori, Yasuo; Suetsugu, Shiro
TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P-2
NATURE COMMUNICATIONS, 5 Art. No. 4994, SEP 2014
abstract, full text, DOI:10.1038/ncomms5994

Cornejo, Isabel; Andrini, Olga; Isabel Niemeyer, Maria; Maraboli, Vanessa; Danilo Gonzalez-Nilo, F.; Teulon, Jacques; Sepulveda, Francisco V.; Pablo Cid, L.
Identification and Functional Expression of a Glutamate and Avermectin-Gated Chloride Channel from Caligus rogercresseyi, a Southern Hemisphere Sea Louse Affecting Farmed Fish
PLOS PATHOGENS, 10 Art. No. e1004402, SEP 2014
abstract, full text, DOI:10.1371/journal.ppat.1004402

Gao Wen-Xiu; Wang Hong-Lei; Li Shen-Min
Molecular Dynamics Simulation Study of Structural and Transport Properties of Methanol-Water Mixture in Carbon Nanotubes
ACTA PHYSICO-CHIMICA SINICA, 30:1625-1633, SEP 2014
abstract, full text, DOI:10.3866/PKU.WHXB201407031

Serra-Vinardell, Jenny; Diaz, Lucia; Guitierrez-de Teran, Hugo; Sanchez-Olle, Gessarni; Bujons, Jordi; Michelakakis, Helen; Mavridou, Irene; Aerts, Johannes M. F. G.; Delgado, Antonio; Grinberg, Daniel; Vilageliu, Lluisa; Casas, Josefina
Selective chaperone effect of aminocyclitol derivatives on G202R and other mutant glucocerebrosidases causing Gaucher disease
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 54:245-254, SEP 2014
abstract, full text, DOI:10.1016/j.biocel.2014.07.017

Daddam, Jayasimha Rayalu; Dowlathabad, Muralidhara Rao; Panthangi, Seshapani; Jasti, Pramodakumari
Molecular Docking and P-glycoprotein Inhibitory Activity of Flavonoids
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 6:167-175, SEP 2014
abstract, full text, DOI:10.1007/s12539-012-0197-7

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus
xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:2344-2355, SEP 2014
abstract, full text, TCBG publications, DOI:10.1107/S1399004714013856

Feng, Zhiwei; Alqarni, Mohammed Hamed; Yang, Peng; Tong, Qin; Chowdhury, Ananda; Wang, Lirong; Xie, Xiang-Qun
Modeling, Molecular Dynamics Simulation, and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2483-2499, SEP 2014
abstract, full text, DOI:10.1021/ci5002718

Guardiani, Carlo; Di Marino, Daniele; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio
Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3589-3597, SEP 2014
abstract, full text, DOI:10.1021/ct500283s

Huggins, David J.
Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3617-3625, SEP 2014
abstract, full text, DOI:10.1021/ct500415g

Dama, James F.; Rotskoff, Grant; Parrinello, Michele; Voth, Gregory A.
Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3626-3633, SEP 2014
abstract, full text, DOI:10.1021/ct500441q

Komuro, Yasuaki; Re, Suyong; Kobayashi, Chigusa; Muneyuki, Eiro; Sugita, Yuji
CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4133-4142, SEP 2014
abstract, full text, DOI:10.1021/ct5004143

Milanovsky, Georgy E.; Ptushenko, Vasily V.; Golbeck, John H.; Semenov, Alexey Yu.; Cherepanov, Dmitry A.
Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A(0)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1472-1483, SEP 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.03.001

Chu, Brian K.; Fu, Iris W.; Markegard, Cade B.; Choi, Seong E.; Nguyen, Hung D.
A Tail of Two Peptide Amphiphiles: Effect of Conjugation with Hydrophobic Polymer on Folding of Peptide Sequences
BIOMACROMOLECULES, 15:3313-3320, SEP 2014
abstract, full text, DOI:10.1021/bm500733h

Gao, Yi; Olsen, Kenneth W.
Unique Mechanism of Facile Polymorphic Conversion of Acetaminophen in Aqueous Medium
MOLECULAR PHARMACEUTICS, 11:3056-3067, SEP 2014
abstract, full text, DOI:10.1021/mp500251w

Alberto Batista-Garcia, Ramon; Sanchez-Reyes, Ayixon; Millan-Pacheco, Cesar; Manuel Gonzalez-Zuniga, Victor; Juarez, Soledad; Luis Folch-Mallol, Jorge; Pastor, Nina
A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1756-1764, SEP 2014
abstract, full text, DOI:10.1002/prot.24529

Varol, Onur; Yuret, Deniz; Erman, Burak; Kabakcioglu, Alkan
Mode coupling points to functionally important residues in myosin II
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1777-1786, SEP 2014
abstract, full text, DOI:10.1002/prot.24531

Joseph, Dmitri D. A.; Jiao, Wanting; Kessans, Sarah A.; Parker, Emily J.
Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N-acetylneuraminic acid synthase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2054-2066, SEP 2014
abstract, full text, DOI:10.1002/prot.24558

Sharp, Kim A.; Kasinath, Vignesh; Wand, A. Joshua
Banding of NMR-derived methyl order parameters: Implications for protein dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2106-2117, SEP 2014
abstract, full text, DOI:10.1002/prot.24566

Legare, Sebastien; Lagguee, Patrick
The influenza fusion peptide promotes lipid polar head intrusion through hydrogen bonding withphosphates and N-terminal membrane insertion depth
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2118-2127, SEP 2014
abstract, full text, DOI:10.1002/prot.24568

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Multiple conformational states and gate opening of outer membrane protein ToIC revealed by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2169-2179, SEP 2014
abstract, full text, DOI:10.1002/prot.24573

Fataftah, Hiba; Karain, Wael
Detecting protein atom correlations using correlation of probability of recurrence
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2180-2189, SEP 2014
abstract, full text, DOI:10.1002/prot.24574

Kanodia, Shivani; Kumar, Gautam; Rizzi, Luca; Pedretti, Alessandro; Hodder, Anthony N.; Romeo, Sergio; Malhotra, Pawan
Synthetic peptides derived from the C-terminal 6 kDa region of Plasmodium falciparum SERA5 inhibit the enzyme activity and malaria parasite development
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:2765-2775, SEP 2014
abstract, full text, DOI:10.1016/j.bbagen.2014.04.013

Friedrichs, Wenke; Langel, Walter
Atomistic modeling of peptide adsorption on rutile (100) in the presence of water and of contamination by low molecular weight alcohols
BIOINTERPHASES, 9 Art. No. 031006, SEP 2014
abstract, full text, DOI:10.1116/1.4883555

Venthur, Herbert; Mutis, Ana; Zhou, Jing-Jiang; Quiroz, Andres
Ligand binding and homology modelling of insect odorant-binding proteins
PHYSIOLOGICAL ENTOMOLOGY, 39:183-198, SEP 2014
abstract, full text, DOI:10.1111/phen.12066

Ding, Yun-Qiao; Chen, Cheng-lung; Gu, Qi-Rui; Fu, Li-Hong
Molecular simulation study of the effects of inorganic anions on the properties of chrome-crosslinked collagen
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 22 Art. No. 065008, SEP 2014
abstract, full text, DOI:10.1088/0965-0393/22/6/065008

Firouzi, M. A. Mahdjour; Pishkenari, H. Nejat; Mahboobi, H.; Meghdari, A.
Manipulation of biomolecules: A molecular dynamics study
CURRENT APPLIED PHYSICS, 14:1216-1227, SEP 2014
abstract, full text, DOI:10.1016/j.cap.2014.06.014

Sedighi, Mina; Mohebbi, Ali
Investigation of nanoparticle aggregation effect on thermal properties of nanofluid by a combined equilibrium and non-equilibrium molecular dynamics simulation
JOURNAL OF MOLECULAR LIQUIDS, 197:14-22, SEP 2014
abstract, full text, DOI:10.1016/j.molliq.2014.04.019

Huang, Yu-ming M.; Kang, Myungshim; Chang, Chia-en A.
Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics
JOURNAL OF MOLECULAR RECOGNITION, 27:537-548, SEP 2014
abstract, full text, DOI:10.1002/jmr.2377

Baul, Upayan; Kuroda, Kenichi; Vemparala, Satyavani
Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 084902, AUG 28 2014
abstract, full text, DOI:10.1063/1.4893440

Hamulakova, Slavka; Janovec, Ladislav; Hrabinova, Martina; Spilovska, Katarina; Korabecny, Jan; Kristian, Pavol; Kuca, Kamil; Imrich, Jan
Synthesis and Biological Evaluation of Novel Tacrine Derivatives and Tacrine-Coumarin Hybrids as Cholinesterase Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 57:7073-7084, AUG 28 2014
abstract, full text, DOI:10.1021/jm5008648

Mino, German; Barriga, Raul; Gutierrez, Gonzalo
Hydrogen Bonds and Heat Diffusion in alpha-Helices: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10025-10034, AUG 28 2014
abstract, full text, DOI:10.1021/jp503420e

Gomez-Castro, Carlos Z.; Vela, Alberto; Quintanar, Liliana; Grande-Aztatzi, Rafael; Mineva, Tzonka; Goursot, Annick
Insights into the Oxygen-Based Ligand of the Low pH Component of the Cu2+-Amyloid-beta Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10052-10064, AUG 28 2014
abstract, full text, DOI:10.1021/jp5047529

Koukos, Panagiotis I.; Glykos, Nicholas M.
Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10076-10084, AUG 28 2014
abstract, full text, DOI:10.1021/jp5046113

Schonbeck, Christian; Westh, Peter; Holm, Rene
Complexation Thermodynamics of Modified Cyclodextrins: Extended Cavities and Distorted Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10120-10129, AUG 28 2014
abstract, full text, DOI:10.1021/jp506001j

Guo, Xiang-Yang; Watermann, Tobias; Sebastiani, Daniel
Local Microphase Separation of a Binary Liquid under Nanoscale Confinement
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10207-10213, AUG 28 2014
abstract, full text, DOI:10.1021/jp505203t

He, Chengzhi; Lamour, Guillaume; Xiao, Adam; Gsponer, Joerg; Li, Hongbin
Mechanically Tightening a Protein Slipknot into a Trefoil Knot
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:11946-11955, AUG 27 2014
abstract, full text, DOI:10.1021/ja503997h

Shi, Mingsong; Zhang, Chunchun; Xie, Yani; Xu, Dingguo
Stereoselective inclusion mechanism of ketoprofen into beta-cyclodextrin: insights from molecular dynamics simulations and free energy calculations
THEORETICAL CHEMISTRY ACCOUNTS, 133 Art. No. 1556, AUG 26 2014
abstract, full text, DOI:10.1007/s00214-014-1556-8

Farimani, A. Barati; Aluru, N. R.; Tajkhorshid, Emad
Thermodynamic insight into spontaneous hydration and rapid water permeation in aquaporins
APPLIED PHYSICS LETTERS, 105 Art. No. 083702, AUG 25 2014
abstract, full text, DOI:10.1063/1.4893782

Teijido, Oscar; Rappaport, Shay M.; Chamberlin, Adam; Noskov, Sergei Y.; Aguilella, Vicente M.; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.
Acidification Asymmetrically Affects Voltage-dependent Anion Channel Implicating the Involvement of Salt Bridges
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23670-23682, AUG 22 2014
abstract, full text, DOI:10.1074/jbc.M114.576314

Keov, Peter; Lopez, Laura; Devine, Shane M.; Valant, Celine; Lane, J. Robert; Scammells, Peter J.; Sexton, Patrick M.; Christopoulos, Arthur
Molecular Mechanisms of Bitopic Ligand Engagement with the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23817-23837, AUG 22 2014
abstract, full text, DOI:10.1074/jbc.M114.582874

Bellucci, Michael A.; Trout, Bernhardt L.
Bezier curve string method for the study of rare events in complex chemical systems
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 074110, AUG 21 2014
abstract, full text, DOI:10.1063/1.4893216

Weiser, Brian P.; Salari, Reza; Eckenhoff, Roderic G.; Brannigan, Grace
Computational Investigation of Cholesterol Binding Sites on Mitochondrial VDAC
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9852-9860, AUG 21 2014
abstract, full text, DOI:10.1021/jp504516a

Kubiak-Ossowska, Karina; Mulheran, Paul A.; Nowak, Wieslaw
Fibronectin Module FN(III)9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9900-9908, AUG 21 2014
abstract, full text, DOI:10.1021/jp5020077

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Threading or Tumbling? Insight into the Self-Inclusion Mechanism of an altro-alpha-Cyclodextrin Derivative
JOURNAL OF PHYSICAL CHEMISTRY C, 118:19380-19386, AUG 21 2014
abstract, full text, DOI:10.1021/jp503866q

Calandrini, Vania; Arnesano, Fabio; Galliani, Angela; Nguyen, Trung Hai; Lppoliti, Emiliano; Carloni, Paolo; Natile, Giovanni
Platination of the copper transporter ATP7A involved in anticancer drug resistance
DALTON TRANSACTIONS, 43:12085-12094, AUG 21 2014
abstract, full text, DOI:10.1039/c4dt01339e

Bansode, Sneha B.; Jana, Asis K.; Batkulwar, Kedar B.; Warkad, Shrikant D.; Joshi, Rakesh S.; Sengupta, Neelanjana; Kulkarni, Mahesh J.
Molecular Investigations of Protriptyline as a Multi-Target Directed Ligand in Alzheimer's Disease
PLOS ONE, 9 Art. No. e105196, AUG 20 2014
abstract, full text, DOI:10.1371/journal.pone.0105196

Fuller, Jonathan C.; Martinez, Michael; Wade, Rebecca C.
On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics
PLOS ONE, 9 Art. No. e104778, AUG 20 2014
abstract, full text, DOI:10.1371/journal.pone.0104778

Biswas, Mithun; Burghardt, Irene
Azobenzene Photoisomerization-Induced Destabilization of B-DNA
BIOPHYSICAL JOURNAL, 107:932-940, AUG 19 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.044

Agazzi, Federico M.; Mariano Correa, N.; Rodriguez, Javier
Molecular Dynamics Simulation of Water/BHDC Cationic Reverse Micelles. Structural Characterization, Dynamical Properties, and Influence of Solvent on Intermicellar Interactions
LANGMUIR, 30:9643-9653, AUG 19 2014
abstract, full text, DOI:10.1021/la501964q

Mahdavi, Somayeh; Kuyucak, Serdar
Molecular Dynamics Study of Binding of mu-Conotoxin GIIIA to the Voltage-Gated Sodium Channel Na(v)1.4
PLOS ONE, 9 Art. No. e105300, AUG 18 2014
abstract, full text, DOI:10.1371/journal.pone.0105300

Rui, Xianliang; Mehrbod, Mehrdad; Van Agthoven, Johannes F.; Anand, Saurabh; Xiong, Jian-Ping; Mofrad, Mohammad R. K.; Arnaout, M. Amin
The alpha-Subunit Regulates Stability of the Metal Ion at the Ligand-associated Metal Ion-binding Site in beta(3) Integrins
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23256-23263, AUG 15 2014
abstract, full text, DOI:10.1074/jbc.M114.581470

Tardia, Piero; Stefanachi, Angela; Niso, Mauro; Stolfa, Diana Antonella; Mangiatordi, Giuseppe Felice; Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Carotti, Angelo; Leonetti, Francesco; Perrone, Roberto; Berardi, Francesco; Azzariti, Amalia; Colabufo, Nicola Antonio; Cellamare, Saverio
Trimethoxybenzanilide-Based P-Glycoprotein Modulators: An Interesting Case of Lipophilicity Tuning by Intramolecular Hydrogen Bonding
JOURNAL OF MEDICINAL CHEMISTRY, 57:6403-6418, AUG 14 2014
abstract, full text, DOI:10.1021/jm500697c

Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
Multiple branched adaptive steered molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 064101, AUG 14 2014
abstract, full text, DOI:10.1063/1.4891807

Bernini, Caterina; Arezzini, Elena; Basosi, Riccardo; Sinicropi, Adalgisa
In Silico Spectroscopy of Tryptophan and Tyrosine Radicals Involved in the Long-Range Electron Transfer of Cytochrome c Peroxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9525-9537, AUG 14 2014
abstract, full text, DOI:10.1021/jp5025153

Karandur, Deepti; Wong, Ka-Yiu; Pettitt, B. Montgomery
Solubility and Aggregation of Gly5 in Water
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9565-9572, AUG 14 2014
abstract, full text, DOI:10.1021/jp503358n

Dong, Hao; Klein, Michael L.; Fiorin, Giacomo
Counterion-Assisted Cation Transport in a Biological Calcium Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9668-9676, AUG 14 2014
abstract, full text, DOI:10.1021/jp5059897

Hill, Eric H.; Whitten, David G.; Evans, Deborah G.
Computational Study of Bacterial Membrane Disruption by Cationic Biocides: Structural Basis for Water Pore Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9722-9732, AUG 14 2014
abstract, full text, DOI:10.1021/jp504297s

Tah, Bidisha; Pal, Prabir; Roy, Sourav; Dutta, Debodyuti; Mishra, Sabyashachi; Ghosh, Manash; Talapatra, G. B.
Quantum-mechanical DFT calculation supported Raman spectroscopic study of some amino acids in bovine insulin
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 129:345-351, AUG 14 2014
abstract, full text, DOI:10.1016/j.saa.2014.03.044

Kokhan, Oleksandr; Ponomarenko, Nina; Pokkuluri, P. Raj; Schiffer, Marianne; Tiede, David M.
Multimerization of Solution-State Proteins by Tetrakis(4-sulfonatophenyl)porphyrin
BIOCHEMISTRY, 53:5070-5079, AUG 12 2014
abstract, full text, DOI:10.1021/bi500278g

Shang, Yi; LeRouzic, Valerie; Schneider, Sebastian; Bisignano, Paola; Pasternak, Gavril W.; Filizola, Marta
Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions
BIOCHEMISTRY, 53:5140-5149, AUG 12 2014
abstract, full text, DOI:10.1021/bi5006915

Kramer, Mitchell; Halleran, Daniel; Rahman, Moazur; Iqbal, Mazhar; Anwar, Muhmad Ikram; Sabet, Salwa; Ackad, Edward; Yousef, Mohammad
Comparative Molecular Dynamics Simulation of Hepatitis C Virus NS3/4A Protease (Genotypes 1b, 3a and 4b) Predicts Conformational Instability of the Catalytic Triad in Drug Resistant Strains
PLOS ONE, 9 Art. No. e104425, AUG 11 2014
abstract, full text, DOI:10.1371/journal.pone.0104425

Masiero, Alessandro; Aufiero, Simona; Minervini, Giovanni; Moro, Stefano; Costa, Rodolfo; Tosatto, Silvio C. E.
Evaluation of the steric impact of flavin adenine dinucleotide in Drosophila melanogaster cryptochrome function
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 450:1606-1611, AUG 8 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.07.038

Wang, Yong; Luan, Bin-Quan; Yang, Zhiyu; Zhang, Xinyue; Ritzo, Brandon; Gates, Kent; Gu, Li-Qun
Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore
SCIENTIFIC REPORTS, 4 Art. No. 5883, AUG 8 2014
abstract, full text, DOI:10.1038/srep05883

Zhu, Yuhong; Chen, Shi-Jie
Many-body effect in ion binding to RNA
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 055101, AUG 7 2014
abstract, full text, DOI:10.1063/1.4890656

Jia, Minyue; Yang, Boyun; Li, Zhongyi; Shen, Huiling; Song, Xiaoxiao; Gu, Wei
Computational Analysis of Functional Single Nucleotide Polymorphisms Associated with the CYP11B2 Gene
PLOS ONE, 9 Art. No. e104311, AUG 7 2014
abstract, full text, DOI:10.1371/journal.pone.0104311

Markosyan, Suren; De Biase, Pablo M.; Czapla, Luke; Samoylova, Olga; Singh, Gurpreet; Cuervo, Javier; Tieleman, D. Peter; Noskov, Sergei Yu.
Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore
NANOSCALE, 6:9006-9016, AUG 7 2014
abstract, full text, DOI:10.1039/c3nr06559f

Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto
MDGRAPE-4: a special-purpose computer system formolecular dynamics simulations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 372 Art. No. 20130387, AUG 6 2014
abstract, full text, DOI:10.1098/rsta.2013.0387

Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martinez, Agustin D.; Garcia, Isaac E.; Saez, Juan C.; Zhou, Ruhong
Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure
BIOPHYSICAL JOURNAL, 107:599-612, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.037

Orzechowski, Marek; Li, Xiaochuan (Edward); Fischer, Stefan; Lehman, William
An Atomic Model of the Tropomyosin Cable on F-actin
BIOPHYSICAL JOURNAL, 107:694-699, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.034

Shoura, Massa J.; Ranatunga, R. J. K. Udayana; Harris, Sarah A.; Nielsen, Steven O.; Levene, Stephen D.
Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: A Molecular-Dynamics Study
BIOPHYSICAL JOURNAL, 107:700-710, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.023

Ayoub, Ahmed T.; Craddock, Travis J. A.; Klobukowski, Mariusz; Tuszynski, Jack
Analysis of the Strength of Interfacial Hydrogen Bonds between Tubulin Dimers Using Quantum Theory of Atoms in Molecules
BIOPHYSICAL JOURNAL, 107:740-750, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.047

Manni, Sandro; Mineev, Konstantin S.; Usmanova, Dinara; Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Kirpichnikov, Mikhail P.; Winter, Jonas; Matkovic, Milos; Deupi, Xavier; Arseniev, Alexander S.; Ballmer-Hofer, Kurt
Structural and Functional Characterization of Alternative Transmembrane Domain Conformations in VEGF Receptor 2 Activation
STRUCTURE, 22:1077-1089, AUG 5 2014
abstract, full text, DOI:10.1016/j.str.2014.05.010

Harpole, Tyler J.; Grosman, Claudio
Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E3196-E3205, AUG 5 2014
abstract, full text, DOI:10.1073/pnas.1408950111

Sakuraba, Shun; Matubayasi, Nobuyuki
ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1592-1608, AUG 5 2014
abstract, full text, DOI:10.1002/jcc.23651

Bracke, Nathalie; Wynendaele, Evelien; D'Hondt, Matthias; Haselberg, Rob; Somsen, Govert W.; Pauwels, Ewald; Van de Wiele, Christoph; De Spiegeleer, Bart
Analytical characterization of NOTA-modified somatropins
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 96:1-9, AUG 5 2014
abstract, full text, DOI:10.1016/j.jpba.2014.03.014

Popadic, A.; Walther, J. H.; Koumoutsakos, P.; Praprotnik, M.
Continuum simulations of water flow in carbon nanotube membranes
NEW JOURNAL OF PHYSICS, 16 Art. No. 082001, AUG 4 2014
abstract, full text, DOI:10.1088/1367-2630/16/8/082001

Bairagya, Hridoy R.; Mishra, Deepak K.; Mukhopadhyay, Bishnu P.; Sekar, K.
Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1248-1262, AUG 3 2014
abstract, full text, DOI:10.1080/07391102.2013.812982

Noel, Jeffrey K.; Whitford, Paul Charles
How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function
ISRAEL JOURNAL OF CHEMISTRY, 54:1093-1107, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400018

Leuchter, Jessica D.; Green, Adam T.; Gilyard, Julian; Rambarat, Cecilia G.; Cho, Samuel S.
Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding
ISRAEL JOURNAL OF CHEMISTRY, 54:1152-1164, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400022

Larsson, Per; Pouya, Iman; Lindahl, Erik
From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding
ISRAEL JOURNAL OF CHEMISTRY, 54:1274-1285, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400020

Reboul, Cyril F.; Whisstock, James C.; Dunstone, Michelle A.
A New Model for Pore Formation by Cholesterol-Dependent Cytolysins
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003791, AUG 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003791

Mateo, Lidia; Ullastres, Anna; Gonzalec, Josefa
A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila
PLOS GENETICS, 10 Art. No. e1004560, AUG 2014
abstract, full text, DOI:10.1371/journal.pgen.1004560

Pietra, Francesco
Binding Pockets and Pathways for Dioxygen through the KijD3 N-Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3-Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations
CHEMISTRY & BIODIVERSITY, 11:1151-1162, AUG 2014
abstract, full text, DOI:10.1002/cbdv.201400081

Devi, J. Meena
A simulation study on the thermal and wetting behavior of alkane thiol SAM on gold (111) surface
PROGRESS IN NATURAL SCIENCE-MATERIALS INTERNATIONAL, 24:405-411, AUG 2014
abstract, full text, DOI:10.1016/j.pnsc.2014.06.009

Paracha, Rehan Zafar; Ali, Amjad; Ahmad, Jamil; Hussain, Riaz; Niazi, Umar; Muhammad, Syed Aun
Structural evaluation of BTK and PKC delta mediated phosphorylation of MAL at positions Tyr86 and Tyr106
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 51:22-35, AUG 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.04.001

Albareda, Marta; Pacios, Luis F.; Manyani, Hamid; Rey, Luis; Brito, Belen; Imperial, Juan; Ruiz-Argueeso, Tomas; Palacios, Jose M.
Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:21217-21229, AUG 1 2014
abstract, full text, DOI:10.1074/jbc.M114.577403

Pavsic, Miha; Guncar, Gregor; Djinovic-Carugo, Kristina; Lenarcic, Brigita
Crystal structure and its bearing towards an understanding of key biological functions of EpCAM
NATURE COMMUNICATIONS, 5 Art. No. 4764, AUG 2014
abstract, full text, DOI:10.1038/ncomms5764

Sixto-Lopez, Yudibeth; Gomez-Vidal, Jose A.; Correa-Basurto, Jose
Exploring the Potential binding Sites of Some Known HDAC Inhibitors on Some HDAC8 Conformers by Docking Studies
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, 173:1907-1926, AUG 2014
abstract, full text, DOI:10.1007/s12010-014-0976-1

Roy, Sourav; Basu, Sankar; Datta, Alok K.; Bhattacharyya, Dhananjay; Banerjee, Rahul; Dasgupta, Dipak
Equilibrium unfolding of cyclophilin from Leishmania donovani: Characterization of intermediate states
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 69:353-360, AUG 2014
abstract, full text, DOI:10.1016/j.ijbiomac.2014.05.063

Lote, Asawari R.; Kolhatkar, Vidula R.; Insley, Thomas; Kral, Petr; Kolhatkar, Rohit
Oligospermines and Nucleic Acid Interaction: A Structure Property Relationship Study
ACS MACRO LETTERS, 3:829-833, AUG 2014
abstract, full text, DOI:10.1021/mz500358w

Lauro, G.; Ferruz, N.; Fulle, S.; Harvey, M. J.; Finn, P. W.; De Fabritiis, G.
Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2185-2189, AUG 2014
abstract, full text, DOI:10.1021/ci500309a

Leonis, Georgios; Avramopoulos, Aggelos; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Yurtsever, Mine; Papadopoulos, Manthos G.
Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human kappa-Opioid Receptor Complexes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2294-2308, AUG 2014
abstract, full text, DOI:10.1021/ci5002873

Schmidtke, Peter; Ciantar, Marine; Theret, Isabelle; Ducrott, Pierre
Dynamics of hERG Closure Allow Novel Insights into hERG Blocking by Small Molecules
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2320-2333, AUG 2014
abstract, full text, DOI:10.1021/ci5001373

Li, Hui; Fan, Jianfen F.; Li, Rui; Yu, Yi; Yan, Xiliang L.
Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2370, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2370-x

Librando, Vito; Pappalardo, Matteo
Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase: a molecular dynamics and docking study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2354, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2354-x

Tekpinar, Mustafa; Zheng, Wenjun
Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2381, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2381-7

Wang, Yu; Xi, Lei; Yao, Jie; Yang, Jiao; Du, Lin-Fang
Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2376, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2376-4

Yang, Jintao; Zhang, Mingzhen; Chen, Hong; Chang, Yung; Chen, Zhan; Zheng, Jie
Probing the Structural Dependence of Carbon Space Lengths of Poly(N-hydroxyalkyl acrylamide)-Based Brushes on Antifouling Performance
BIOMACROMOLECULES, 15:2982-2991, AUG 2014
abstract, full text, DOI:10.1021/bm500598a

Busse-Wicher, Marta; Gomes, Thiago C. F.; Tryfona, Theodora; Nikolovski, Nino; Stott, Katherine; Grantham, Nicholas J.; Bolam, David N.; Skaf, Munir S.; Dupree, Paul
The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana
PLANT JOURNAL, 79:492-506, AUG 2014
abstract, full text, DOI:10.1111/tpj.12575

Maffeo, Christopher; Ngo, Thuy T. M.; Ha, Taekjip; Aksimentiev, Aleksei
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2891-2896, AUG 2014
abstract, full text, DOI:10.1021/ct500193u

Dixit, Purushottam D.; Dill, Ken A.
Inferring Microscopic Kinetic Rates from Stationary State Distributions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3002-3005, AUG 2014
abstract, full text, DOI:10.1021/ct5001389

White, Andrew D.; Voth, Gregory A.
Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3023-3030, AUG 2014
abstract, full text, DOI:10.1021/ct500320c

Amodeo, Giuseppe Federico; Scorciapino, Mariano Andrea; Messina, Angela; De Pinto, Vito; Ceccarelli, Matteo
Charged Residues Distribution Modulates Selectivity of the Open State of Human Isoforms of the Voltage Dependent Anion-Selective Channel
PLOS ONE, 9 Art. No. e103879, AUG 1 2014
abstract, full text, DOI:10.1371/journal.pone.0103879

Yang, Shang; Wang, Xi; Cui, Lei; Ding, Xiang; Niu, Lili; Yang, Fuquan; Wang, Chao; Wang, Chih-chen; Lou, Jizhong
Compact Conformations of Human Protein Disulfide Isomerase
PLOS ONE, 9 Art. No. e103472, AUG 1 2014
abstract, full text, DOI:10.1371/journal.pone.0103472

Anderson, Janet S.; Mustafi, Sourajit M.; Hernandez, Griselda; LeMaster, David M.
Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain
BIOPHYSICAL CHEMISTRY, 192:41-48, AUG 2014
abstract, full text, DOI:10.1016/j.bpc.2014.06.004

Collins, Carleton G.; Johnson, Andrew T.; Connell, Richard D.; Nelson, Ruth A.; Murgu, Ivan; Oliver, Allen G.; Smith, Bradley D.
Effect of 1,3-adamantane bridging units within the surrounding macrocycle of squaraine rotaxanes
NEW JOURNAL OF CHEMISTRY, 38:3992-3998, AUG 2014
abstract, full text, DOI:10.1039/c4nj00726c

Manna, Moutusi; Rog, Tomasz; Vattulainen, Ilpo
The challenges of understanding glycolipid functions: An open outlook based on molecular simulations
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1841:1130-1145, AUG 2014
abstract, full text, DOI:10.1016/j.bbalip.2013.12.016

Parasuraman, Ponnusamy; Murugan, Veeramani; Selvin, Jeyasigamani F. A.; Gromiha, M. Michael; Fukui, Kazuhiko; Veluraja, Kasinadar
Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Ac alpha(2-3)Gal: a study by in silico mutations and molecular dynamics simulations
JOURNAL OF MOLECULAR RECOGNITION, 27:482-492, AUG 2014
abstract, full text, DOI:10.1002/jmr.2369

Sela, Hanan; Spiridon, Laurentiu N.; Ashkenazi, Haim; Bhullar, Navreet K.; Brunner, Susanne; Petrescu, Andrei-Jose; Fahima, Tzion; Keller, Beat; Jordan, Tina
Three-Dimensional Modeling and Diversity Analysis Reveals Distinct AVR Recognition Sites and Evolutionary Pathways in Wild and Domesticated Wheat Pm3 R Genes
MOLECULAR PLANT-MICROBE INTERACTIONS, 27:835-845, AUG 2014
abstract, full text, DOI:10.1094/MPMI-01-14-0009-R

Grosse, Wolfgang; Psakis, Georgios; Mertins, Barbara; Reiss, Philipp; Windisch, Dirk; Brademann, Felix; Buerck, Jochen; Ulrich, Anne; Koert, Ulrich; Essen, Lars-Oliver
Structure-Based Engineering of a Minimal Porin Reveals Loop-Independent Channel Closure
BIOCHEMISTRY, 53:4826-4838, JUL 29 2014
abstract, full text, DOI:10.1021/bi500660q

Zhu, Hong; Xiao, Shiyan; Wang, Lei; Liang, Haojun
Communication: Asymmetrical cation movements through G-quadruplex DNA
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 041103, JUL 28 2014
abstract, full text, DOI:10.1063/1.4891218

Yu, H.; Liu, T.; Zhao, Z.; Chen, Y.; Zeng, J.; Liu, S.; Zhu, F.
Mutations in 3 '-long terminal repeat of HERV-W family in chromosome 7 upregulate syncytin-1 expression in urothelial cell carcinoma of the bladder through interacting with c-Myb
ONCOGENE, 33:3947-3958, JUL 24 2014
abstract, full text, DOI:10.1038/onc.2013.366

Rastaedter, Dominique; Biswas, Mithun; Burghardt, Irene
Molecular Dynamics Study of the Controlled Destabilization of an RNA Hairpin Structure by a Covalently Attached Azobenzene Switch
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8478-8488, JUL 24 2014
abstract, full text, DOI:10.1021/jp501399k

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.
Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8559-8565, JUL 24 2014
abstract, full text, DOI:10.1021/jp503956m

Haverkort, Frank; Stradomska, Anna; Knoester, Jasper
First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8877-8890, JUL 24 2014
abstract, full text, DOI:10.1021/jp5049277

Delacour, Herve; Lushchekina, Sofya; Mabboux, Isabelle; Bousquet, Aurore; Ceppa, Franck; Schopfer, Lawrence M.; Lockridge, Oksana; Masson, Patrick
Characterization of a Novel BCHE "Silent'' Allele: Point Mutation (p. Val204Asp) Causes Loss of Activity and Prolonged Apnea with Suxamethonium
PLOS ONE, 9 Art. No. e101552, JUL 23 2014
abstract, full text, DOI:10.1371/journal.pone.0101552

Polak, Andraz; Tarek, Mounir; Tomsic, Matija; Valant, Janez; Ulrih, Natasa Poklar; Jamnik, Andrej; Kramar, Peter; Miklavcic, Damijan
Structural Properties of Archaeal Lipid Bilayers: Small-Angle X-ray Scattering and Molecular Dynamics Simulation Study
LANGMUIR, 30:8308-8315, JUL 22 2014
abstract, full text, DOI:10.1021/la5014208

Rajapaksha, Harinda; Petrovsky, Nikolai
In Silico Structural Homology Modelling and Docking for Assessment of Pandemic Potential of a Novel H7N9 Influenza Virus and Its Ability to Be Neutralized by Existing Anti-Hemagglutinin Antibodies
PLOS ONE, 9 Art. No. e102618, JUL 21 2014
abstract, full text, DOI:10.1371/journal.pone.0102618

Cui, Youtian; Cui, Wenjing; Liu, Zhongmei; Zhou, Li; Kobayashi, Michihiko; Zhou, Zhemin
Improvement of stability of nitrile hydratase via protein fragment swapping
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 450:401-408, JUL 18 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.05.127

Mnpotra, Jagjeet S.; Qiao, Zhuanhong; Cai, Jian; Lynch, Diane L.; Grossfield, Alan; Leioatts, Nicholas; Hurst, Dow P.; Pitman, Michael C.; Song, Zhao-Hui; Reggio, Patricia H.
Structural Basis of G Protein-coupled Receptor-G(i) Protein Interaction FORMATION OF THE CANNABINOID CB2 RECEPTOR-G(i) PROTEIN COMPLEX
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:20259-20272, JUL 18 2014
abstract, full text, DOI:10.1074/jbc.M113.539916

Fogarty, Aoife C.; Laage, Damien
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7715-7729, JUL 17 2014
abstract, full text, DOI:10.1021/jp409805p

Malolepsza, Edyta; Straub, John E.
Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7848-7855, JUL 17 2014
abstract, full text, DOI:10.1021/jp412827s

Yoon, Jeseong; Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D.
Dynamical Transition and Heterogeneous Hydration Dynamics in RNA
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7910-7919, JUL 17 2014
abstract, full text, DOI:10.1021/jp500643u

Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.
Non-Gaussian Lineshapes and Dynamics of Time-Resolved Linear and Nonlinear (Correlation) Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7925-7936, JUL 17 2014
abstract, full text, DOI:10.1021/jp500733s

Chao, Shu-Han; Matthews, Sam S.; Paxman, Ryan; Aksimentiev, Aleksei; Gruebele, Martin; Price, Joshua L.
Two Structural Scenarios for Protein Stabilization by PEG
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8388-8395, JUL 17 2014
abstract, full text, DOI:10.1021/jp502234s

Galan, Jhenny F.; Germany, Edward; Pawlowski, Amanda; Strickland, Lynette; Galinato, Mary Grace I.
Theoretical and Spectroscopic Analysis of N,N '-Diphenylurea and N,N '-Dimethyl-N,N '-diphenylurea Conformations
JOURNAL OF PHYSICAL CHEMISTRY A, 118:5304-5315, JUL 17 2014
abstract, full text, DOI:10.1021/jp503539m

Hilder, Tamsyn A.; Ridone, Pietro; Nakayama, Yoshitaka; Martinac, Boris; Chung, Shin-Ho
Binding of fullerenes and nanotubes to MscL
SCIENTIFIC REPORTS, 4 Art. No. 5609, JUL 17 2014
abstract, full text, DOI:10.1038/srep05609

Schwander, P.; Fung, R.; Ourmazd, A.
Conformations of macromolecules and their complexes from heterogeneous datasets
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 369 Art. No. 20130567, JUL 17 2014
abstract, full text, DOI:10.1098/rstb.2013.0567

Chibani, Siwar; Jacquemin, Denis; Laurent, Adele D.
Modelling solvent effects on the absorption and emission spectra of constrained cyanines with both implicit and explicit QM/EFP models
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:321-327, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.033

Goez, Albrecht; Jacob, Christoph R.; Neugebauer, Johannes
Modeling environment effects on pigment site energies: Frozen density embedding with fully quantum-chemical protein densities
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:347-359, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.02.009

Etienne, Thibaud; Gattuso, Hugo; Monari, Antonio; Assfeld, Xavier
QM/MM modeling of Harmane cation fluorescence spectrum in water solution and interacting with DNA
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:367-372, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.026

Hamed, Elham; Keten, Sinan
Hierarchical Cascades of Instability Govern the Mechanics of Coiled Coils: Helix Unfolding Precedes Coil Unzipping
BIOPHYSICAL JOURNAL, 107:477-484, JUL 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.009

Dewan, Shalaka; Carnevale, Vincenzo; Bankura, Arindam; Eftekhari-Bafrooei, Ali; Fiorin, Giacomo; Klein, Michael L.; Borguet, Eric
Structure of Water at Charged Interfaces: A Molecular Dynamics Study
LANGMUIR, 30:8056-8065, JUL 15 2014
abstract, full text, DOI:10.1021/la5011055

Bossis, Fabrizio; De Grassi, Anna; Palese, Luigi Leonardo; Pierri, Ciro Leonardo
Prediction of high- and low-affinity quinol-analogue-binding sites in the aa(3) and bo(3) terminal oxidases from Bacillus subtilis and Escherichia coli
BIOCHEMICAL JOURNAL, 461:305-314, JUL 15 2014
abstract, full text, DOI:10.1042/BJ20140082

Raczynski, Przemyslaw; Gorny, Krzysztof; Dawid, Aleksander; Gburski, Zygmunt
Delivery of nitric oxide to the interior of mammalian cell by carbon nanotube: MD simulation
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 554:6-10, JUL 15 2014
abstract, full text, DOI:10.1016/j.abb.2014.04.014

Chang, Hsin-Yang; Chou, Chia-Cheng; Hsu, Min-Feng; Wang, Andrew H. J.
Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase from Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:18719-18735, JUL 11 2014
abstract, full text, DOI:10.1074/jbc.M114.575076

Bovigny, Christophe; Degiacomi, Matteo Thomas; Lemmin, Thomas; Dal Peraro, Matteo; Stenta, Marco
Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7457-7466, JUL 10 2014
abstract, full text, DOI:10.1021/jp411786z

Noinaj, Nicholas; Kuszak, Adam J.; Balusek, Curtis; Gumbart, James C.; Buchanan, Susan K.
Lateral Opening and Exit Pore Formation Are Required for BamA Function
STRUCTURE, 22:1055-1062, JUL 8 2014
abstract, full text, DOI:10.1016/j.str.2014.05.008

Fu, Iris W.; Markegard, Cade B.; Chu, Brian K.; Nguyen, Hung D.
Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations
LANGMUIR, 30:7745-7754, JUL 8 2014
abstract, full text, DOI:10.1021/la5012988

Korotchenko, Vasiliy N.; Saydmohammed, Manush; Vollmer, Laura L.; Bakan, Ahmet; Sheetz, Kyle; Debiec, Karl T.; Greene, Kristina A.; Agliori, Christine S.; Bahar, Ivet; Day, Billy W.; Vogt, Andreas; Tsang, Michael
In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase
CHEMBIOCHEM, 15:1436-1445, JUL 7 2014
abstract, full text, DOI:10.1002/cbic.201402000

Watly, Joanna; Simonoysky, Eyal; Wieczorek, Robert; Barbosa, Nuno; Miller, Yifat; Kozlowski, Henryk
Insight into the Coordination and the Binding Sites of Cu2+ by the Histidyl-6-Tag using Experimental and Computational Tools
INORGANIC CHEMISTRY, 53:6675-6683, JUL 7 2014
abstract, full text, DOI:10.1021/ic500387u

Bae, Jungeun; Nael, Manal A.; Jiang, Lingzhou; Hwang, Patrick TaeJoon; Mahdi, Fakhri; Jun, Ho-Wook; Elshamy, Wael M.; Zhou, Yu-Dong; Murthy, S. Narasimha; Doerksen, Robert J.; Jo, Seongbong
Quinone Propionic Acid- Based Redox- Triggered Polymer Nanoparticles for Drug Delivery: Computational Analysis and In Vitro Evaluation
JOURNAL OF APPLIED POLYMER SCIENCE, 131 Art. No. 40461, JUL 5 2014
abstract, full text, DOI:10.1002/app.40461

Luan, Binquan; Wang, Chao; Royyuru, Ajay; Stolovitzky, Gustavo
Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages
NANOTECHNOLOGY, 25 Art. No. 265101, JUL 4 2014
abstract, full text, DOI:10.1088/0957-4484/25/26/265101

Zhang, Liqun; Centa, Thomas; Buck, Matthias
Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7302-7311, JUL 3 2014
abstract, full text, DOI:10.1021/jp503668k

Gillman, Alan L.; Jang, Hyunbum; Lee, Joon; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Arce, Fernando Teran
Activity and Architecture of Pyroglutamate-Modified Amyloid-beta (A beta(pE3-42)) Pores
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7335-7344, JUL 3 2014
abstract, full text, DOI:10.1021/jp5040954

Shi, Wei; Thompson, Robert L.; Albenze, Erik; Steckel, Janice A.; Nulwala, Hunaid B.; Luebke, David R.
Contribution of the Acetate Anion to CO2 Solubility in Ionic Liquids: Theoretical Method Development and Experimental Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7383-7394, JUL 3 2014
abstract, full text, DOI:10.1021/jp502425a

Mukhametov, Azat; Newhouse, E. Irene; Ab Aziz, Nurohaida; Saito, Jennifer A.; Alam, Maqsudul
Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 52:103-113, JUL 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.06.008

Lisse, Thomas S.; Vadivel, Kanagasabai; Bajaj, S. Paul; Zhou, Rui; Chun, Rene F.; Hewison, Martin; Adams, John S.
The heterodimeric structure of heterogeneous nuclear ribonucleoprotein C1/C2 dictates 1,25-dihydroxyvitamin D-directed transcriptional events in osteoblasts
BONE RESEARCH, 2 Art. No. 14011, JUL 1 2014
abstract, full text, DOI:10.1038/boneres.2014.11

Modak, Brenda; Torres, Paulina; Mascayano, Carolina; Torres, Rene; Urzua, Alejandro; Valenzuela, Beatriz
Derivatives of 3H-spiro1-benzofuran-2, 1'-cyclohexanes: immunostimulants for veterinary use
BOLETIN LATINOAMERICANO Y DEL CARIBE DE PLANTAS MEDICINALES Y AROMATICAS, 13:375-380, JUL 2014
abstract, full text

Cardone, Giovanni; Moyer, Adam L.; Cheng, Naiqian; Thompson, Cynthia D.; Dvoretzky, Israel; Lowy, Douglas R.; Schiller, John T.; Steven, Alasdair C.; Buck, Christopher B.; Trus, Benes L.
Maturation of the Human Papillomavirus 16 Capsid
MBIO, 5 Art. No. e01104-14, JUL-AUG 2014
abstract, full text, DOI:10.1128/mBio.01104-14

Nevidimov, A. V.
Molecular dynamics simulation of reverse micelles: Standing problems after 25 years of research
RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B, 8:554-558, JUL 2014
abstract, full text, DOI:10.1134/S199079311404023X

Perez, Camilo; Faust, Belinda; Mehdipour, Ahmad Reza; Francesconi, Kevin A.; Forrest, Lucy R.; Ziegler, Christine
Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling
NATURE COMMUNICATIONS, 5 Art. No. 4231, JUL 2014
abstract, full text, DOI:10.1038/ncomms5231

Ricci, Maria; Spijker, Peter; Voitchovsky, Kislon
Water-induced correlation between single ions imaged at the solid-liquid interface
NATURE COMMUNICATIONS, 5 Art. No. 4400, JUL 2014
abstract, full text, DOI:10.1038/ncomms5400

Farelli, Jeremiah D.; Galvin, Brendan D.; Li, Zhiru; Liu, Chunliang; Aono, Miyuki; Garland, Megan; Hallett, Olivia E.; Causey, Thomas B.; Ali-Reynolds, Alana; Saltzberg, Daniel J.; Carlow, Clotilde K. S.; Dunaway-Mariano, Debra; Allen, Karen N.
Structure of the Trehalose-6-phosphate Phosphatase from Brugia malayi Reveals Key Design Principles for Anthelmintic Drugs
PLOS PATHOGENS, 10 Art. No. e1004245, JUL 2014
abstract, full text, DOI:10.1371/journal.ppat.1004245

Shen, Ning; Fan, Ye; Pamidighantam, Sudhakar
E-science infrastructures for molecular modeling and parametrization
JOURNAL OF COMPUTATIONAL SCIENCE, 5:576-589, JUL 2014
abstract, full text, DOI:10.1016/j.jocs.2014.01.005

Kossmann, Bradley; Ivanov, Ivaylo
Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003704, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003704

Lonsdale, Richard; Rouse, Sarah L.; Sansom, Mark S. P.; Mulholland, Adrian J.
A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003714, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003714

Sun, Huiyong; Li, Youyong; Tian, Sheng; Wang, Junmei; Hou, Tingjun
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003729, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003729

Chen, Rong; Chung, Shin-Ho
Binding Modes of Two Scorpion Toxins to the Voltage-Gated Potassium Channel Kv1.3 Revealed from Molecular Dynamics
TOXINS, 6:2149-2161, JUL 2014
abstract, full text, DOI:10.3390/toxins6072149

Mukherjee, Sanchita; Kundu, Sangeeta; Bhattacharyya, Dhananjay
Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:735-749, JUL 2014
abstract, full text, DOI:10.1007/s10822-014-9755-x

Kumari, Rashmi; Kumar, Rajendra; Lynn, Andrew
g_mmpbsa-A GROMACS Tool for High-Throughput MM-PBSA Calculations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1951-1962, JUL 2014
abstract, full text, DOI:10.1021/ci500020m

Campbell, Arthur J.; Lamb, Michelle L.; Joseph-McCarthy, Diane
Ensemble-Based Docking Using Biased Molecular Dynamics
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2127-2138, JUL 2014
abstract, full text, DOI:10.1021/ci400729j

Faginas-Lago, Noelia; Alberti, Margarita; Costantini, Alessandro; Lagana, Antonio; Lombardi, Andrea; Pacifici, Leonardo
An innovative synergistic grid approach to the computational study of protein aggregation mechanisms
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2226, JUL 2014
abstract, full text, DOI:10.1007/s00894-014-2226-4

You, Yong; Liu, Fang; Du, Ke-Jie; Wen, Ge-Bo; Lin, Ying-Wu
Structural and functional alterations of myoglobin by glucose-protein interactions
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2358, JUL 2014
abstract, full text, DOI:10.1007/s00894-014-2358-6

Ye, Jun; Nadar, S. Venkadesh; Li, Jiaojiao; Rosen, Barry P.
Structure of Escherichia coli Grx2 in complex with glutathione: a dual-function hybrid of glutaredoxin and glutathione S-transferase
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:1907-1913, JUL 2014
abstract, full text, DOI:10.1107/S1399004714009250

Taxt, Arne M.; Diaz, Yuleima; Bacle, Amelie; Grauffel, Cedric; Reuter, Nathalie; Aasland, Rein; Sommerfelt, Halvor; Puntervoll, Pal
Characterization of Immunological Cross-Reactivity between Enterotoxigenic Escherichia coli Heat-Stable Toxin and Human Guanylin and Uroguanylin
INFECTION AND IMMUNITY, 82:2913-2922, JUL 2014
abstract, full text, DOI:10.1128/IAI.01749-14

Bucci, Anthony; Abrams, Cameron F.
Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2668-2676, JUL 2014
abstract, full text, DOI:10.1021/ct500088z

Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe
Diffusive Models of Membrane Permeation with Explicit Orientational Freedom
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2710-2718, JUL 2014
abstract, full text, TCBG publications, DOI:10.1021/ct500209j

Ge, Zhenpeng; Li, Quan; Wang, Yi
Free Energy Calculation of Nanodiamond-Membrane Association-The Effect of Shape and Surface Functionalization
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2751-2758, JUL 2014
abstract, full text, DOI:10.1021/ct500194s

Roy, Amitava; Hua, Duy P.; Ward, Joshua M.; Post, Carol Beth
Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2759-2768, JUL 2014
abstract, full text, DOI:10.1021/ct500200n

Procacci, Piero; Cardelli, Chiara
Fast Switching Alchemical Transformations in Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2813-2823, JUL 2014
abstract, full text, DOI:10.1021/ct500142c

Hazel, Anthony; Chipot, Christophe; Gumbart, James C.
Thermodynamics of Deca-alanine Folding in Water
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2836-2844, JUL 2014
abstract, full text, DOI:10.1021/ct5002076

Hansen, Freja H.; Skjorringe, Tina; Yasmeen, Saiqa; Arends, Natascha V.; Sahai, Michelle A.; Erreger, Kevin; Andreassen, Thorvald F.; Holy, Marion; Hamilton, Peter J.; Neergheen, Viruna; Karlsborg, Merete; Newman, Amy H.; Pope, Simon; Heales, Simon J. R.; Friberg, Lars; Law, Ian; Pinborg, Lars H.; Sitte, Harald H.; Loland, Claus; Shi, Lei; Weinstein, Harel; Galli, Aurelio; Hjermind, Lena E.; Moller, Lisbeth B.; Gether, Ulrik
Missense dopamine transporter mutations associate with adult parkinsonism and ADHD
JOURNAL OF CLINICAL INVESTIGATION, 124:3107-3120, JUL 2014
abstract, full text, DOI:10.1172/JCI73778

Pessoa, Joao; Fonseca, Fatima; Furini, Simone; Morais-Cabral, Joao H.
Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel
JOURNAL OF GENERAL PHYSIOLOGY, 144:39-52, JUL 2014
abstract, full text, DOI:10.1085/jgp.201311145

Salomone, Fabrizio; Breton, Marie; Leray, Isabelle; Cardarelli, Francesco; Boccardi, Claudia; Bonhenry, Daniel; Tarek, Mounir; Mir, Lluis M.; Beltram, Fabio
High-Yield Nontoxic Gene Transfer through Conjugation of the CM18-Tat(11) Chimeric Peptide with Nanosecond Electric Pulses
MOLECULAR PHARMACEUTICS, 11:2466-2474, JUL 2014
abstract, full text, DOI:10.1021/mp500223t

Bai, Qifeng; Shen, Yulin; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun
Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:2128-2138, JUL 2014
abstract, full text, DOI:10.1016/j.bbagen.2014.03.010

Arenas, F. A.; Leal, C. A.; Pinto, C. A.; Arenas-Salinas, M. A.; Morales, W. A.; Cornejo, F. A.; Diaz-Vasquez, W. A.; Vasquez, C. C.
On the mechanism underlying tellurite reduction by Aeromonas caviae ST dihydrolipoamide dehydrogenase
BIOCHIMIE, 102:174-182, JUL 2014
abstract, full text, DOI:10.1016/j.biochi.2014.03.008

Vogel, Alexander; Scheidt, Holger A.; Feller, Scott E.; Metso, Jari; Badeau, Robert M.; Tikkanen, Matti J.; Wahala, Kristiina; Jauhiainen, Matti; Huster, Daniel
The Orientation and Dynamics of Estradiol and Estradiol Oleate in Lipid Membranes and HDL Disc Models
BIOPHYSICAL JOURNAL, 107:114-125, JUL 1 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.060

Aitha, Mahesh; Richmond, Timothy K.; Hu, Zhenxin; Hetrick, Alyssa; Reese, Raquel; Gunther, Althea; McCarrick, Robert; Bennett, Brian; Crowder, Michael W.
Dilution of dipolar interactions in a spin-labeled, multimeric metalloenzyme for DEER studies
JOURNAL OF INORGANIC BIOCHEMISTRY, 136:40-46, JUL 2014
abstract, full text, DOI:10.1016/j.jinorgbio.2014.03.010

Jennings, Gareth K.; Modi, Anuja; Elenewski, Justin E.; Ritchie, Caroline M.; Thuy Nguyen; Ellis, Keith C.; Hackett, John C.
Spin equilibrium and O-2-binding kinetics of Mycobacterium tuberculosis CYP51 with mutations in the histidine-threonine dyad
JOURNAL OF INORGANIC BIOCHEMISTRY, 136:81-91, JUL 2014
abstract, full text, DOI:10.1016/j.jinorgbio.2014.03.017

Cui, Di; Ou, Shuching; Patel, Sandeep
Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1453-1468, JUL 2014
abstract, full text, DOI:10.1002/prot.24513

Grunzke, Richard; Breuers, Sebastian; Gesing, Sandra; Herres-Pawlis, Sonja; Kruse, Martin; Blunk, Dirk; de la Garza, Luis; Packschies, Lars; Schaefer, Patrick; Schaerfe, Charlotta; Schlemmer, Tobias; Steinke, Thomas; Schuller, Bernd; Mueller-Pfefferkorn, Ralph; Jaekel, Rene; Nagel, Wolfgang E.; Atkinson, Malcolm; Krueger, Jens
Standards-based metadata management for molecular simulations
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 26:1744-1759, JUL 2014
abstract, full text, DOI:10.1002/cpe.3116

Jackson, Colin J.; Coppin, Christopher W.; Carr, Paul D.; Aleksandrov, Alexey; Wilding, Matthew; Sugrue, Elena; Ubels, Joanna; Paks, Michael; Newman, Janet; Peat, Thomas S.; Russell, Robyn J.; Field, Martin; Weik, Martin; Oakeshott, John G.; Scott, Colin
300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:4003-4011, JUL 2014
abstract, full text, DOI:10.1128/AEM.00916-14

Mueller, Gerald; Benkhai, Hicham; Matthes, Rutger; Finke, Birgit; Friedrichs, Wenke; Geist, Norman; Langel, Walter; Kramer, Axel
Poly (hexamethylene biguanide) adsorption on hydrogen peroxide treated Ti-Al-V alloys and effects on wettability, antimicrobial efficacy, and cytotoxicity
BIOMATERIALS, 35:5261-5277, JUL 2014
abstract, full text, DOI:10.1016/j.biometerials.2014.03.033

Moon, Jun Hyuk; Katha, Anki Reddy; Pandian, Shanthi; Kolake, Subramanya Mayya; Han, Sungsoo
Polyamide-POSS hybrid membranes for seawater desalination: Effect of POSS inclusion on membrane properties
JOURNAL OF MEMBRANE SCIENCE, 461:89-95, JUL 1 2014
abstract, full text, DOI:10.1016/j.memsci.2014.03.004

Wise, Olivia; Coskuner, Orkid
New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1278-1289, JUN 30 2014
abstract, full text, DOI:10.1002/jcc.23622

Panshenskov, Mikhail; Solov'yov, Ilia A.; Solov'yov, Andrey V.
Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1317-1329, JUN 30 2014
abstract, full text, DOI:10.1002/jcc.23613

Xia, Bo; Liu, Yinling; Li, Wei; Brice, Allyn R.; Dominy, Brian N.; Cao, Weiguo
Specificity and Catalytic Mechanism in Family 5 Uracil DNA Glycosylase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:18413-18426, JUN 27 2014
abstract, full text, DOI:10.1074/jbc.M114.567354

Zhang, Mingzhen; Hu, Rundong; Liang, Guizhao; Chang, Yung; Sun, Yan; Peng, Zhenmeng; Zheng, Jie
Structural and Energetic Insight into the Cross-Seeding Amyloid Assemblies of Human IAPP and Rat IAPP
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7026-7036, JUN 26 2014
abstract, full text, DOI:10.1021/jp5022246

Bagai, Sampada; Sun, Chongbo; Tang, Tian
Lipid-Modified Polyethylenimine-Mediated DNA Attraction Evaluated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7070-7076, JUN 26 2014
abstract, full text, DOI:10.1021/jp503381r

Kamath, Ganesh; Cutler, Richard W.; Deshmukh, Sanket A.; Shakourian-Fard, Mehdi; Parrish, Riley; Huether, Joshua; Butt, Darryl P.; Xiong, H.; Sankaranarayanan, Subramanian K. R. S.
In Silico Based Rank-Order Determination and Experiments on Nonaqueous Electrolytes for Sodium Ion Battery Applications
JOURNAL OF PHYSICAL CHEMISTRY C, 118:13406-13416, JUN 26 2014
abstract, full text, DOI:10.1021/jp502319p

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Svedas, Vytas
Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions
PLOS ONE, 9 Art. No. e100643, JUN 24 2014
abstract, full text, DOI:10.1371/journal.pone.0100643

Tossavainen, Helena; Kukkurainen, Sampo; Maatta, Juha A. E.; Kahkonen, Niklas; Pihlajamaa, Tero; Hytonen, Vesa P.; Kulomaa, Markku S.; Permi, Perttu
Chimeric Avidin - NMR Structure and Dynamics of a 56 kDa Homotetrameric Thermostable Protein
PLOS ONE, 9 Art. No. e100564, JUN 24 2014
abstract, full text, DOI:10.1371/journal.pone.0100564

Vitorovic-Todorovic, Maja D.; Koukoulitsa, Catherine; Juranic, Ivan O.; Mandic, Ljuba M.; Drakulic, Branko J.
Structural modifications of 4-aryl-4-oxo-2-aminylbutanamides and their acetyl- and butyrylcholinesterase inhibitory activity. Investigation of AChE-ligand interactions by docking calculations and molecular dynamics simulations
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 81:158-175, JUN 23 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.05.008

Yakubovich, Alexander V.; Solov'yov, Andrey V.
Quantitative thermodynamic model for globular protein folding
EUROPEAN PHYSICAL JOURNAL D, 68 Art. No. 145, JUN 23 2014
abstract, full text, DOI:10.1140/epjd/e2014-50097-3

Moore, Stan G.; Crozier, Paul S.
Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 234112, JUN 21 2014
abstract, full text, DOI:10.1063/1.4883695

Scopelliti, Amanda J.; Heinzelmann, Germano; Kuyucak, Serdar; Ryan, Renae M.; Vandenberg, Robert J.
Na+ Interactions with the Neutral Amino Acid Transporter ASCT1
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:17468-17479, JUN 20 2014
abstract, full text, DOI:10.1074/jbc.M114.565242

Pandolfi, Ronald J.; Edwards, Lauren; Johnston, David; Becich, Peter; Hirst, Linda S.
Designing highly tunable semiflexible filament networks
PHYSICAL REVIEW E, 89 Art. No. 062602, JUN 20 2014
abstract, full text, DOI:10.1103/PhysRevE.89.062602

Goodman, J. S.; Chao, S. -H.; Pogorelov, T. V.; Gruebele, M.
Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding
JOURNAL OF PHYSICAL CHEMISTRY B, 118:6511-6518, JUN 19 2014
abstract, full text, DOI:10.1021/jp412459z

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 118:6742-6757, JUN 19 2014
abstract, full text, DOI:10.1021/jp503469s

Vukovic, Lela; Vokac, Elizabeth; Kral, Petr
Molecular Friction-Induced Electroosmotic Phenomena in Thin Neutral Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:2131-2137, JUN 19 2014
abstract, full text, DOI:10.1021/jz500761s

Rajeshwar, Rajitha T.; Smith, Jeremy C.; Krishnan, Marimuthu
Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:8590-8605, JUN 18 2014
abstract, full text, DOI:10.1021/ja5024783

Knott, Brandon C.; Crowley, Michael F.; Himmel, Michael E.; Stahlberg, Jerry; Beckham, Gregg T.
Carbohydrate-Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:8810-8819, JUN 18 2014
abstract, full text, DOI:10.1021/ja504074g

Sikdar, Samapan; Ghosh, Mahua; De Raychaudhury, Molly; Chakrabarti, J.
Quantum chemical studies on the role of residues in calcium ion binding to Calmodulin
CHEMICAL PHYSICS LETTERS, 605:103-107, JUN 17 2014
abstract, full text, DOI:10.1016/j.cplett.2014.05.017

Heinzelmann, Germano; Kuyucak, Serdar
Molecular Dynamics Simulations Elucidate the Mechanism of Proton Transport in the Glutamate Transporter EAAT3
BIOPHYSICAL JOURNAL, 106:2675-2683, JUN 17 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.010

Mielke, Clinton; Lefort, Natalie; McLean, Carrie G.; Cordova, Jeanine M.; Langlais, Paul R.; Bordner, Andrew J.; Te, Jerez A.; Ozkan, S. Banu; Willis, Wayne T.; Mandarino, Lawrence J.
Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation
BIOCHEMISTRY, 53:3817-3829, JUN 17 2014
abstract, full text, DOI:10.1021/bi401651e

Clingman, Carina C.; Deveau, Laura M.; Hay, Samantha A.; Genga, Ryan M.; Shandilya, Shivender M. D.; Massi, Francesca; Ryder, Sean P.
Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite
ELIFE, 3 Art. No. e02848, JUN 16 2014
abstract, full text, DOI:10.7554/eLife.02848

Sinha, Sudipta K.; Saiz, Leonor
Determinants of protein-ligand complex formation in the thyroid hormone receptor alpha: A molecular dynamics simulation study
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1038:57-66, JUN 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.034

Savelyev, Alexey; MacKerell, Alexander D., Jr.
All- Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1219-1239, JUN 15 2014
abstract, full text, DOI:10.1002/jcc.23611

Anoop, Arunagiri; Ranganathan, Srivastav; Das Dhaked, Bhagwan; Jha, Narendra Nath; Pratihar, Supriya; Ghosh, Saikat; Sahay, Shruti; Kumar, Santosh; Das, Subhadeep; Kombrabail, Mamata; Agarwal, Kumud; Jacob, Reeba S.; Singru, Praful; Bhaumik, Prasenjit; Padinhateeri, Ranjith; Kumar, Ashutosh; Maji, Samir K.
Elucidating the Role of Disulfide Bond on Amyloid Formation and Fibril Reversibility of Somatostatin-14 RELEVANCE TO ITS STORAGE AND SECRETION
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:16884-16903, JUN 13 2014
abstract, full text, DOI:10.1074/jbc.M114.548354

Belorusova, Anna Y.; Eberhardt, Jerome; Potier, Noelle; Stote, Roland H.; Dejaegere, Annick; Rochel, Natacha
Structural Insights into the Molecular Mechanism of Vitamin D Receptor Activation by Lithocholic Acid Involving a New Mode of Ligand Recognition
JOURNAL OF MEDICINAL CHEMISTRY, 57:4710-4719, JUN 12 2014
abstract, full text, DOI:10.1021/jm5002524

Mieda, Shunsuke; Ikeda, Atsushi; Shigeri, Yasushi; Shinoda, Wataru
Thermodynamic Stability of [60]Fullerene and gamma-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 118:12555-12561, JUN 12 2014
abstract, full text, DOI:10.1021/jp5029905

Liu, Peng; Chipot, Christophe; Cai, Wensheng; Shao, Xueguang
Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine
JOURNAL OF PHYSICAL CHEMISTRY C, 118:12562-12567, JUN 12 2014
abstract, full text, DOI:10.1021/jp503241p

Lasso, Gorka; Yu, Linda P. C.; Gil, David; Lazaro, Melisa; Tong, Liang; Valle, Mikel
Functional Conformations for Pyruvate Carboxylase during Catalysis Explored by Cryoelectron Microscopy
STRUCTURE, 22:911-922, JUN 10 2014
abstract, full text, DOI:10.1016/j.str.2014.04.011

Chen, Qu; Wang, Qi; Liu, Ying-Chun; Wu, Tao
The effect of hydrogen bonds on diffusion mechanism of water inside single-walled carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 214507, JUN 7 2014
abstract, full text, DOI:10.1063/1.4879796

Bernardi, Rafael C.; Cann, Isaac; Schulten, Klaus
Molecular dynamics study of enhanced Man5B enzymatic activity
BIOTECHNOLOGY FOR BIOFUELS, 7 Art. No. 83, JUN 5 2014
abstract, full text, TCBG publications, DOI:10.1186/1754-6834-7-83

Mahmood, Mohammed Arif I.; Ali, Waqas; Adnan, Ashfaq; Iqbal, Samir M.
3D Structural Integrity and Interactions of Single-Stranded Protein-Binding DNA in a Functionalized Nanopore
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5799-5806, JUN 5 2014
abstract, full text, DOI:10.1021/jp411820w

Suresh, Gorle; Priyakumar, U. Deva
Atomistic Investigation of the Effect of Incremental Modification of Deoxyribose Sugars by Locked Nucleic Acid (beta-D-LNA and alpha-L-LNA) Moieties on the Structures and Thermodynamics of DNA-RNA Hybrid Duplexes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5853-5863, JUN 5 2014
abstract, full text, DOI:10.1021/jp5014779

Subramanian, Deepa; Klauda, Jeffery B.; Collings, Peter J.; Anisimov, Mikhail A.
Mesoscale Phenomena in Ternary Solutions of Tertiary Butyl Alcohol, Water, and Propylene Oxide
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5994-6006, JUN 5 2014
abstract, full text, DOI:10.1021/jp4125183

Heldenbrand, Hugh; Janowski, Pawel A.; Giambasu, George; Giese, Timothy J.; Wedekind, Joseph E.; York, Darrin M.
Evidence for the Role of Active Site Residues in the Hairpin Ribozyme from Molecular Simulations along the Reaction Path
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:7789-7792, JUN 4 2014
abstract, full text, DOI:10.1021/ja500180q

Barrios, David A.; D'Antonio, Jennifer; McCombs, Nikolette L.; Zhao, Jing; Franzen, Stefan; Schmidt, Andreas C.; Sombers, Leslie A.; Ghiladi, Reza A.
Peroxygenase and Oxidase Activities of Dehaloperoxidase-Hemoglobin from Amphitrite ornata
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:7914-7925, JUN 4 2014
abstract, full text, DOI:10.1021/ja500293c

Watson, Max C.; Curtis, Joseph E.
Probing the Average Local Structure of Biomolecules Using Small-Angle Scattering and Scaling Laws
BIOPHYSICAL JOURNAL, 106:2474-2482, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.050

Sharma, Monika; Predeus, Alexander V.; Kovacs, Nicholas; Feig, Michael
Differential Mismatch Recognition Specificities of Eukaryotic MutS Homologs, MutS alpha and MutS beta
BIOPHYSICAL JOURNAL, 106:2483-2492, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.026

Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun; Widmalm, Goran; Klauda, Jeffery B.; Fleming, Karen G.; Im, Wonpil
E. coli Outer Membrane and Interactions with OmpLA
BIOPHYSICAL JOURNAL, 106:2493-2502, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.024

Chandler, Danielle E.; Struempfer, Johan; Sener, Melih; Scheuring, Simon; Schulten, Klaus
Light Harvesting by Lamellar Chromatophores in Rhodospirillum photometricum
BIOPHYSICAL JOURNAL, 106:2503-2510, JUN 3 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.04.030

Emileh, Ali; Duffy, Caitlin; Holmes, Andrew P.; Bastian, Arangassery Rosemary; Aneja, Rachna; Tuzer, Ferit; Rajagopal, Srivats; Li, Huiyuan; Abrams, Cameron F.; Chaiken, Irwin M.
Covalent Conjugation of a Peptide Triazole to HIV-1 gp120 Enables Intramolecular Binding Site Occupancy
BIOCHEMISTRY, 53:3403-3414, JUN 3 2014
abstract, full text, DOI:10.1021/bi500136f

Vukovic, Lela; Koh, Hye Ran; Myong, Sua; Schulten, Klaus
Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins
BIOCHEMISTRY, 53:3457-3466, JUN 3 2014
abstract, full text, TCBG publications, DOI:10.1021/bi500352s

Rimmert, Bradley; Sabet, Salwa; Ackad, Edward; Yousef, Mohammad S.
A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: implications in catalysis and drug resistivity
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:950-958, JUN 3 2014
abstract, full text, DOI:10.1080/07391102.2013.800001

Negureanu, Lacramioara; Salsbury, Freddie R., Jr.
Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutS alpha-DNA recognition complex
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:969-992, JUN 3 2014
abstract, full text, DOI:10.1080/07391102.2013.799437

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Free energy profiles of ion permeation and doxorubicin translocation in TolC
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 13 Art. No. 1450031, JUN 2014
abstract, full text, DOI:10.1142/S021963361450031X

Blacklock, Kristin; Verkhivker, Gennady M.
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003679, JUN 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003679

Oliveira, Denilson F.; dos Santos Junior, Helvecio M.; Nunes, Alexandro S.; Campos, Vicente P.; de Pinho, Renata S. C.; Gajo, Giovanna C.
Purification and identification of metabolites produced by Bacillus cereus and B. subtilis active against Meloidogyne exigua, and their in silico interaction with a putative phosphoribosyltransferase from M. incognita
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS, 86:525-538, JUN 2014
abstract, full text, DOI:10.1590/0001-3765201402412

Khrenova, Maria G.; Nemukhin, Alexander V.; Grigorenko, Bella L.; Wang, Peng; Zhang, Jian-Ping
All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2287, JUN 2014
abstract, full text, DOI:10.1007/s00894-014-2287-4

Kucukkal, Tugba G.; Yang, Ye; Chapman, Susan C.; Cao, Weiguo; Alexov, Emil
Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 15:9670-9717, JUN 2014
abstract, full text, DOI:10.3390/ijms15069670

Gentili, D.; Bolognesi, G.; Giacomello, A.; Chinappi, M.; Casciola, C. M.
Pressure effects on water slippage over silane-coated rough surfaces: pillars and holes
MICROFLUIDICS AND NANOFLUIDICS, 16:1009-1018, JUN 2014
abstract, full text, DOI:10.1007/s10404-014-1376-0

Ling, Zhenmin; Kang, Zhen; Liu, Yi; Liu, Song; Chen, Jian; Du, Guocheng
Improvement of catalytic efficiency and thermostability of recombinant Streptomyces griseus trypsin by introducing artificial peptide
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, 30:1819-1827, JUN 2014
abstract, full text, DOI:10.1007/s11274-014-1608-1

Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lu, Shou-Qin; Long, Mian
The impact of N-terminal phosphorylation on LHCII conformation in state transition
ACTA MECHANICA SINICA, 30:447-456, JUN 2014
abstract, full text, DOI:10.1007/s10409-014-0044-7

Clark, Richard; Takeda, Kyozaburo
Multistage conformational transition in peptide nanotube induced by temperature and/or external electric field
JAPANESE JOURNAL OF APPLIED PHYSICS, 53 Art. No. 065201, JUN 2014
abstract, full text, DOI:10.7567/JJAP.53.065201

Martinez-Olivan, Juan; Rozado-Aguirre, Zurine; Arias-Moreno, Xabier; Angarica, Vladimir E.; Velazquez-Campoy, Adrian; Sancho, Javier
Low-density lipoprotein receptor is a calcium/magnesium sensor-role of LR4 and LR5 ion interaction kinetics in low-density lipoprotein release in the endosome
FEBS JOURNAL, 281:2638-2658, JUN 2014
abstract, full text, DOI:10.1111/febs.12811

Pietra, Francesco
Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3-Hydroxy-2-methylquinolin-4-one 2,4-Dioxygenase in Association with Its Natural Substrate, 3-Hydroxy-2-methylquinolin-4(1H)-one. A Perspective from Molecular Dynamics Simulations
CHEMISTRY & BIODIVERSITY, 11:861-871, JUN 2014
abstract, full text, DOI:10.1002/cbdv.201400054

de Buyl, Pierre; Colberg, Peter H.; Hoefling, Felix
H5MD: A structured, efficient, and portable file format for molecular data
COMPUTER PHYSICS COMMUNICATIONS, 185:1546-1553, JUN 2014
abstract, full text, DOI:10.1016/j.cpc.2014.01.018

Thibault, Julien C.; Cheatham, Thomas E., I.I.I.; Facelli, Julio C.
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1810-1819, JUN 2014
abstract, full text, DOI:10.1021/ci500173w

Yu Tao; Guo Xu; Zou Xian-Wu; Sang Jian-Ping
Ion Binding Energies Determining Functional Transport of ClC Proteins
CHINESE PHYSICS LETTERS, 31 Art. No. 068701, JUN 2014
abstract, full text, DOI:10.1088/0256-307X/31/6/068701

Jiang, Jianfei; Bakan, Ahmet; Kapralov, Alexandr A.; Silva, K. Ishara; Huang, Zhentai; Amoscato, Andrew A.; Peterson, James; Garapati, Venkata Krishna; Saxena, Sunil; Bayir, Huelya; Atkinson, Jeffrey; Bahar, Ivet; Kagan, Valerian E.
Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids
FREE RADICAL BIOLOGY AND MEDICINE, 71:221-230, JUN 2014
abstract, full text, DOI:10.1016/j.freeradbiomed.2014.02.029

Krueger, Jens; Grunzke, Richard; Gesing, Sandra; Breuers, Sebastian; Brinkmann, Andre; de la Garza, Luis; Kohlbacher, Oliver; Kruse, Martin; Nagel, Wolfgang E.; Packschies, Lars; Mueller-Pfefferkorn, Ralph; Schaefer, Patrick; Schaerfe, Charlotta; Steinke, Thomas; Schlemmer, Tobias; Warzecha, Klaus Dieter; Zink, Andreas; Herres-Pawlis, Sonja
The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2232-2245, JUN 2014
abstract, full text, DOI:10.1021/ct500159h

Azamat, Jafar; Sardroodi, Jaber Jahanbin
The permeation of potassium and chloride ions through nanotubes: a molecular simulation study
MONATSHEFTE FUR CHEMIE, 145:881-890, JUN 2014
abstract, full text, DOI:10.1007/s00706-013-1136-y

Yennamalli, Ragothaman; Arangarasan, Raj; Bryden, Aaron; Gleicher, Michael; Phillips, George N., Jr.
Using a commodity high-definition television for collaborative structural biology
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 47:1153-1157, JUN 2014
abstract, full text, DOI:10.1107/S160057671400939X

Imtong, Chompounoot; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan
Bacillus thuringiensis Cry4Aa insecticidal protein: Functional importance of the intrinsic stability of the unique alpha 4-alpha 5 loop comprising the Pro-rich sequence
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844:1111-1118, JUN 2014
abstract, full text, DOI:10.1016/j.bbapap.2014.03.003

Ortiz, Ernesto; Rendon-Anaya, Martha; Rego, Solange Cristina; Schwartz, Elisabeth Ferroni; Domingos Possani, Lourival
Antarease-like Zn-metalloproteases are ubiquitous in the venom of different scorpion genera
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:1738-1746, JUN 2014
abstract, full text, DOI:10.1016/j.bbagen.2013.12.012

Morrison, Ann Michelle Stanley; Goldstone, Jared V.; Lamb, David C.; Kubota, Akira; Lemaire, Benjamin; Stegeman, John J.
Identification, modeling and ligand affinity of early deuterostome CYP51s, and functional characterization of recombinant zebrafish sterol 14 alpha-demethylase
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:1825-1836, JUN 2014
abstract, full text, DOI:10.1016/j.bbagen.2013.12.009

Abriata, Luciano A.; Vila, Alejandro J.; Dal Peraro, Matteo
Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 19:565-575, JUN 2014
abstract, full text, DOI:10.1007/s00775-014-1108-7

Mutis, A.; Palma, R.; Venthur, H.; Iturriaga-Vasquez, P.; Faundez-Parraguez, M.; Mella-Herrera, R.; Kontodimas, D.; Lobos, C.; Quiroz, A.
Molecular Characterization and In Silico Analysis of the Pheromone-Binding Protein of the European Grapevine Moth Lobesia botrana (Denis & Schiffermuller) (Lepidoptera, Tortricidae)
NEOTROPICAL ENTOMOLOGY, 43:266-275, JUN 2014
abstract, full text, DOI:10.1007/s13744-014-0212-2

Fujita, Takatoshi; Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer C.; Aspuru-Guzik, Alan
Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria
PHOTOSYNTHESIS RESEARCH, 120:273-289, JUN 2014
abstract, full text, DOI:10.1007/s11120-014-9978-7

Sencanski, Milan; Dosen-Micovic, Ljiljana
In Silico Study of the Structurally Similar ORL1 Receptor Agonist and Antagonist Pairs Reveal Possible Mechanism of Receptor Activation
PROTEIN JOURNAL, 33:231-242, JUN 2014
abstract, full text, DOI:10.1007/s10930-014-9555-0

Tsai, Hui-Hsu Gavin; Chang, Che-Ming; Lee, Jian-Bin
Multi-step formation of a hemifusion diaphragm for vesicle fusion revealed by all-atom molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1529-1535, JUN 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.018

Jung, Jaewoon; Mori, Takaharu; Sugita, Yuji
Midpoint Cell Method for Hybrid ( MPI1OpenMP) Parallelization of Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1064-1072, MAY 30 2014
abstract, full text, DOI:10.1002/jcc.23591

Wang, Zunliang; Han, Xiaofeng; He, Nongyue; Chen, Zhan; Brooks, Charles L., I.I.I.
Molecular Structures of C- and N-Terminus Cysteine Modified Cecropin P1 Chemically Immobilized onto Maleimide-Terminated Self-Assembled Mono layers Investigated by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5670-5680, MAY 29 2014
abstract, full text, DOI:10.1021/jp5023482

Lee, Cheng-Kuang; Pao, Chun-Wei
Nanomorphology Evolution of P3HT/PCBM Blends during Solution-Processing from Coarse-Grained Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY C, 118:11224-11233, MAY 29 2014
abstract, full text, DOI:10.1021/jp501323p

Huang, Yu-ming M.; Chang, Chia-en A.
Achieving Peptide Binding Specificity and Promiscuity by Loops: Case of the Forkhead-Associated Domain
PLOS ONE, 9 Art. No. e98291, MAY 28 2014
abstract, full text, DOI:10.1371/journal.pone.0098291

Sun, Xiaotian; Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Mechanism of Graphene Oxide as an Enzyme Inhibitor from Molecular Dynamics Simulations
ACS APPLIED MATERIALS & INTERFACES, 6:7153-7163, MAY 28 2014
abstract, full text, DOI:10.1021/am500167c

Mazack, Michael J. M.; Gao, Jiali
Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 204501, MAY 28 2014
abstract, full text, DOI:10.1063/1.4875922

Zorba, Adelajda; Buosi, Vanessa; Kutter, Steffen; Kern, Nadja; Pontiggia, Francesco; Cho, Young-Jin; Kern, Dorothee
Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2
ELIFE, 3 Art. No. e02667, MAY 27 2014
abstract, full text, DOI:10.7554/eLife.02667

Kumazaki, Kaoru; Chiba, Shinobu; Takemoto, Mizuki; Furukawa, Arata; Nishiyama, Ken-ichi; Sugano, Yasunori; Mori, Takaharu; Dohmae, Naoshi; Hirata, Kunio; Nakada-Nakura, Yoshiko; Maturana, Andres D.; Tanaka, Yoshiki; Mori, Hiroyuki; Sugita, Yuji; Arisaka, Fumio; Ito, Koreaki; Ishitani, Ryuichiro; Tsukazaki, Tomoya; Nureki, Osamu
Structural basis of Sec-independent membrane protein insertion by YidC
NATURE, 509:516-+, MAY 22 2014
abstract, full text, DOI:10.1038/nature13167

Spiga, Enrico; Abriata, Luciano A.; Piazza, Francesco; Dal Peraro, Matteo
Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5310-5321, MAY 22 2014
abstract, full text, DOI:10.1021/jp4126705

Kuttel, Michelle; Gordon, Marc; Ravenscroft, Neil
Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields
CARBOHYDRATE RESEARCH, 390:20-27, MAY 22 2014
abstract, full text, DOI:10.1016/j.carres.2014.02.026

Furini, Simone; Barbini, Paolo; Domene, Carmen
Effects of the Protonation State of the EEEE Motif of a Bacterial Na+-channel on Conduction and Pore Structure
BIOPHYSICAL JOURNAL, 106:2175-2183, MAY 20 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.005

Olivier, Yoann; Muccioli, Luca; Zannoni, Claudio
Quinquephenyl: The Simplest Rigid-Rod-Like Nematic Liquid Crystal, or is it? An Atomistic Simulation
CHEMPHYSCHEM, 15:1345-1355, MAY 19 2014
abstract, full text, DOI:10.1002/cphc.201301126

Pizzirusso, Antonio; Di Pietro, Maria Enrica; De Luca, Giuseppina; Celebre, Giorgio; Longeri, Marcello; Muccioli, Luca; Zannoni, Claudio
Order and Conformation of Biphenyl in Cyanobiphenyl Liquid Crystals: A Combined Atomistic Molecular Dynamics and H-1 NMR Study
CHEMPHYSCHEM, 15:1356-1367, MAY 19 2014
abstract, full text, DOI:10.1002/cphc.201400082

Abad, Enrique; Rommel, Judith B.; Kaestner, Johannes
Reaction Mechanism of the Bicopper Enzyme Peptidylglycine alpha-Hydroxylating Monooxygenase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:13726-13738, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M114.558494

Mahalingam, Bhuvaneshwari; Van Agthoven, Johannes F.; Xiong, Jian-Ping; Alonso, Jose Luis; Adair, Brian D.; Rui, Xianliang; Anand, Saurabh; Mehrbod, Mehrdad; Mofrad, Mohammad R. K.; Burger, Christa; Goodman, Simon L.; Arnaout, M. Amin
Atomic Basis for the Species-specific Inhibition of alpha V Integrins by Monoclonal Antibody 17E6 Is Revealed by the Crystal Structure of alpha V beta 3 Ectodomain-17E6 Fab Complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:13801-13809, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M113.546929

Korneeva, Vera A.; Trubetskov, Mikhail M.; Korshunova, Alena V.; Lushchekina, Sofya V.; Kolyadko, Vladimir N.; Sergienko, Olga V.; Lunin, Vladimir G.; Panteleev, Mikhail A.; Ataullakhanov, Fazoil I.
Interactions Outside the Proteinase-binding Loop Contribute Significantly to the Inhibition of Activated Coagulation Factor XII by Its Canonical Inhibitor from Corn
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:14109-14120, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M114.553735

Casanovas, J.; Revilla-Lopez, G.; Bertran, O.; del Valle, L. J.; Turon, P.; Puiggali, J.; Aleman, C.
Restricted Puckering of Mineralized RNA-Like Riboses
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5075-5081, MAY 15 2014
abstract, full text, DOI:10.1021/jp501714q

Gc, Jeevan B.; Bhandari, Yuba R.; Gerstman, Bernard S.; Chapagain, Prem P.
Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription Factor
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5101-5108, MAY 15 2014
abstract, full text, DOI:10.1021/jp502193v

Hansen, Sara K.; Vestergaard, Mikkel; Thogersen, Lea; Schiott, Birgit; Nielsen, Niels Chr.; Vosegaard, Thomas
Lipid Dynamics Studied by Calculation of P-31 Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5119-5129, MAY 15 2014
abstract, full text, DOI:10.1021/jp5000304

Wang, Kefeng; Leng, Yang; Lu, Xiong; Ren, Fuzeng
Molecular dynamics simulation of protein effects on interfacial energy between HA surfaces and solutions
MATERIALS LETTERS, 123:191-194, MAY 15 2014
abstract, full text, DOI:10.1016/j.matlet.2014.02.089

Zhang, Cunzheng; Wang, Li; Tu, Zhui; Sun, Xing; He, Qinghua; Lei, Zhaojing; Xu, Chongxin; Liu, Yuan; Zhang, Xiao; Yang, Jingyi; Liu, Xianjin; Xu, Yang
Organophosphorus pesticides detection using broad-specific single-stranded DNA based fluorescence polarization aptamer assay
BIOSENSORS & BIOELECTRONICS, 55:216-219, MAY 15 2014
abstract, full text, DOI:10.1016/j.bios.2013.12.020

Tempkin, Jeremy O. B.; Qi, Bo; Saunders, Marissa G.; Roux, Benoit; Dinner, Aaron R.; Weare, Jonathan
Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 184114, MAY 14 2014
abstract, full text, DOI:10.1063/1.4872021

Hu, Rundong; Zhang, Mingzhen; Patel, Kunal; Wang, Qiuming; Chang, Yung; Gong, Xiong; Zhang, Ge; Zheng, Jie
Cross-Sequence Interactions between Human and Rat Islet Amyloid Polypeptides
LANGMUIR, 30:5193-5201, MAY 13 2014
abstract, full text, DOI:10.1021/la500632d

Kaila, Ville R. I.; Wikstrom, Marten; Hummer, Gerhard
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:6988-6993, MAY 13 2014
abstract, full text, DOI:10.1073/pnas.1319156111

Cheng, Dong-Qiang; Li, Ying; Huang, Jing-Fei
Molecular Evolution of the Primate alpha-/theta-Defensin Multigene Family
PLOS ONE, 9 Art. No. e97425, MAY 12 2014
abstract, full text, DOI:10.1371/journal.pone.0097425

Zeytuni, Natalie; Uebe, Rene; Maes, Michal; Davidov, Geula; Baram, Michal; Raschdorf, Oliver; Friedler, Assaf; Miller, Yifat; Schueler, Dirk; Zarivach, Raz
Bacterial Magnetosome Biomineralization - A Novel Platform to Study Molecular Mechanisms of Human CDF-Related Type-II Diabetes
PLOS ONE, 9 Art. No. e97154, MAY 12 2014
abstract, full text, DOI:10.1371/journal.pone.0097154

Nibali, Valeria Conti; D'Angelo, Giovanna; Tarek, Mounir
Molecular dynamics simulation of short-wavelength collective dynamics of phospholipid membranes
PHYSICAL REVIEW E, 89 Art. No. 050301, MAY 12 2014
abstract, full text, DOI:10.1103/PhysRevE.89.050301

Gamble, Trevor; Decker, Karl; Plett, Timothy S.; Pevarnik, Matthew; Pietschmann, Jan-Frederik; Vlassiouk, Ivan; Aksimentiev, Aleksei; Siwy, Zuzanna S.
Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling
JOURNAL OF PHYSICAL CHEMISTRY C, 118:9809-9819, MAY 8 2014
abstract, full text, DOI:10.1021/jp501492g

Midya, Uday Sankar; Bandyopadhyay, Sanjoy
Hydration Behavior at the Ice-Binding Surface of the Tenebrio molitor Antifreeze Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4743-4752, MAY 8 2014
abstract, full text, DOI:10.1021/jp412528b

Nocek, Boguslaw; Starus, Anna; Makowska-Grzyska, Magdalena; Gutierrez, Blanca; Sanchez, Stephen; Jedrzejczak, Robert; Mack, Jamey C.; Olsen, Kenneth W.; Joachimiak, Andrzej; Holz, Richard C.
The Dimerization Domain in DapE Enzymes Is required for Catalysis
PLOS ONE, 9 Art. No. e93593, MAY 7 2014
abstract, full text, DOI:10.1371/journal.pone.0093593

Harrach, Michael F.; Drossel, Barbara
Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 174501, MAY 7 2014
abstract, full text, DOI:10.1063/1.4872239

Ovchinnikov, Victor; Karplus, Martin
Investigations of alpha-helix <->beta-sheet transition pathways in a miniprotein using the finite-temperature string method
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 175103, MAY 7 2014
abstract, full text, DOI:10.1063/1.4871685

Henin, Jerome; Salari, Reza; Murlidaran, Sruthi; Brannigan, Grace
A Predicted Binding Site for Cholesterol on the GABA(A) Receptor
BIOPHYSICAL JOURNAL, 106:1938-1949, MAY 6 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.024

Kumar, Raj; Kukreja, Roshan V.; Li, Li; Zhmurov, Artem; Kononova, Olga; Cai, Shuowei; Ahmed, Syed A.; Barsegov, Valeri; Singh, Bal Ram
Botulinum neurotoxin: unique folding of enzyme domain of the most-poisonous poison
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:804-815, MAY 4 2014
abstract, full text, DOI:10.1080/07391102.2013.791878

Bernini, Caterina; Pogni, Rebecca; Basosi, Riccardo; Sinicropi, Adalgisa
Prediction of hydrogen-bonding networks around tyrosyl radical in P. eryngii versatile peroxidase W164Y variants: a QM/MMMD study
MOLECULAR SIMULATION, 40:485-490, MAY 3 2014
abstract, full text, DOI:10.1080/08927022.2013.822967

Chen, Xin; Zhu, Shuyan; Wang, Shoubin; Yang, Dagang; Zhang, Jinglai
Molecular dynamics study on the stability of wild-type and the R220K mutant of human prion protein
MOLECULAR SIMULATION, 40:504-513, MAY 3 2014
abstract, full text, DOI:10.1080/08927022.2013.824572

Kaczmarski, Joe A.; Corry, Ben
Investigating the size and dynamics of voltage-gated sodium channel fenestrations A molecular dynamics study
CHANNELS, 8, MAY-JUN 2014
abstract, full text, DOI:10.4161/chan.28136

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
Modelling and enhanced molecular dynamics to steer structure-based drug discovery
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 114:123-136, MAY 2014
abstract, full text, DOI:10.1016/j.pbiomolbio.2013.06.004

Zaraiskaya, Tatiana; Vassiliev, Sergey; Bruce, Doug
Discovering oxygen channel topology in photosystem II using implicit ligand sampling and wavefront propagation
JOURNAL OF COMPUTATIONAL SCIENCE, 5:549-555, MAY 2014
abstract, full text, DOI:10.1016/j.jocs.2013.10.001

LeVine, Michael V.; Weinstein, Harel
NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003603, MAY 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003603

Randjelovic, Jelena; Eric, Slavica; Savic, Vladimir
In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 50:100-112, MAY 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.04.002

Asciutto, Eliana K.; Gaborek, Timothy; Madura, Jeffry D.
Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 13 Art. No. 1440004, MAY 2014
abstract, full text, DOI:10.1142/S0219633614400045

Chen, Xinyu; Wehle, Sarah; Kuzmanovic, Natascha; Merget, Benjamin; Holzgrabe, Ulrike; Koenig, Burkhard; Sotriffer, Christoph A.; Decker, Michael
Acetylcholinesterase Inhibitors with Photoswitchable Inhibition of beta-Amyloid Aggregation
ACS CHEMICAL NEUROSCIENCE, 5:377-389, MAY 2014
abstract, full text, DOI:10.1021/cn500016p

Nguyen, Phuong T. V.; Yu, Haibo; Keller, Paul A.
Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2216, MAY 2014
abstract, full text, DOI:10.1007/s00894-014-2216-6

Strom, Alexander M.; Fehling, Samuel C.; Bhattacharyya, Sudeep; Hati, Sanchita
Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations
JOURNAL OF MOLECULAR MODELING, 20, MAY 2014
abstract, full text, DOI:10.1007/s00894-014-2245-1

Lei Dongsheng; Tong Huimin; Zhang Lei; Zhang Xing; Zhang Shengli; Ren Gang
Structure and Function of Cholesteryl Ester Transfer Protein in Transferring Cholesteryl Ester
PROGRESS IN CHEMISTRY, 26:879-888, MAY 2014
abstract, full text, DOI:10.7536/PC131028

Li, Jie; Yang, Lixin; Gaur, Shikha; Zhang, Keqiang; Wu, Xiwei; Yuan, Yate-Ching; Li, Hongzhi; Hu, Shuya; Weng, Yaguang; Yen, Yun
Mutants TP53 p.R273H and p.R273C but not p.R273G Enhance Cancer Cell Malignancy
HUMAN MUTATION, 35:575-584, MAY 2014
abstract, full text, DOI:10.1002/humu.22528

Yang, Lin; da Rocha, Sandro R. P.
PEGylated, NH2-Terminated PAMAM Dendrimers: A Microscopic View from Atomistic Computer Simulations
MOLECULAR PHARMACEUTICS, 11:1459-1470, MAY 2014
abstract, full text, DOI:10.1021/mp400630z

Hall, Benjamin A.; Abd Halim, Khairul Bariyyah; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S. P.
Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2165-2175, MAY 2014
abstract, full text, DOI:10.1021/ct500003g

Dasari, Surendra; Theis, Jason D.; Vrana, Julie A.; Zenka, Roman M.; Zimmermann, Michael T.; Kocher, Jean-Pierre A.; Highsmith, W. Edward, Jr.; Kurtin, Paul J.; Dogan, Ahmet
Clinical Proteome Informatics Workbench Detects Pathogenic Mutations in Hereditary Amyloidoses
JOURNAL OF PROTEOME RESEARCH, 13:2352-2358, MAY 2014
abstract, full text, DOI:10.1021/pr4011475

Nevidimov, A. V.; Razumov, V. F.
The monoatomic solvent model in molecular dynamics study of reverse micelles
HIGH ENERGY CHEMISTRY, 48:202-205, MAY 2014
abstract, full text, DOI:10.1134/S0018143914030084

Geng, Hong-Li; Bian, Mei-Ru; Liu, Yang; Cao, Jiang; Chen, Chong; Wang, Zhi-Yuan; Li, Zhen-Yu; Zeng, Ling-Yu; Wang, Xiao-Yun; Wu, Qing-Yun; Xu, Kai-Lin
The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 66:302-310, MAY 2014
abstract, full text, DOI:10.1016/j.ijbiomac.2014.02.039

Yang, Zhixiu; Guo, Qiang; Goto, Simon; Chen, Yuling; Li, Ningning; Yan, Kaige; Zhang, Yixiao; Muto, Akira; Deng, Haiteng; Himeno, Hyouta; Lei, Jianlin; Gao, Ning
Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence
PROTEIN & CELL, 5:394-407, MAY 2014
abstract, full text, DOI:10.1007/s13238-014-0044-1

Brice, Allyn R.; Lazaridis, Themis
Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4461-4470, MAY 1 2014
abstract, full text, DOI:10.1021/jp409412g

Cui, Di; Ou, Shuching; Peters, Eric; Patel, Sandeep
Ion-Specific Induced Fluctuations and Free Energetics of Aqueous Protein Hydrophobic Interfaces: Toward Connecting to Specific-Ion Behaviors at Aqueous Liquid-Vapor Interfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4490-4504, MAY 1 2014
abstract, full text, DOI:10.1021/jp4105294

Aleksandrov, Alexey; Zvereva, Elena; Field, Martin
The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4505-4513, MAY 1 2014
abstract, full text, DOI:10.1021/jp412346g

Liu, Lan; Jalili, Nobar; Baergen, Alyson; Ng, Simon; Bailey, Justin; Derda, Ratmir; Klassen, John S.
Fluorine Bonding Enhances the Energetics of Protein-Lipid Binding in the Gas Phase
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 25:751-757, MAY 2014
abstract, full text, DOI:10.1007/s13361-014-0837-8

Qu, Tao; Tomar, Vikas
An analysis of the effects of temperature and structural arrangements on the thermal conductivity and thermal diffusivity of tropocollagen-hydroxyapatite interfaces
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 38:28-38, MAY 1 2014
abstract, full text, DOI:10.1016/j.msec.2014.01.039

Kasimova, Marina A.; Tarek, Mounir; Shaytan, Alexey K.; Shaitan, Konstantin V.; Delemotte, Lucie
Voltage-gated ion channel modulation by lipids: Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1322-1331, MAY 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.024

Baker, Michelle K.; Gangupomu, Vamshi K.; Abrams, Cameron F.
Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1396-1405, MAY 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.009

Kiani, F.; Khosravi, T.; Moradi, F.; Rahbari, P.; Aghaei, M. J.; Arabi, M.; Tajik, H.; Kalantarinejad, R.
Computational Investigation of Carbon Nanotubes-Enhanced Membrane for Water Desalination Based on Flux and Rejection Characteristics
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:1237-1243, MAY 2014
abstract, full text, DOI:10.1166/jctn.2014.3488

Hoshyarmanesh, S.; Bahrami, M.; Kalantarinejad, R.
A Multiscale Approach in the Computational Modeling of Bio-Physical Environment of Micro-Mechanical Biosensor Towards the Prostate Specific Antigen Diagnosis
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:1374-1384, MAY 2014
abstract, full text, DOI:10.1166/jctn.2014.3507

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel
A Principal Component Analysis of the Dynamics of Subdomains and Binding Sites in Human Serum Albumin
BIOPOLYMERS, 101:561-572, MAY 2014
abstract, full text, DOI:10.1002/bip.22418

Lee, Myeongsang; Baek, Inchul; Chang, Hyun Joon; Yoon, Gwonchan; Na, Sungsoo
The bond survival time variation of polymorphic amyloid fibrils in the mechanical insight
CHEMICAL PHYSICS LETTERS, 600:68-72, APR 29 2014
abstract, full text, DOI:10.1016/j.cplett.2014.03.043

Xu, Yingzhi; Li, He; Jin, Ying-Hua; Fan, Jun; Sun, Fei
Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate
PLOS ONE, 9 Art. No. e95965, APR 24 2014
abstract, full text, DOI:10.1371/journal.pone.0095965

Mori, Masahiko; Wichukchinda, Nuanjun; Miyahara, Reiko; Rojanawiwat, Archawin; Pathipvanich, Panita; Maekawa, Tomoyuki; Miura, Toshiyuki; Goulder, Philip; Yasunami, Michio; Ariyoshi, Koya; Sawanpanyalert, Pathom
HLA-B(*)35:05 is a protective allele with a unique structure among HIV-1 CRF01_AE-infected Thais, in whom the B(*)57 frequency is low
AIDS, 28:959-967, APR 24 2014
abstract, full text, DOI:10.1097/QAD.0000000000000206

Wu, Emilia L.; Qi, Yifei; Song, Kevin C.; Klauda, Jeffery B.; Im, Wonpil
Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4315-4325, APR 24 2014
abstract, full text, DOI:10.1021/jp500610t

Khrenova, Maria G.; Nemukhin, Alexander V.; Savitsky, Alexander P.
Computational Characterization of Ketone-Ketal Transformations at the Active Site of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4345-4350, APR 24 2014
abstract, full text, DOI:10.1021/jp501674b

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Torsi, Luisa; Lattanzi, Gianluca
Effects of Annealing and Residual Solvents on Amorphous P3HT and PBTTT Films
JOURNAL OF PHYSICAL CHEMISTRY C, 118:8641-8655, APR 24 2014
abstract, full text, DOI:10.1021/jp410936t

Espinoza-Fonseca, L. Michel; Autry, Joseph M.; Thomas, David D.
Microsecond Molecular Dynamics Simulations of Mg2+- and K+- Bound E1 Intermediate States of the Calcium Pump
PLOS ONE, 9 Art. No. e95979, APR 23 2014
abstract, full text, DOI:10.1371/journal.pone.0095979

Zhao, Junjie; de Serrano, Vesna; Franzen, Stefan
A Model for the Flexibility of the Distal Histidine in Dehaloperoxidase-Hemoglobin A Based on X-ray Crystal Structures of the Carbon Monoxide Adduct
BIOCHEMISTRY, 53:2474-2482, APR 22 2014
abstract, full text, DOI:10.1021/bi5001905

Elder, Robert M.; Jayaraman, Arthi
Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 155103, APR 21 2014
abstract, full text, DOI:10.1063/1.4870776

Gongadze, Ekaterina; Velikonja, Aljaz; Perutkova, Sarka; Kramar, Peter; Macek-Lebar, Alenka; Kralj-Iglic, Veronika; Iglic, Ales
Ions and water molecules in an electrolyte solution in contact with charged and dipolar surfaces
ELECTROCHIMICA ACTA, 126:42-60, APR 20 2014
abstract, full text, DOI:10.1016/j.electacta.2013.07.147

Kannam, Sridhar Kumar; Kim, Sung Cheol; Rogers, Priscilla R.; Gunn, Natalie; Wagner, John; Harrer, Stefan; Downton, Matthew T.
Sensing of protein molecules through nanopores: a molecular dynamics study
NANOTECHNOLOGY, 25 Art. No. 155502, APR 18 2014
abstract, full text, DOI:10.1088/0957-4484/25/15/155502

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji
Origin of subdiffusion of water molecules on cell membrane surfaces
SCIENTIFIC REPORTS, 4 Art. No. 4720, APR 17 2014
abstract, full text, DOI:10.1038/srep04720

Wang, Qianqian; Guo, Jingjing; Jiao, Pingzu; Liu, Huanxiang; Yao, Xiaojun
Exploring the Influence of EGCG on the beta-Sheet-Rich Oligomers of Human Islet Amyloid Polypeptide (hIAPP(1-37)) and Identifying Its Possible Binding Sites from Molecular Dynamics Simulation
PLOS ONE, 9 Art. No. e94796, APR 16 2014
abstract, full text, DOI:10.1371/journal.pone.0094796

Spencer, Ryan K.; Li, Hao; Nowick, James S.
X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from A beta(17-36)
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:5595-5598, APR 16 2014
abstract, full text, DOI:10.1021/ja5017409

Masetti, Matteo; Falchi, Federico; Recanatini, Maurizio
Protein Dynamics of the HIF-2 alpha PAS-B Domain upon Heterodimerization and Ligand Binding
PLOS ONE, 9 Art. No. e94986, APR 15 2014
abstract, full text, DOI:10.1371/journal.pone.0094986

Nogueira, Juan J.; Gonzalez, Leticia
Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences
BIOCHEMISTRY, 53:2391-2412, APR 15 2014
abstract, full text, DOI:10.1021/bi500068z

Smith, Natalie E.; Vrielink, Alice; Attwood, Paul V.; Corry, Ben
Binding and Channeling of Alternative Substrates in the Enzyme DmpFG: a Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 106:1681-1690, APR 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.013

Saunders, Marissa G.; Tempkin, Jeremy; Weare, Jonathan; Dinner, Aaron R.; Roux, Benoit; Voth, Gregory A.
Nucleotide Regulation of the Structure and Dynamics of G-Actin
BIOPHYSICAL JOURNAL, 106:1710-1720, APR 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.012

Devi, J. Meena
Aggregation of thiol coated gold nanoparticles: A simulation study on the effect of polymer coverage density and solvent
COMPUTATIONAL MATERIALS SCIENCE, 86:174-179, APR 15 2014
abstract, full text, DOI:10.1016/j.commatsci.2014.01.042

Nakano, Shogo; Okazaki, Seiji; Tokiwa, Hiroaki; Asano, Yasuhisa
Binding of NAD(+) and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:10445-10454, APR 11 2014
abstract, full text, DOI:10.1074/jbc.M113.540773

Zhao, Charles L.; Mahboobi, Seyed Hanif; Moussavi-Baygi, Ruhollah; Mofrad, Mohammad R. K.
The Interaction of CRM1 and the Nuclear Pore Protein Tpr
PLOS ONE, 9 Art. No. e93709, APR 10 2014
abstract, full text, DOI:10.1371/journal.pone.0093709

Garcia-Beltran, Olimpo; Yanez, Osvaldo; Caballero, Julio; Galdamez, Antonio; Mena, Natalia; Nunez, Marco T.; Cassels, Bruce K.
Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 76:79-86, APR 9 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.016

Vestergaard, Anna L.; Coleman, Jonathan A.; Lemmin, Thomas; Mikkelsen, Stine A.; Molday, Laurie L.; Vilsen, Bente; Molday, Robert S.; Dal Peraro, Matteo; Andersen, Jens Peter
Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E1334-E1343, APR 8 2014
abstract, full text, DOI:10.1073/pnas.1321165111

Martin, Hugh S. C.; Jha, Shantenu; Coveney, Peter V.
Comparative Analysis of Nucleotide Translocation through Protein Nanopores Using Steered Molecular Dynamics and an Adaptive Biasing Force
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:692-702, APR 5 2014
abstract, full text, DOI:10.1002/jcc.23525

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei
Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:711-721, APR 5 2014
abstract, full text, DOI:10.1002/jcc.23544

Heinrich, Frank; Nanda, Hirsh; Goh, Haw Zan; Bachert, Collin; Loesche, Mathias; Linstedt, Adam D.
Myristoylation Restricts Orientation of the GRASP Domain on Membranes and Promotes Membrane Tethering*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:9683-9691, APR 4 2014
abstract, full text, DOI:10.1074/jbc.M113.543561

Villali, Janice; Pontiggia, Francesco; Clarkson, Michael W.; Hagan, Michael F.; Kern, Dorothee
Evidence Against the "Y-T Coupling" Mechanism of Activation in the Response Regulator NtrC
JOURNAL OF MOLECULAR BIOLOGY, 426:1554-1567, APR 3 2014
abstract, full text, DOI:10.1016/j.jmb.2013.12.027

Dehez, Francois; Delemotte, Lucie; Kramar, Peter; Miklavcic, Damijan; Tarek, Mounir
Evidence of Conducting Hydrophobic Nanopores Across Membranes in Response to an Electric Field
JOURNAL OF PHYSICAL CHEMISTRY C, 118:6752-6757, APR 3 2014
abstract, full text, DOI:10.1021/jp4114865

Nibali, Valeria Conti; D'Angelo, Giovanna; Paciaroni, Alessandro; Tobias, Douglas J.; Tarek, Mounir
On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:1181-1186, APR 3 2014
abstract, full text, DOI:10.1021/jz500023e

Sachdeva, Ruchi; Singh, Balvinder
Phosphorylation of Ser-180 of rat aquaporin-4 shows marginal affect on regulation of water permeability: molecular dynamics study
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:555-566, APR 3 2014
abstract, full text, DOI:10.1080/07391102.2013.780981

Ying, Tianlei; Ju, Tina W.; Wang, Yanping; Prabakaran, Ponraj; Dimitrov, Dimiter S.
Interactions of IgG1 CH2 and CH3 domains with FcRn
FRONTIERS IN IMMUNOLOGY, 5, APR 2 2014
abstract, full text, DOI:10.3389/fimmu.2014.00146

Rogacheva, Olga N.; Stefanov, Vasiliy E.; Shchegolev, Boris F.; Vershinina, Elena A.; Savvateeva-Popova, Elena V.
Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RI alpha A-domain
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 12 Art. No. 1441005, APR 2014
abstract, full text, DOI:10.1142/S0219720014410054

Hsiao, Ya-Wen; Soderhjelm, Par
Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:443-454, APR 2014
abstract, full text, DOI:10.1007/s10822-014-9724-4

Guardingo, Mireia; Bellido, Elena; Miralles-Lluma, Rosa; Faraudo, Jordi; Sedo, Josep; Tatay, Sergio; Verdaguer, Albert; Busque, Felix; Ruiz-Molina, Daniel
Bioinspired Catechol-Terminated Self-Assembled Monolayers with Enhanced Adhesion Properties
SMALL, 10:1594-1602, APR 2014
abstract, full text, DOI:10.1002/smll.201302406

Meurillon, Maia; Marton, Zsuzsanna; Hospital, Audrey; Jordheim, Lars Petter; Bejaud, Jerome; Lionne, Corinne; Dumontet, Charles; Perigaud, Christian; Chaloin, Laurent; Peyrottes, Suzanne
Structure activity relationships of beta-hydroxyphosphonate nucleoside analogues as cytosolic 5 '-nucleotidase II potential inhibitors: Synthesis, in vitro evaluation and molecular modeling studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 77:18-37, APR 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.055

Vass, Marton; Schmidt, Eva; Horti, Ferenc; Keseru, Gyorgy M.
Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 77:38-46, APR 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.034

Ding, Yun-Qiao; Chen, Cheng-Lung; Gu, Qi-Rui; Liao, Jun-Min; Chuang, Po-Hsiang
Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 22 Art. No. 035007, APR 2014
abstract, full text, DOI:10.1088/0965-0393/22/3/035007

Souza, P. C. T.; Puhl, A. C.; Martinez, L.; Aparicio, R.; Nascimento, A. S.; Figueira, A. C. M.; Nguyen, P.; Webb, P.; Skaf, M. S.; Polikarpov, I.
Identification of a New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor
MOLECULAR ENDOCRINOLOGY, 28:534-545, APR 2014
abstract, full text, DOI:10.1210/me.2013-1359

Wu, Ming; He, Jia; Ren, Xiao; Cai, Wen-Sheng; Fang, Yong-Chun; Feng, Xi-Zeng
Development of functional biointerfaces by surface modification of polydimethylsiloxane with bioactive chlorogenic acid
COLLOIDS AND SURFACES B-BIOINTERFACES, 116:700-706, APR 1 2014
abstract, full text, DOI:10.1016/j.colsurfb.2013.11.010

Roberts, Justine J.; Elder, Robert M.; Neumann, Alexander J.; Jayaraman, Arthi; Bryant, Stephanie J.
Interaction of Hyaluronan Binding Peptides with Glycosaminoglycans in Poly(ethylene glycol) Hydrogels
BIOMACROMOLECULES, 15:1132-1141, APR 2014
abstract, full text, DOI:10.1021/bm401524h

Castro-Fernandez, Victor; Bravo-Moraga, Felipe; Herrera-Morande, Alejandra; Guixe, Victoria
Bifunctional ADP-dependent phosphofructokinase/ glucokinase activity in the order Methanococcales biochemical characterization of the mesophilic enzyme from Methanococcus maripaludis
FEBS JOURNAL, 281:2017-2029, APR 2014
abstract, full text, DOI:10.1111/febs.12757

Ermakova, Elena; Kurbanov, Rauf
Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 49:99-109, APR 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.02.001

Jin Zhao; Liu Jian; Wang Li-Li; Cao Feng-Lei; Sun Huai
Development and Validation of an All-Atom Force Field for the Energetic Materials TATB, RDX and HMX
ACTA PHYSICO-CHIMICA SINICA, 30:654-661, APR 2014
abstract, full text, DOI:10.3866/PKU.WHXB201402113

Cilurzo, Francesco; Vistoli, Giulio; Gennari, Chiara G. M.; Selmin, Francesca; Gardoni, Fabrizio; Franze, Silvia; Campisi, Monica; Minghetti, Paola
The Role of the Conformational Profile of Polysaccharides on Skin Penetration: The Case of Hyaluronan and Its Sulfates
CHEMISTRY & BIODIVERSITY, 11:551-561, APR 2014
abstract, full text, DOI:10.1002/cbdv.201300130

Basile, Livia; Pappalardo, Matteo; Guccione, Salvatore; Milardi, Danilo; Ramsay, Rona R.
Computational Comparison of Imidazoline Association with the 12 Binding Site in Human Monoamine Oxidases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1200-1207, APR 2014
abstract, full text, DOI:10.1021/ci400346k

Li, Minghui; Petukh, Marharyta; Alexov, Emil; Panchenko, Anna R.
Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1770-1780, APR 2014
abstract, full text, DOI:10.1021/ct401022c

Malac, Kamil; Barvik, Ivan
Recognition of 2 ',5 '-linked oligoadenylates by human ribonuclease L: molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2123, APR 2014
abstract, full text, DOI:10.1007/s00894-014-2123-x

Raj, Fredrick Robin Devadoss Victor Paul; Exner, Thomas E.
C-alpha torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2196, APR 2014
abstract, full text, DOI:10.1007/s00894-014-2196-6

Drinkwater, Nyssa; Cossins, Benjamin P.; Keeble, Anthony H.; Wright, Michael; Cain, Katharine; Hailu, Hanna; Oxbrow, Amanda; Delgado, Jean; Shuttleworth, Lindsay K.; Kao, Michael W.-.P.; McDonnell, James M.; Beavil, Andrew J.; Henry, Alistair J.; Sutton, Brian J.
Human immunoglobulin E flexes between acutely bent and extended conformations
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:397-U142, APR 2014
abstract, full text, DOI:10.1038/nsmb.2795

Friedt, Jenna; Leavens, Fern M. V.; Mercier, Evan; Wieden, Hans-Joachim; Kothe, Ute
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation
NUCLEIC ACIDS RESEARCH, 42:3857-3870, APR 2014
abstract, full text, DOI:10.1093/nar/gkt1331

Zhang Xiaoyi; Deng Dongjie; Tan Jianjun; He Yu; Li Chunhua; Wang Cunxin
Pharmacophore and Docking-based 3D-QSAR Studies on HIV-1 Integrase Inhibitors
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 30:297-305, APR 2014
abstract, full text, DOI:10.1007/s40242-014-3395-5

Geng Yi-Zhao; Zhang Hui; Ji Qing; Yan Shi-Wei
Locking Function of a Key Residue in Kinesin's Gating Mechanism
CHINESE PHYSICS LETTERS, 31 Art. No. 048702, APR 2014
abstract, full text, DOI:10.1088/0256-307X/31/4/048702

Holm, Rene; Ostergaard, Jesper; Schonbeck, Christian; Jensen, Henrik; Shi, Wei; Peters, Gunther H.; Westh, Peter
Determination of stability constants of tauro- and glyco-conjugated bile salts with the negatively charged sulfobutylether-beta-cyclodextrin: comparison of affinity capillary electrophoresis and isothermal titration calorimetry and thermodynamic analysis of the interaction
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 78:185-194, APR 2014
abstract, full text, DOI:10.1007/s10847-013-0287-0

Schonbeck, Christian; Holm, Rene; Westh, Peter; Peters, Gunther H.
Extending the hydrophobic cavity of beta-cyclodextrin results in more negative heat capacity changes but reduced binding affinities
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 78:351-361, APR 2014
abstract, full text, DOI:10.1007/s10847-013-0305-2

Karachevtsev, Maksym V.; Gladchenko, Galyna O.; Leontiev, Victor S.; Karachevtsev, Victor A.
Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface
NANOSCALE RESEARCH LETTERS, 9 Art. No. 157, APR 1 2014
abstract, full text, DOI:10.1186/1556-276X-9-157

Politis, Argyris; Stengel, Florian; Hall, Zoe; Hernandez, Helena; Leitner, Alexander; Walzthoeni, Thomas; Robinson, Carol V.; Aebersold, Ruedi
A mass spectrometry-based hybrid method for structural modeling of protein complexes
NATURE METHODS, 11:403-+, APR 2014
abstract, full text, DOI:10.1038/NMETH.2841

Braun, Christian J.; Lachnit, Christine; Becker, Patrick; Henkes, Leonhard M.; Arrigoni, Cristina; Kast, Stefan M.; Moroni, Anna; Thiel, Gerhard; Schroeder, Indra
Viral potassium channels as a robust model system for studies of membrane-protein interaction
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1096-1103, APR 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.06.010

Alekozai, Emal M.; GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Crowley, Michael F.; Smith, Jeremy C.; Cheng, Xiaolin
Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose I beta
CELLULOSE, 21:951-971, APR 2014
abstract, full text, DOI:10.1007/s10570-013-0026-0

Sencanski, Milan; Sukalovic, Vladimir; Shakib, Kaveh; Soskic, Vukic; Dosen-Micovic, Ljiljana; Kostic-Rajacic, Sladjana
Molecular Modeling of 5HT(2A) Receptor - Arylpiperazine Ligands Interactions
CHEMICAL BIOLOGY & DRUG DESIGN, 83:462-471, APR 2014
abstract, full text, DOI:10.1111/cbdd.12261

Wang, Kun; Luo, Huiying; Tian, Jian; Turunen, Ossi; Huang, Huoqing; Shi, Pengjun; Hua, Huifang; Wang, Caihong; Wang, Shuanghe; Yao, Bin
Thermostability Improvement of a Streptomyces Xylanase by Introducing Proline and Glutamic Acid Residues
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:2158-2165, APR 2014
abstract, full text, DOI:10.1128/AEM.03458-13

Warren, Nicholas; Strom, Alexander; Nicolet, Brianna; Albin, Kristine; Albrecht, Joshua; Bausch, Brenna; Dobbe, Megan; Dudek, Megan; Firgens, Samuel; Fritsche, Chad; Gunderson, Anthony; Heimann, Joseph; Her, Cheng; Hurt, Jordan; Konorev, Dmitri; Lively, Matthew; Meacham, Stephanie; Rodriguez, Valentina; Tadayon, Stephanie; Trcka, David; Yang, Yer; Bhattacharyya, Sudeep; Hati, Sanchita
Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases
PROTEIN JOURNAL, 33:184-198, APR 2014
abstract, full text, DOI:10.1007/s10930-014-9548-z

Howard, Rebecca J.; Trudell, James R.; Harris, R. Adron
Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics
PHARMACOLOGICAL REVIEWS, 66:396-412, APR 2014
abstract, full text, DOI:10.1124/pr.113.007468

Simard, Jean; Ammi, Mehdi; Mayeur, Anais
Comparative study of the bimanual and collaborative modes for closely coupled manipulations
INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES, 72:408-421, APR 2014
abstract, full text, DOI:10.1016/j.ijhcs.2013.12.002

Mernea, Maria; Calborean, Octavian; Grigore, Oana; Dascalu, Traian; Mihailescu, Dan Florin
Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures
OPTICAL AND QUANTUM ELECTRONICS, 46:505-514, APR 2014
abstract, full text, DOI:10.1007/s11082-013-9872-0

Ma, Jun
A molecular dynamics study on the nucleation of calcium phosphate regulated by collagen
JOURNAL OF MATERIALS SCIENCE, 49:3099-3106, APR 2014
abstract, full text, DOI:10.1007/s10853-013-8011-4

Jacobitz, Alex W.; Wereszczynski, Jeff; Yi, Sung Wook; Amer, Brendan R.; Huang, Grace L.; Nguyen, Angelyn V.; Sawaya, Michael R.; Jung, Michael E.; McCammon, J. Andrew; Clubb, Robert T.
Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:8891-8902, MAR 28 2014
abstract, full text, DOI:10.1074/jbc.M113.509273

Li, Xiaochuan Edward; Orzechowski, Marek; Lehman, William; Fischer, Stefan
Structure and flexibility of the tropomyosin overlap junction
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 446:304-308, MAR 28 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.02.097

Chen, Rong; Chung, Shin-Ho
Mechanism of tetrodotoxin block and resistance in sodium channels
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 446:370-374, MAR 28 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.02.115

Rashid, M. Harunur; Huq, Redwan; Tanner, Mark R.; Chhabra, Sandeep; Khoo, Keith K.; Estrada, Rosendo; Dhawan, Vikas; Chauhan, Satendra; Pennington, Michael W.; Beeton, Christine; Kuyucak, Serdar; Norton, Raymond S.
A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases
SCIENTIFIC REPORTS, 4 Art. No. 4509, MAR 28 2014
abstract, full text, DOI:10.1038/srep04509

Chen, Rong; Robinson, Anna; Chung, Shin-Ho
Mechanism of mu-Conotoxin PIIIA Binding to the Voltage-Gated Na+ Channel Na(V)1.4
PLOS ONE, 9 Art. No. e93267, MAR 27 2014
abstract, full text, DOI:10.1371/journal.pone.0093267

Yan, Leilei; Yan, Chunli; Qian, Kun; Su, Hairui; Kofsky-Wofford, Stephanie A.; Lee, Wei-Chao; Zhao, Xinyang; Ho, Meng-Chiao; Ivanov, Ivaylo; Zheng, Yujun George
Diamidine Compounds for Selective Inhibition of Protein Arginine Methyltransferase 1
JOURNAL OF MEDICINAL CHEMISTRY, 57:2611-2622, MAR 27 2014
abstract, full text, DOI:10.1021/jm401884z

Mansoorabadi, Steven O.; Wu, Meilan; Tao, Zhihua; Gao, Peng; Pingali, Sai Venkatesh; Guo, Liang; Liu, Hung-wen
Conformational Activation of Poly(ADP-ribose) Polymerase-1 upon DNA Binding Revealed by Small-Angle X-ray Scattering
BIOCHEMISTRY, 53:1779-1788, MAR 25 2014
abstract, full text, DOI:10.1021/bi401439n

Colzani, Mara; Criscuolo, Angela; De Maddis, Danilo; Garzon, Davide; Yeum, Kyung-Jin; Vistoli, Giulio; Carini, Marina; Aldini, Giancarlo
A novel high resolution MS approach for the screening of 4-hydroxy-trans-2-nonenal sequestering agents
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 91:108-118, MAR 25 2014
abstract, full text, DOI:10.1016/j.jpba.2013.12.024

Sethi, Ritika; Seppala, Jonne; Tossavainen, Helena; Ylilauri, Mikko; Ruskamo, Salla; Pentikainen, Olli T.; Pentikainen, Ulla; Permi, Perttu; Ylanne, Jari
A Novel Structural Unit in the N-terminal Region of Filamins
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:8588-8598, MAR 21 2014
abstract, full text, DOI:10.1074/jbc.M113.537456

Lindert, Steffen; Maslennikov, Innokentiy; Chiu, Ellis J. C.; Pierce, Levi C.; McCammon, J. Andrew; Choe, Senyon
Drug screening strategy for human membrane proteins: From NMR protein backbone structure to in silica- and NMR-screened hits
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 445:724-733, MAR 21 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.01.179

Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
Mg2+ coordinating dynamics in Mg:ATP fueled motor proteins
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 115102, MAR 21 2014
abstract, full text, DOI:10.1063/1.4867898

Tomasic, Tihomir; Hajsek, David; Svajger, Urban; Luzar, Jernej; Obermajer, Natasa; Petit-Haertlein, Isabelle; Fieschi, Franck; Anderluh, Marko
Monovalent mannose-based DC-SIGN antagonists: Targeting the hydrophobic groove of the receptor
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 75:308-326, MAR 21 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.01.047

Fiorillo, Annarita; di Marino, Daniele; Bertuccini, Lucia; Via, Allegra; Pozio, Edoardo; Camerini, Serena; Ilari, Andrea; Lalle, Marco
The Crystal Structure of Giardia duodenalis 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference
PLOS ONE, 9 Art. No. e92902, MAR 21 2014
abstract, full text, DOI:10.1371/journal.pone.0092902

Zeytuni, Natalie; Uebe, Rene; Maes, Michal; Davidov, Geula; Baram, Michal; Raschdorf, Oliver; Nadav-Tsubery, Merav; Kolusheva, Sofiya; Bitton, Ronit; Goobes, Gil; Friedler, Assaf; Miller, Yifat; Schueler, Dirk; Zarivach, Raz
Cation Diffusion Facilitators Transport Initiation and Regulation Is Mediated by Cation Induced Conformational Changes of the Cytoplasmic Domain
PLOS ONE, 9 Art. No. e92141, MAR 21 2014
abstract, full text, DOI:10.1371/journal.pone.0092141

Sen, Kakali; Thiel, Walter
Role of Two Alternate Water Networks in Compound I Formation in P450eryF
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2810-2820, MAR 20 2014
abstract, full text, DOI:10.1021/jp411272h

Vidossich, Pietro; Loewen, Peter C.; Carpena, Xavi; Fiorin, Giacomo; Fita, Ignacio; Rovira, Carme
Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (KatG). A Combined Structural and Metadynamics Investigation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2924-2931, MAR 20 2014
abstract, full text, DOI:10.1021/jp4123425

Konold, Patrick; Regmi, Chola K.; Chapagain, Prem P.; Gerstman, Bernard S.; Jimenez, Ralph
Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2940-2948, MAR 20 2014
abstract, full text, DOI:10.1021/jp412371y

Liu, Yanxin; Prigozhin, Maxim B.; Schulten, Klaus; Gruebele, Martin
Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:4265-4272, MAR 19 2014
abstract, full text, TCBG publications, DOI:10.1021/ja412639u

Heinzelmann, Germano; Kuyucak, Serdar
Molecular Dynamics Simulations of the Mammalian Glutamate Transporter EAAT3
PLOS ONE, 9 Art. No. e92089, MAR 18 2014
abstract, full text, DOI:10.1371/journal.pone.0092089

Adelman, Joshua L.; Sheng, Ying; Choe, Seungho; Abramson, Jeff; Wright, Ernest M.; Rosenberg, John M.; Grabe, Michael
Structural Determinants of Water Permeation through the Sodium-Galactose Transporter vSGLT
BIOPHYSICAL JOURNAL, 106:1280-1289, MAR 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.006

Scharnagl, Christina; Pester, Oxana; Hornburg, Philipp; Hornburg, Daniel; Goetz, Alexander; Langosch, Dieter
Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix
BIOPHYSICAL JOURNAL, 106:1318-1326, MAR 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.02.013

Yang, J.; Calero, C.; Marti, J.
Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 104901, MAR 14 2014
abstract, full text, DOI:10.1063/1.4867385

Yzeiri, Irena; Patra, Niladri; Kral, Petr
Porous carbon nanotubes: Molecular absorption, transport, and separation
JOURNAL OF CHEMICAL PHYSICS, 140, MAR 14 2014
abstract, full text, DOI:10.1063/1.4867542

Lockhart, Christopher; Klimov, Dmitri K.
Alzheimer's A beta 10-40 Peptide Binds and Penetrates DMPC Bilayer: An Isobaric-Isothermal Replica Exchange Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2638-2648, MAR 13 2014
abstract, full text, DOI:10.1021/jp412153s

Madrona, Yarrow; Hollingsworth, Scott A.; Tripathi, Sarvind; Fields, James B.; Rwigema, Jean-Christophe N.; Tobias, Douglas J.; Poulos, Thomas L.
Crystal Structure of Cindoxin, the P450cin Redox Partner
BIOCHEMISTRY, 53:1435-1446, MAR 11 2014
abstract, full text, DOI:10.1021/bi500010m

Guillotin, Laure; Lafite, Pierre; Daniellou, Richard
Unraveling the Substrate Recognition Mechanism and Specificity of the Unusual Glycosyl Hydrolase Family 29 BT2192 from Bacteroides thetaiotaomicron
BIOCHEMISTRY, 53:1447-1455, MAR 11 2014
abstract, full text, DOI:10.1021/bi400951q

Jiang, Xiaoxu; Villafuerte, Maria Katerina R.; Andersson, Magnus; White, Stephen H.; Kaback, H. Ronald
Galactoside-Binding Site in LacY
BIOCHEMISTRY, 53:1536-1543, MAR 11 2014
abstract, full text, DOI:10.1021/bi401716z

Serrano, Soraya; Araujo, Aitziber; Apellaniz, Beatriz; Bryson, Steve; Carravilla, Pablo; de la Arada, Igor; Huarte, Nerea; Rujas, Edurne; Pai, Emil F.; Arrondo, Jose L. R.; Domene, Carmen; Angeles Jimenez, Maria; Nieva, Jose L.
Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope IMPLICATIONS FOR ANTIBODY RECOGNITION MECHANISM AND IMMUNOGEN DESIGN
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6565-6580, MAR 7 2014
abstract, full text, DOI:10.1074/jbc.M113.527747

Lemmin, Thomas; Dimitrov, Mitko; Fraering, Patrick C.; Dal Peraro, Matteo
Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6763-6774, MAR 7 2014
abstract, full text, DOI:10.1074/jbc.M113.470781

Pang, Xiaodong; Zhou, Huan-Xiang
Design Rules for Selective Binding of Nuclear Localization Signals to Minor Site of Importin alpha
PLOS ONE, 9 Art. No. e91025, MAR 7 2014
abstract, full text, DOI:10.1371/journal.pone.0091025

Padilla-Sanchez, Victor; Gao, Song; Kim, Hyung Rae; Kihara, Daisuke; Sun, Lei; Rossmann, Michael G.; Rao, Venigalla B.
Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine
JOURNAL OF MOLECULAR BIOLOGY, 426:1019-1038, MAR 6 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.011

Tseng, Wen-Chi; Lin, Chia-Ray; Hung, Xing-Guang; Wei, Tsen-Yun; Chen, Yu-Chun; Fang, Tsuei-Yun
Identification of substrate-binding and selectivity-related residues of maltooligosyltrehalose synthase from the thermophilic archaeon Sulfolobus solfataricus ATCC 35092
ENZYME AND MICROBIAL TECHNOLOGY, 56:53-59, MAR 5 2014
abstract, full text, DOI:10.1016/j.enzmictic.2014.01.003

Li, Yunlang; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.; Schlick, Tamar
Optimal and Variant Metal-Ion Routes in DNA Polymerase beta's Conformational Pathways
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:3630-3639, MAR 5 2014
abstract, full text, DOI:10.1021/ja412701f

Zhang, Fan; Tian, Yi; Gao, Feng; Chen, Shulin; Li, Demao; Zhou, Yuxia
Bacterial community in the intestine of the sea urchin Strongylocentrotus intermedius during digestion of Macrocystis pyrifera
MARINE AND FRESHWATER BEHAVIOUR AND PHYSIOLOGY, 47:117-127, MAR 4 2014
abstract, full text, DOI:10.1080/10236244.2014.906095

Boiteux, Celine; Vorobyov, Igor; Allen, Toby W.
Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3454-3459, MAR 4 2014
abstract, full text, DOI:10.1073/pnas.1320907111

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey
Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3585-3590, MAR 4 2014
abstract, full text, DOI:10.1073/pnas.1317061111

Gorham, Ronald D., Jr.; Rodriguez, Wilson; Morikis, Dimitrios
Molecular Analysis of the Interaction between Staphylococcal Virulence Factor Sbi-IV and Complement C3d
BIOPHYSICAL JOURNAL, 106:1164-1173, MAR 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.033

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun
Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:372-393, MAR 4 2014
abstract, full text, DOI:10.1080/07391102.2013.770372

Yu, Haoran; Huang, He
Engineering proteins for thermostability through rigidifying flexible sites
BIOTECHNOLOGY ADVANCES, 32:308-315, MAR-APR 2014
abstract, full text, DOI:10.1016/j.biotechadv.2013.10.012

Pradhan, S. M.; Katti, K. S.; Katti, D. R.
Multiscale Modeling of Collagen Fibril in Bone at Various Crosslink Densities: An Insight into Its Deformation Mechanisms
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES, 98:181-201, MAR 2014
abstract, full text

Tu, Qing Song; Lee, Michelle; Zhang, Samuel; Li, Shaofan
Molecular Dynamics Simulations of Ions Diffusion in Carbon Nanotubes Embedded in Cell Membrane
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES, 98:247-259, MAR 2014
abstract, full text

Song, Zhen; Ming, Jie; Yang, Binsheng
The effect of metals on SDS-induced partially folded states of CopC
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 19:359-374, MAR 2014
abstract, full text, DOI:10.1007/s00775-013-1071-8

Gamini, Ramya; Han, Wei; Stone, John E.; Schulten, Klaus
Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003488, MAR 2014
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1003488

Adhireksan, Zenita; Davey, Gabriela E.; Campomanes, Pablo; Groessl, Michael; Clavel, Catherine M.; Yu, Haojie; Nazarov, Alexey A.; Yeo, Charmian Hui Fang; Ang, Wee Han; Droege, Peter; Rothlisberger, Ursula; Dyson, Paul J.; Davey, Curt A.
Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity
NATURE COMMUNICATIONS, 5 Art. No. 3462, MAR 2014
abstract, full text, DOI:10.1038/ncomms4462

Zhou, Qiangjun; Li, Jiangmei; Yu, Hang; Zhai, Yujia; Gao, Zhen; Liu, Yanxin; Pang, Xiaoyun; Zhang, Lunfeng; Schulten, Klaus; Sun, Fei; Chen, Chang
Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II alpha
NATURE COMMUNICATIONS, 5 Art. No. 3552, MAR 2014
abstract, full text, TCBG publications, DOI:10.1038/ncomms4552

Kunze, Jens; Todoroff, Nickolay; Schneider, Petra; Rodrigues, Tiago; Geppert, Tim; Reisen, Felix; Schreuder, Herman; Saas, Joachim; Hessler, Gerhard; Baringhaus, Karl-Heinz; Schneider, Gisbert
Targeting Dynamic Pockets of HIV-1 Protease by Structure-Based Computational Screening for Allosteric Inhibitors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:987-991, MAR 2014
abstract, full text, DOI:10.1021/ci400712h

des Georges, Amedee; Hashem, Yaser; Unbehaun, Anett; Grassucci, Robert A.; Taylor, Derek; Hellen, Christopher U. T.; Pestova, Tatyana V.; Frank, Joachim
Structure of the mammalian ribosomal pre-termination complex associated with eRF1 center dot eRF3 center dot GDPNP
NUCLEIC ACIDS RESEARCH, 42:3409-3418, MAR 2014
abstract, full text, DOI:10.1093/nar/gkt1279

Llatser, Ignacio; Demiray, Deniz; Cabellos-Aparicio, Albert; Altilar, D. Turgay; Alarcon, Eduard
N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks
SIMULATION MODELLING PRACTICE AND THEORY, 42:210-222, MAR 2014
abstract, full text, DOI:10.1016/j.simpat.2013.11.004

Wright, David W.; Hall, Benjamin A.; Kenway, Owain A.; Jha, Shantenu; Coveney, Peter V.
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1228-1241, MAR 2014
abstract, full text, DOI:10.1021/ct4007037

Aytenfisu, Asaminew H.; Spasic, Aleksandar; Seetin, Matthew G.; Serafini, John; Mathews, David H.
Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1292-1301, MAR 2014
abstract, full text, DOI:10.1021/ct400861g

Ferrari, Florent; Paris, Cedric; Maigret, Bernard; Bidouil, Christelle; Delaunay, Stephane; Humeau, Catherine; Chevalot, Isabelle
Molecular rules for chemo- and regio-selectivity of Candida antarctica lipase B in peptide acylation reactions
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 101:122-132, MAR 2014
abstract, full text, DOI:10.1016/j.molcatb.2013.12.007

Huang, Lan; Cao, Yang; Zhou, Jianfang; Qin, Kun; Zhu, Wenfei; Zhu, Yun; Yang, Lei; Wang, Dayan; Wei, Hong; Shu, Yuelong
A Conformational Restriction in the Influenza A Virus Neuraminidase Binding Site by R152 Results in a Combinational Effect of I222T and H274Y on Oseltamivir Resistance
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 58:1639-1645, MAR 2014
abstract, full text, DOI:10.1128/AAC.01848-13

Fibriansah, Guntur; Tan, Joanne L.; Smith, Scott A.; de Alwis, Adamberage R.; Thiam-Seng Ng; Kostyuchenko, Victor A.; Ibarra, Kristie D.; Wang, Jiaqi; Harris, Eva; de Silva, Aravinda; Crowe, James E., Jr.; Lok, Shee-Mei
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface
EMBO MOLECULAR MEDICINE, 6:358-371, MAR 2014
abstract, full text, DOI:10.1002/emmm.201303404

Rusu, Victor H.; Horta, Vitor A. C.; Horta, Bruno A. C.; Lins, Roberto D.; Baron, Riccardo
MDWiZ: A platform for the automated translation of molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 48:80-86, MAR 2014
abstract, full text, DOI:10.1016/j.jmgm.2013.12.006

Hirtz, Michael; Kumar, Naresh; Chi, Lifeng
Simulation Modeling of Supported Lipid Membranes - A Review
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:617-623, MAR 2014
abstract, full text, DOI:10.2174/1568026614666140118204332

Jiang, Wei; Phillips, James C.; Huang, Lei; Fajer, Mikolai; Meng, Yilin; Gumbart, James C.; Luo, Yun; Schulten, Klaus; Roux, Benoit
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD
COMPUTER PHYSICS COMMUNICATIONS, 185:908-916, MAR 2014
abstract, full text, TCBG publications, DOI:10.1016/j.cpc.2013.12.014

Ai, Haixin; Zhang, Li; Chang, Alan K.; Wei, Hongyun; Che, Yuchen; Liu, Hongsheng
Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2142, MAR 2014
abstract, full text, DOI:10.1007/s00894-014-2142-7

Mikulska, Karolina; Strzelecki, Janusz; Nowak, Wieslaw
Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2144, MAR 2014
abstract, full text, DOI:10.1007/s00894-014-2144-5

Geng, Yi-Zhao; Li, Tie; Ji, Qing; Yan, Shiwei
Simulation Study of Interactions Between Kinesin's Neck Linker and Motor Domain
CELLULAR AND MOLECULAR BIOENGINEERING, 7:99-105, MAR 2014
abstract, full text, DOI:10.1007/s12195-014-0320-4

Lushchekina, Sofya V.; Nemukhin, Alexander V.; Varfolomeev, Sergei D.; Masson, Patrick
Molecular Modeling Evidence for His438 Flip in the Mechanism of Butyrylcholinesterase Hysteretic Behavior
JOURNAL OF MOLECULAR NEUROSCIENCE, 52:434-445, MAR 2014
abstract, full text, DOI:10.1007/s12031-013-0178-2

Ruiz, Luis; Keten, Sinan
Multiscale Modeling of Elasticity and Fracture in Organic Nanotubes
JOURNAL OF ENGINEERING MECHANICS, 140:431-442, MAR 1 2014
abstract, full text, DOI:10.1061/(ASCE)EM.1943-7889.0000471

Pal, Anirban; Agarwala, Abhishek; Raha, Spumyendu; Bhattacharya, Baidurya
Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 74:2203-2214, MAR 2014
abstract, full text, DOI:10.1016/j.jpdc.2013.12.008

Citlalli Contreras-Romo, M.; Correa-Basurto, Jose; Padilla-Martinez, Itzia; Martinez-Archundia, Marlet; Martinez-Ramos, Federico; Slusarz, Magdalena J.; Lopez-Perez, Gilberto; Quintanar-Stephano, Andres
Theoretical studies, synthesis, and biological activity of 1-[(4-methylphenyl)sulfonyl]-5-oxo-2,3,4,5-tetrahydro-1H-1-benzazepine-4 -carbonitrile (C9) as a non-peptide antagonist of the arginine vasopressin V1a and V2 receptors
MEDICINAL CHEMISTRY RESEARCH, 23:1581-1590, MAR 2014
abstract, full text, DOI:10.1007/s00044-013-0739-5

Walker, Ryan G.; Deng, Xiaodi; Melchior, John T.; Morris, Jamie; Tso, Patrick; Jones, Martin K.; Segrest, Jere P.; Thompson, Thomas B.; Davidson, W. Sean
The Structure of Human Apolipoprotein A-IV as Revealed by Stable Isotope-assisted Cross-linking, Molecular Dynamics, and Small Angle X-ray Scattering
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:5596-5608, FEB 28 2014
abstract, full text, DOI:10.1074/jbc.M113.541037

Abdul-Ridha, Alaa; Lopez, Laura; Keov, Peter; Thal, David M.; Mistry, Shailesh N.; Sexton, Patrick M.; Lane, J. Robert; Canals, Meritxell; Christopoulos, Arthur
Molecular Determinants of Allosteric Modulation at the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6067-6079, FEB 28 2014
abstract, full text, DOI:10.1074/jbc.M113.539080

Ljubetic, Ajasja; Urbancic, Iztok; Strancar, Janez
Recovering position-dependent diffusion from biased molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 084109, FEB 28 2014
abstract, full text, DOI:10.1063/1.4866448

Meyer, Austin G.; Sawyer, Sara L.; Ellington, Andrew D.; Wilke, Claus O.
Analyzing machupo virus-receptor binding by molecular dynamics simulations
PEERJ, 2 Art. No. e266, FEB 27 2014
abstract, full text, DOI:10.7717/peerj.266

Volpert, Marianna; Mangum, Jonathan E.; Jamsai, Duangporn; D'Sylva, Rebecca; O'Bryan, Moira K.; McIntyre, Peter
Eukaryotic expression, purification and structure/function analysis of native, recombinant CRISP3 from human and mouse
SCIENTIFIC REPORTS, 4 Art. No. 4217, FEB 27 2014
abstract, full text, DOI:10.1038/srep04217

Johnson, Quentin R.; Lindsay, Richard J.; Raval, Sherin R.; Dobbs, Jeremy S.; Nellas, Ricky B.; Shen, Tongye
Effects of Branched O-Glycosylation on a Semiflexible Peptide Linker
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2050-2057, FEB 27 2014
abstract, full text, DOI:10.1021/jp410788r

Strzelecki, Janusz; Peplowski, Lukasz; Lenartowski, Robert; Nowak, Wieslaw; Balter, Aleksander
Mechanical transition in a highly stretched and torsionally constrained DNA
PHYSICAL REVIEW E, 89 Art. No. 020701, FEB 27 2014
abstract, full text, DOI:10.1103/PhysRevE.89.020701

Murciano-Calles, Javier; Corbi-Verge, Carles; Candel, Adela M.; Luque, Irene; Martinez, Jose C.
Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95
PLOS ONE, 9 Art. No. e90030, FEB 26 2014
abstract, full text, DOI:10.1371/journal.pone.0090030

Correa-Basurto, J.; Bello, M.; Rosales-Hernandez, M. C.; Hernandez-Rodriguez, M.; Nicolas-Vazquez, I.; Rojo-Dominguez, A.; Trujillo-Ferrara, J. G.; Miranda, Rene; Flores-Sandoval, C. A.
QSAR, docking, dynamic simulation and quantum mechanics studies to explore the recognition properties of cholinesterase binding sites
CHEMICO-BIOLOGICAL INTERACTIONS, 209:1-13, FEB 25 2014
abstract, full text, DOI:10.1016/j.cbi.2013.12.001

Sheng, Jia; Li, Li; Engelhart, Aaron E.; Gan, Jianhua; Wang, Jiawei; Szostak, Jack W.
Structural insights into the effects of 2 '-5 ' linkages on the RNA duplex
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3050-3055, FEB 25 2014
abstract, full text, DOI:10.1073/pnas.1317799111

Megow, Joerg; Renger, Thomas; May, Volkhard
Mixed Quantum-Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Screening of the Excitonic Coupling
CHEMPHYSCHEM, 15:478-485, FEB 24 2014
abstract, full text, DOI:10.1002/cphc.201300625

Li, Min; Chang, Shan; Yang, Longjin; Shi, Jingyi; McFarland, Kelli; Yang, Xiao; Moller, Alyssa; Wang, Chunguang; Zou, Xiaoqin; Chi, Chengwu; Cui, Jianmin
Conopeptide Vt3.1 Preferentially Inhibits BK Potassium Channels Containing beta 4 Subunits via Electrostatic Interactions*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:4735-4742, FEB 21 2014
abstract, full text, DOI:10.1074/jbc.M113.535898

Tanaka, Naoto; Delemotte, Lucie; Klein, Michael L.; Komaromy, Andras M.; Tanaka, Jacqueline C.
A Cyclic Nucleotide-Gated Channel Mutation Associated with Canine Daylight Blindness Provides Insight into a Role for the S2 Segment Tri-Asp motif in Channel Biogenesis
PLOS ONE, 9 Art. No. e88768, FEB 21 2014
abstract, full text, DOI:10.1371/journal.pone.0088768

Temmerman, Koen; de Diego, Inaki; Pogenberg, Vivian; Simon, Bertrand; Jonko, Weronika; Li, Xun; Wilmanns, Matthias
A PEF/Y Substrate Recognition and Signature Motif Plays a Critical Role in DAPK-Related Kinase Activity
CHEMISTRY & BIOLOGY, 21:264-273, FEB 20 2014
abstract, full text, DOI:10.1016/j.chembiol.2013.12.008

Feil, Susanne C.; Ascher, David B.; Kuiper, Michael J.; Tweten, Rodney K.; Parker, Michael W.
Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration
JOURNAL OF MOLECULAR BIOLOGY, 426:785-792, FEB 20 2014
abstract, full text, DOI:10.1016/j.jmb.2013.11.020

Kim, Hajin; Abeysirigunawarden, Sanjaya C.; Chen, Ke; Mayerle, Megan; Ragunathan, Kaushik; Luthey-Schulten, Zaida; Ha, Taekjip; Woodson, Sarah A.
Protein-guided RNA dynamics during early ribosome assembly
NATURE, 506:334-+, FEB 20 2014
abstract, full text, DOI:10.1038/nature13039

Vermaas, Josh V.; Tajkhorshid, Emad
A Microscopic View of Phospholipid Insertion into Biological Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1754-1764, FEB 20 2014
abstract, full text, DOI:10.1021/jp409854w

Heinzelmann, Germano; Chen, Po-Chia; Kuyucak, Serdar
Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1813-1824, FEB 20 2014
abstract, full text, DOI:10.1021/jp412195m

Li, Li; Szostak, Jack W.
The Free Energy Landscape of Pseudorotation in 3 '-5 ' and 2 '-5 ' Linked Nucleic Acids
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2858-2865, FEB 19 2014
abstract, full text, DOI:10.1021/ja412079b

Ide, Julien; Mereau, Raphael; Ducasse, Laurent; Castet, Frederic; Bock, Harald; Olivier, Yoann; Cornil, Jerome; Beljonne, David; D'Avino, Gabriele; Roscioni, Otello Maria; Muccioli, Luca; Zannoni, Claudio
Charge Dissociation at Interfaces between Discotic Liquid Crystals: The Surprising Role of Column Mismatch
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2911-2920, FEB 19 2014
abstract, full text, DOI:10.1021/ja4114769

Xiong, Feifei; Xia, Liliang; Wang, Jingfang; Wu, Biao; Wang, Dengyu; Yuan, Longfang; Cheng, Yating; Zhu, Hongying; Che, Xiaoyan; Zhang, Qinghua; Zhao, Guoping; Wang, Ying
A High-Affinity CDR-Grafted Antibody against Influenza A H5N1 Viruses Recognizes a Conserved Epitope of H5 Hemagglutinin
PLOS ONE, 9 Art. No. e88777, FEB 18 2014
abstract, full text, DOI:10.1371/journal.pone.0088777

Giambasu, George M.; Luchko, Tyler; Herschlag, Daniel; York, Darrin M.; Case, David A.
Ion Counting from Explicit-Solvent Simulations and 3D-RISM
BIOPHYSICAL JOURNAL, 106:883-894, FEB 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.021

Wang, Yong; Liu, Yanxin; DeBerg, Hannah A.; Nomura, Takeshi; Hoffman, Melinda Tonks; Rohde, Paul R.; Schulten, Klaus; Martinac, Boris; Selvin, Paul R.
Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel
ELIFE, 3 Art. No. e01834, FEB 18 2014
abstract, full text, TCBG publications, DOI:10.7554/eLife.01834

Stewart, Matthew B.; Gray, Stephen R.; Vasiljevic, Todor; Orbell, John D.
Exploring the molecular basis for the metal-mediated assembly of alginate gels
CARBOHYDRATE POLYMERS, 102:246-253, FEB 15 2014
abstract, full text, DOI:10.1016/j.carbpol.2013.11.034

Alizadeh, Ali; Parsafar, GolamAbbas
Temperature dependence and the effect of charge configuration on water permeation through modified carbon nanotubes: A simulation study
FLUID PHASE EQUILIBRIA, 363:282-289, FEB 15 2014
abstract, full text, DOI:10.1016/j.fluid.2013.12.005

Huggins, David J.
Comparing Distance Metrics for Rotation Using the k-Nearest Neighbors Algorithm for Entropy Estimation
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:377-385, FEB 15 2014
abstract, full text, DOI:10.1002/jcc.23504

Hynninen, Antti-Pekka; Crowley, Michael F.
New Faster CHARMM Molecular Dynamics Engine
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:406-413, FEB 15 2014
abstract, full text, DOI:10.1002/jcc.23501

Yoon, Gwonchan; Lee, Myeongsang; Kim, Jae In; Na, Sungsoo; Eom, Kilho
Role of Sequence and Structural Polymorphism on the Mechanical Properties of Amyloid Fibrils
PLOS ONE, 9 Art. No. e88502, FEB 14 2014
abstract, full text, DOI:10.1371/journal.pone.0088502

D'Amore, Claudio; Di Leva, Francesco Saverio; Sepe, Valentina; Renga, Barbara; Del Gaudio, Chiara; D'Auria, Maria Valeria; Zampella, Angela; Fiorucci, Stefano; Limongelli, Vittorio
Design, Synthesis, and Biological Evaluation of Potent Dual Agonists of Nuclear and Membrane Bile Acid Receptors
JOURNAL OF MEDICINAL CHEMISTRY, 57:937-954, FEB 13 2014
abstract, full text, DOI:10.1021/jm401873d

Narawane, Shailesh; Budnjo, Adnan; Grauffel, Cedric; Haug, Bengt Erik; Reuter, Nathalie
In Silico Design, Synthesis, and Assays of Specific Substrates for Proteinase 3: Influence of Fluorogenic and Charged Groups
JOURNAL OF MEDICINAL CHEMISTRY, 57:1111-1115, FEB 13 2014
abstract, full text, DOI:10.1021/jm401559r

Pogorelov, Taras V.; Vermaas, Josh V.; Arcario, Mark J.; Tajkhorshid, Emad
Partitioning of Amino Acids into a Model Membrane: Capturing the Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1481-1492, FEB 13 2014
abstract, full text, DOI:10.1021/jp4089113

Duboue-Dijon, Elise; Fogarty, Aoife C.; Laage, Damien
Temperature Dependence of Hydrophobic Hydration Dynamics: From Retardation to Acceleration
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1574-1583, FEB 13 2014
abstract, full text, DOI:10.1021/jp408603n

Carrasco-Sanchez, Veronica; Vergara-Jaque, Ariela; Zuniga, Matias; Comer, Jeffrey; John, Amalraj; Nachtigall, Fabiane M.; Valdes, Oscar; Duran-Lara, Esteban F.; Sandoval, Claudia; Santos, Leonardo S.
In situ and in silico evaluation of amine- and folate-terminated dendrimers as nanocarriers of anesthetics
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 73:250-257, FEB 12 2014
abstract, full text, DOI:10.1016/j.ejmech.2013.11.040

Campomanes, Pablo; Kellett, Whitney R.; Easthon, Lindsey M.; Ozarowski, Andrew; Allen, Karen N.; Angerhofer, Alexander; Rothlisberger, Ursula; Richards, Nigel G. J.
Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2313-2323, FEB 12 2014
abstract, full text, DOI:10.1021/ja408138f

Lee, Wook; Engels, Bernd
The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate
BIOCHEMISTRY, 53:919-931, FEB 11 2014
abstract, full text, DOI:10.1021/bi401308j

Park, Eunyong; Menetret, Jean-Francois; Gumbart, James C.; Ludtke, Steven J.; Li, Weikai; Whynot, Andrew; Rapoport, Tom A.; Akey, Christopher W.
Structure of the SecY channel during initiation of protein translocation
NATURE, 506:102-+, FEB 6 2014
abstract, full text, DOI:10.1038/nature12720

Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer C.; Valleau, Stephanie; Fujita, Takatoshi; Aspuru-Guzik, Alan
Atomistic Study of Energy Funneling in the Light-Harvesting Complex of Green Sulfur Bacteria
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2048-2057, FEB 5 2014
abstract, full text, DOI:10.1021/ja412035q

Wang, Deqiang; Harrer, Stefan; Luan, Binquan; Stolovitzky, Gustavo; Peng, Hongbo; Afzali-Ardakani, Ali
Regulating the Transport of DNA through Biofriendly Nanochannels in a Thin Solid Membrane
SCIENTIFIC REPORTS, 4 Art. No. 3985, FEB 5 2014
abstract, full text, DOI:10.1038/srep03985

Kyrychenko, Alexander; Freites, J. Alfredo; He, Jing; Tobias, Douglas J.; Wimley, William C.; Ladokhin, Alexey S.
Structural Plasticity in the Topology of the Membrane-Interacting Domain of HIV-1 gp41
BIOPHYSICAL JOURNAL, 106:610-620, FEB 4 2014
abstract, full text, DOI:10.1016/j.bpj.2013.12.032

Kwansa, Albert L.; De Vita, Raffaella; Freeman, Joseph W.
Mechanical recruitment of N- and C-crosslinks in collagen type I
MATRIX BIOLOGY, 34:161-169, FEB 2014
abstract, full text, DOI:10.1016/j.matbio.2013.10.012

Gumbart, James C.; Beeby, Morgan; Jensen, Grant J.; Roux, Benoit
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations
PLOS COMPUTATIONAL BIOLOGY, 10, FEB 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003475

Klappenberger, Florian
Two-dimensional functional molecular nanoarchitectures - Complementary investigations with scanning tunneling microscopy and X-ray spectroscopy
PROGRESS IN SURFACE SCIENCE, 89:1-55, FEB 2014
abstract, full text, DOI:10.1016/j.progsurf.2013.10.002

Pang, Xue-qin; Liu, Jian-yong
GPCR A(2A)AR Agonist Binding and Induced Conformation Changes of Functional Switches
CHINESE JOURNAL OF CHEMICAL PHYSICS, 27:29-38, FEB 2014
abstract, full text, DOI:10.1063/1674-0068/27/01/29-38

Newcomb, Christina J.; Sur, Shantanu; Ortony, Julia H.; Lee, One-Sun; Matson, John B.; Boekhoven, Job; Yu, Jeong Min; Schatz, George C.; Stupp, Samuel I.
Cell death versus cell survival instructed by supramolecular cohesion of nanostructuresl
NATURE COMMUNICATIONS, 5 Art. No. 3321, FEB 2014
abstract, full text, DOI:10.1038/ncomms4321

Pietra, Francesco
On Dioxygen Permeation through a Dehydrogenase-Pyrroloquinoline Quinone Complex. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 11:209-216, FEB 2014
abstract, full text, DOI:10.1002/cbdv.201300314

Wu Yun-Long; Xu Xin-Hai; Yang Xue-Jun; Zou Shun; Ren Xiao-Guang
MDSLB: A new static load balancing method for parallel molecular dynamics simulations
CHINESE PHYSICS B, 23 Art. No. 028903, FEB 2014
abstract, full text, DOI:10.1088/1674-1056/23/2/028903

Patel, Jagdish Suresh; Berteotti, Anna; Ronsisvalle, Simone; Rocchia, Walter; Cavalli, Andrea
Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:470-480, FEB 2014
abstract, full text, DOI:10.1021/ci4003574

Ning, Lulu; Guo, Jingjing; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun
The role of Cys179-Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2106, FEB 2014
abstract, full text, DOI:10.1007/s00894-014-2106-y

Barra, Pabla A.; Barraza, Luis; Jimenez, Veronica A.; Gavin, Jose A.; Alderete, Joel B.
Complexation of Mefenamic Acid by Low-Generation PAMAM Dendrimers: Insight from NMR Spectroscopy Studies and Molecular Dynamics Simulations
MACROMOLECULAR CHEMISTRY AND PHYSICS, 215:372-383, FEB 2014
abstract, full text, DOI:10.1002/macp.201300398

Lee, Jooyong; Jeon, Jonggu; Kim, Min-Seok; Lee, Hochan; Cho, Minhaeng
Amide I IR probing of core and shell hydrogen-bond structures in reverse micelles
PURE AND APPLIED CHEMISTRY, 86:135-149, FEB 2014
abstract, full text, DOI:10.1515/pac-2014-5016

Mishra, Panchanand; Dixit, Anshuman; Ray, Mamata; Sabat, Surendra Chandra
Mechanistic study of CuZn-SOD from Ipomoea carnea mutated at dimer interface: Enhancement of peroxidase activity upon monomerization
BIOCHIMIE, 97:181-193, FEB 2014
abstract, full text, DOI:10.1016/j.biochi.2013.10.014

Amarasinghe, Priyanthi M.; Anandarajah, A.; Ghosh, Pijush
Molecular dynamic study of capillary forces on clay particles
APPLIED CLAY SCIENCE, 88-89:170-177, FEB 2014
abstract, full text, DOI:10.1016/j.clay.2013.12.022

Ambrosia, Matthew Stanley; Ha, Man Yeong; Balachandar, S.
Dynamic hydrophobicity on flat and pillared graphite surfaces with different pillar surface fractions
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 28:669-677, FEB 2014
abstract, full text, DOI:10.1007/s12206-013-1178-4

Chen, Bo; Boel, Gregory; Hashem, Yaser; Ning, Wei; Fei, Jingyi; Wang, Chi; Gonzalez, Ruben L., Jr.; Hunt, John F.; Frank, Joachim
EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:152-+, FEB 2014
abstract, full text, DOI:10.1038/nsmb.2741

Rothe, Benjamin; Back, Regis; Quinternet, Marc; Bizarro, Jonathan; Robert, Marie-Cecile; Blaud, Magali; Romier, Christophe; Manival, Xavier; Charpentier, Bruno; Bertrand, Edouard; Branlant, Christiane
Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly
NUCLEIC ACIDS RESEARCH, 42:2015-2036, FEB 2014
abstract, full text, DOI:10.1093/nar/gkt1091

Song, Jianing; Ji, Changge; Zhang, John Z. H.
Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:240-249, FEB 2014
full text

Van Wart, Adam T.; Durrant, Jacob; Votapka, Lane; Amaro, Rommie E.
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:511-517, FEB 2014
abstract, full text, DOI:10.1021/ct4008603

Mansour, Andrew Abi; Ortoleva, Peter J.
Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:518-523, FEB 2014
abstract, full text, DOI:10.1021/ct400615a

Maragliano, Luca; Roux, Benoit; Vanden-Eijnden, Eric
Comparison between Mean Forces and Swarms-of-Trajectories String Methods
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:524-533, FEB 2014
abstract, full text, DOI:10.1021/ct400606c

Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe
Calculation of Lipid-Bilayer Permeabilities Using an Average Force
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:554-564, FEB 2014
abstract, full text, TCBG publications, DOI:10.1021/ct400925s

Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron
Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:659-667, FEB 2014
abstract, full text, DOI:10.1021/ct4009798

Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang
Dynamic Mechanism of Single-Stranded DNA Encapsulated into Single-Wall Carbon Nanotubes: A Molecular Dynamics Simulation Study
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 83 Art. No. 024801, FEB 2014
abstract, full text, DOI:10.7566/JPSJ.83.024801

Geng, Yi-Zhao; Liu, Shu-Xia; Ji, Qing; Yan, Shiwei
Mechanical amplification mechanism of kinesin's beta-domain
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 543:10-14, FEB 1 2014
abstract, full text, DOI:10.1016/j.abb.2013.12.017

Contreras-Romo, Martha C.; Martinez-Archundia, Marlet; Deeb, Omar; Slusarz, Magdalena J.; Ramirez-Salinas, Gema; Garduno-Juarez, Ramon; Quintanar-Stephano, Andres; Ramirez-Galicia, Guillermo; Correa-Basurto, Jose
Exploring the Ligand Recognition Properties of the Human Vasopressin V1a Receptor Using QSAR and Molecular Modeling Studies
CHEMICAL BIOLOGY & DRUG DESIGN, 83:207-223, FEB 2014
abstract, full text, DOI:10.1111/cbdd.12229

Gonzalez, Pablo M.; Lagos, Carlos F.; Ward, Weslyn C.; Polli, James E.
Structural Requirements of the Human Sodium-Dependent Bile Acid Transporter (hASBT): Role of 3-and 7-OH Moieties on Binding and Translocation of Bile Acids
MOLECULAR PHARMACEUTICS, 11:588-598, FEB 2014
abstract, full text, DOI:10.1021/mp400575t

Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.
A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 269:123-138, FEB 1 2014
abstract, full text, DOI:10.1016/j.cma.2013.11.010

Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni
PLUMED 2: New feathers for an old bird
COMPUTER PHYSICS COMMUNICATIONS, 185:604-613, FEB 2014
abstract, full text, DOI:10.1016/j.cpc.2013.09.018

Chen, Dongping; Totton, Tim S.; Akroyd, Jethro W. J.; Mosbach, Sebastian; Kraft, Markus
Size-dependent melting of polycyclic aromatic hydrocarbon nano-clusters: A molecular dynamics study
CARBON, 67:79-91, FEB 2014
abstract, full text, DOI:10.1016/j.carbon.2013.09.058

Bouard, Charlotte; Terreux, Raphael; Hope, Jennifer; Chemelle, Julie Anne; Puisieux, Alain; Ansieau, Stephane; Payen, Lea
Interhelical loops within the bHLH domain are determinant in maintaining TWIST1-DNA complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:226-241, FEB 1 2014
abstract, full text, DOI:10.1080/07391102.2012.762722

Sun, Chongbo; Tang, Tian
Study on the role of polyethylenimine as gene delivery carrier using molecular dynamics simulations
JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY, 28:399-416, FEB 1 2014
abstract, full text, DOI:10.1080/01694243.2012.693830

Spijker, Peter; Hiasa, Takumi; Musso, Tiziana; Nishioka, Rina; Onishi, Hiroshi; Foster, Adam S.
Understanding the Interface of Liquids with an Organic Crystal Surface from Atonnistic Simulations and AFM Experiments
JOURNAL OF PHYSICAL CHEMISTRY C, 118:2058-2066, JAN 30 2014
abstract, full text, DOI:10.1021/jp4106647

Chien, Michael W.; Johnson, Robert R.; Pillai, Shreekumar R.; Singh, Shree Ram; Johnson, A. T. Charlie, Jr.
Mechanics and Energetics of DNA Hybridization on Single-Walled Carbon Nanotubes Explored Using Adaptive Biasing Force Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 118:2209-2214, JAN 30 2014
abstract, full text, DOI:10.1021/jp4102288

Xiao, Shiyan; Klein, Michael L.; LeBard, David N.; Levine, Benjamin G.; Liang, Haojun; MacDermaid, Christopher M.; Afonso-Prieto, Mercedes
Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:873-889, JAN 30 2014
abstract, full text, DOI:10.1021/jp408383g

Lundborg, Magnus; Apostolov, Rossen; Spangberg, Daniel; Gardenas, Anders; van der Spoel, David; Lindahl, Erik
An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:260-269, JAN 30 2014
abstract, full text, DOI:10.1002/jcc.23495

Strauss, Ishai; Chan, Henry; Kral, Petr
Ultralong Polarization Chains Induced by Ions Solvated in Confined Water Monolayers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:1170-1173, JAN 29 2014
abstract, full text, DOI:10.1021/ja4087962

Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron
Communication: An existence test for dividing surfaces without recrossing
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 041104, JAN 28 2014
abstract, full text, DOI:10.1063/1.4862504

Solov'yov, Ilia A.; Domratcheva, Tatiana; Schulten, Klaus
Separation of photo-induced radical pair in cryptochrome to a functionally critical distance
SCIENTIFIC REPORTS, 4 Art. No. 3845, JAN 24 2014
abstract, full text, TCBG publications, DOI:10.1038/srep03845

Sun, Mei-Hui; Liu, Shuang-Quan; Du, Ke-Jie; Nie, Chang-Ming; Lin, Ying-Wu
A spectroscopic study of uranyl-cytochrome b(5)/cytochrome c interactions
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 118:130-137, JAN 24 2014
abstract, full text, DOI:10.1016/j.saa.2013.08.112

Meng, Yilin; Roux, Benoit
Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
JOURNAL OF MOLECULAR BIOLOGY, 426:423-435, JAN 23 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.001

Jean-Francois, Frantz L.; Dai, Jian; Yu, Lu; Myrick, Alissa; Rubin, Eric; Fajer, Piotr G.; Song, Likai; Zhou, Huan-Xiang; Cross, Timothy A.
Binding of MgtR, a Salmonella Transmembrane Regulatory Peptide, to MgtC, a Mycobacterium tuberculosis Virulence Factor: A Structural Study
JOURNAL OF MOLECULAR BIOLOGY, 426:436-446, JAN 23 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.014

Rashid, M. Harunur; Kuyucak, Serdar
Free Energy Simulations of Binding of HsTx1 Toxin to Kv1 Potassium Channels: the Basis of Kv1.3/Kv1.1 Selectivity
JOURNAL OF PHYSICAL CHEMISTRY B, 118:707-716, JAN 23 2014
abstract, full text, DOI:10.1021/jp410950h

Dolores Elola, M.; Rodriguez, Javier
Solvation of Coumarin 480 within nano-confining environments: Structure and dynamics
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 034702, JAN 21 2014
abstract, full text, DOI:10.1063/1.4861586

Jung, Segun; Schlick, Tamar
Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth Disease Virus IRES Captured by Dynamics Simulations
BIOPHYSICAL JOURNAL, 106:447-458, JAN 21 2014
abstract, full text, DOI:10.1016/j.bpj.2013.12.008

Li, Chun-Yang; Wei, Tian-Di; Zhang, Sheng-Hui; Chen, Xiu-Lan; Gao, Xiang; Wang, Peng; Xie, Bin-Bin; Su, Hai-Nan; Qin, Qi-Long; Zhang, Xi-Ying; Yu, Juan; Zhang, Hong-Hai; Zhou, Bai-Cheng; Yang, Gui-Peng; Zhang, Yu-Zhong
Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:1026-1031, JAN 21 2014
abstract, full text, DOI:10.1073/pnas.1312354111

Wakai, Nobuhiko; Takemura, Kazuhiro; Morita, Takami; Kitao, Akio
Mechanism of Deep-Sea Fish alpha-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e85852, JAN 20 2014
abstract, full text, DOI:10.1371/journal.pone.0085852

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Comparative theoretical study of the binding of potential cancer-treatment drugs to Checkpoint kinase 1
CHEMICAL PHYSICS LETTERS, 591:273-276, JAN 20 2014
abstract, full text, DOI:10.1016/j.cplett.2013.11.049

Van Ngo; Stefanovski, Darko; Haas, Stephan; Farley, Robert A.
Non-Equilibrium Dynamics Contribute to Ion Selectivity in the KcsA Channel
PLOS ONE, 9 Art. No. e86079, JAN 17 2014
abstract, full text, DOI:10.1371/journal.pone.0086079

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Correlated Dynamical Crossovers of the Hydration Layer of a Single-Stranded DNA Oligomer
JOURNAL OF PHYSICAL CHEMISTRY B, 118:413-422, JAN 16 2014
abstract, full text, DOI:10.1021/jp408234k

Beecher, Consuelo N.; Young, Robert P.; Langeslay, Derek J.; Mueller, Leonard J.; Larive, Cynthia K.
Hydroxyl-Proton Hydrogen Bonding in the Heparin Oligosaccharide Arixtra in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 118:482-491, JAN 16 2014
abstract, full text, DOI:10.1021/jp410540d

Lee, Sarah; Tran, Alan; Allsopp, Matthew; Lim, Joseph B.; Henin, Jerome; Klauda, Jeffery B.
CHARMM36 United Atom Chain Model for Lipids and Surfactants
JOURNAL OF PHYSICAL CHEMISTRY B, 118:547-556, JAN 16 2014
abstract, full text, DOI:10.1021/jp410344g

Megow, Joerg; May, Volkhard
Plasmon enhanced molecular absorption: A mixed quantum-classical description of supramolecular complexes attached to a metal nanoparticle
CHEMICAL PHYSICS, 428:6-13, JAN 15 2014
abstract, full text, DOI:10.1016/j.chemphys.2013.10.023

Escobar, Francisco Velazquez; Hildebrandt, Thomas; Utesch, Tillmann; Schmitt, Franz Josef; Seuffert, Ina; Michael, Norbert; Schulz, Claudia; Mroginski, Maria Andrea; Friedrich, Thomas; Hildebrandt, Peter
Structural Parameters Controlling the Fluorescence Properties of Phytochromes
BIOCHEMISTRY, 53:20-29, JAN 14 2014
abstract, full text, DOI:10.1021/bi401287u

Chamberlin, Adam; Qiu, Feng; Rebolledo, Santiago; Wang, Yibo; Noskov, Sergei Y.; Larsson, H. Peter
Hydrophobic plug functions as a gate in voltage-gated proton channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E273-E282, JAN 14 2014
abstract, full text, DOI:10.1073/pnas.1318018111

Zhang, Yanxing; Gao, Puyuan; Zhang, Liuyao; Yang, Zongxian
The search for the good Pd-based catalyst for oxygen reduction reaction: core-shell M4@Pd20 nanowires
JOURNAL OF NANOPARTICLE RESEARCH, 16 Art. No. 2225, JAN 10 2014
abstract, full text, DOI:10.1007/s11051-013-2225-x

Pepin, Robert; Laszlo, Kenneth J.; Peng, Bo; Marek, Ales; Bush, Matthew F.; Turecek, Frantisek
Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion-Molecule Complexes, and Fragment Separation
JOURNAL OF PHYSICAL CHEMISTRY A, 118:308-324, JAN 9 2014
abstract, full text, DOI:10.1021/jp411100c

Zhao, Juan; Shi, Jipei; Wang, Jianping
Amide-I Characteristics of Helical beta-Peptides by Linear Infrared Measurement and Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:94-106, JAN 9 2014
abstract, full text, DOI:10.1021/jp4095936

Honarparvar, Bahareh; Govender, Thavendran; Maguire, Glenn E. M.; Soliman, Mahmoud E. S.; Kruger, Hendrik G.
Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity
CHEMICAL REVIEWS, 114:493-537, JAN 8 2014
full text, DOI:10.1021/cr300314q

Cisneros, G. Andres; Karttunen, Mikko; Ren, Pengyu; Sagui, Celeste
Classical Electrostatics for Biomolecular Simulations
CHEMICAL REVIEWS, 114:779-814, JAN 8 2014
full text, DOI:10.1021/cr300461d

Petridis, Loukas; Arnbaye, Haile; Jagadamma, Sindhu; Kilbey, S. Michael, I.I.; Lokitz, Bradley S.; Lauter, Valeria; Mayes, Melanie A.
Spatial Arrangement of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 48:79-84, JAN 7 2014
abstract, full text, DOI:10.1021/es403430k

Duff, Nathan; Dahal, Yuba Raj; Schmit, Jeremy D.; Peters, Baron
Salting out the polar polymorph: Analysis by alchemical solvent transformation
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 014501, JAN 7 2014
abstract, full text, DOI:10.1063/1.4853775

Prieto, Lidia; He, Yi; Lazaridis, Themis
Protein Arcs May Form Stable Pores in Lipid Membranes
BIOPHYSICAL JOURNAL, 106:154-161, JAN 7 2014
abstract, full text, DOI:10.1016/j.bpj.2013.11.4490

Cruz-Chu, Eduardo R.; Malafeev, Alexander; Pajarskas, Tautrimas; Pivkin, Igor V.; Koumoutsakos, Petros
Structure and Response to Flow of the Glycocalyx Layer
BIOPHYSICAL JOURNAL, 106:232-243, JAN 7 2014
abstract, full text, DOI:10.1016/j.bpj.2013.09.060

Cai, Kaicong; Su, Tingting; Lin, Shen; Zheng, Renhui
Molecular mechanics force field-based general map for the solvation effect on amide I probe of peptide in different micro-environments
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 117:548-556, JAN 3 2014
abstract, full text, DOI:10.1016/j.saa.2013.08.058

Comer, Jeffrey; Roux, Benoit; Chipot, Christophe
Achieving ergodic sampling using replica-exchange free-energy calculations
MOLECULAR SIMULATION, 40:218-228, JAN 2 2014
abstract, full text, DOI:10.1080/08927022.2013.841909

Chen, Cong; Zhang, Kun; Wang, Ping; Li, Wei Zhong; Song, Yong Chen; Zhang, Ning
Ion hydration and hydrogen bond structure in NaCl solutions at temperatures and pressures for carbon dioxide sequestration: the effects of solvated CO2 molecules
MOLECULAR PHYSICS, 112:74-84, JAN 2 2014
abstract, full text, DOI:10.1080/00268976.2013.800244

Clark, Kevin M.; Yu, Yang; van der Donk, Wilfred A.; Blackburn, Ninian J.; Lu, Yi
Modulating the copper-sulfur interaction in type 1 blue copper azurin by replacing Cys112 with nonproteinogenic homocysteine
INORGANIC CHEMISTRY FRONTIERS, 1:153-158, 2014
abstract, full text, DOI:10.1039/c3qi00096f

Zobnina, V.G.; Chagovets, V.V.; Boryak, O.A.; Kosevich, M.V.
Mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers
Mass-spektrometriya, 11:97-106, 2014
abstract, full text

Fazenda, Alvaro Luiz; Mendes, Celso L.; Kale, Laxmikant V.; Panetta, Jairo; Rodrigues, Eduardo Rocha
Dynamic Load Balancing in GPU-Based Systems for a MPI program
2014 INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING & SIMULATION (HPCS), 154-161, 2014
abstract, full text

Drakulic, Branko J.; Gavrovic-Jankulovic, Marija
Dynamics of Uninhibited and Covalently Inhibited Cysteine Protease on Non-physiological pH
HIGH-PERFORMANCE COMPUTING INFRASTRUCTURE FOR SOUTH EAST EUROPE'S RESEARCH COMMUNITIES: RESULTS OF THE HP-SEE USER FORUM 2012, 2:75-82, 2014
abstract, full text, DOI:10.1007/978-3-319-01520-0_9

Damirchi, Behzad; Rouhollahi, Amir; Sohrabi, Salman; Mehr, Seyyed Mandi Nemati
MODELING AND STABILITY ANALYSIS OF TRUNCATED HIGH DENSITY LIPOPROTEIN (HDL) SYSTEM USING MARTINI COARSE GRAIN TECHNIQUE
PROCEEDINGS OF THE ASME INTERNATIONAL MECHANICAL ENGINEERING CONGRESS AND EXPOSITION, 2013, VOL 3A, Art. No. V03AT03A069, 2014
abstract, full text

Kondratyev, Maxim Sergeevich; Kabanov, Artem Valerievich; Samchenko, Alexander Anatolievich; Komarov, Vladislav Mikhailovich
High performance computations in the problem of increasing the thermostability of antioxidant enzymes
Vestnik MGTU Stankin, Issue 2, 106-110, 2014
abstract, full text

Baird, Nathan J.; West, Jeremey; Sosnick, Tobin R.
RNA Structure and Folding Analyzed Using Small-Angle X-Ray Scattering
HANDBOOK OF RNA BIOCHEMISTRY, VOLS 1 AND 2, 2ND EDITION, 407-425, 2014
full text

Auffinger, Pascal
Molecular Dynamics Simulations of RNA Systems
HANDBOOK OF RNA BIOCHEMISTRY, VOLS 1 AND 2, 2ND EDITION, 687-717, 2014
full text

Schmidt, Thomas C.; Paasche, Alexander; Grebner, Christoph; Ansorg, Kay; Becker, Johannes; Lee, Wook; Engels, Bernd
QM/MM Investigations Of Organic Chemistry Oriented Questions
ELECTRONIC EFFECTS IN ORGANIC CHEMISTRY, 351:25-101, 2014
abstract, full text, DOI:10.1007/128_2011_309

Lee, Michael D.; Graham, Bim; Swarbrick, James D.
Metal Complexes as Tools for Structural Biology
INORGANIC CHEMICAL BIOLOGY: PRINCIPLES, TECHNIQUES AND APPLICATIONS, 37-62, 2014
full text

Muccioli, Luca; D'Avino, Gabriele; Berardi, Roberto; Orlandi, Silvia; Pizzirusso, Antonio; Ricci, Matteo; Roscioni, Otello Maria; Zannoni, Claudio
Supramolecular Organization of Functional Organic Materials in the Bulk and at Organic/Organic Interfaces: A Modeling and Computer Simulation Approach
MULTISCALE MODELLING OF ORGANIC AND HYBRID PHOTOVOLTAICS, 352:39-101, 2014
abstract, full text, DOI:10.1007/128_2013_470

Borreguero, Jose M.; Campbell, Stuart I.; Delaire, Olivier A.; Doucet, Mathieu; Goswami, Monojoy; Hagen, Mark E.; Lynch, Vickie E.; Proffen, Thomas E.; Ren, Shelly; Savici, Andrei T.; Sumpter, Bobby G.
Integrating Advanced Materials Simulation Techniques into an Automated Data Analysis Workflow at the Spallation Neutron Source
TMS 2014 SUPPLEMENTAL PROCEEDINGS, 297-308, 2014
abstract, full text

Zarudnev, E. S.; Karachevtsev, V. A.
Controlled Aggregation of Biopolymer-Wrapped Carbon Nanotubes in Aqueous Suspension, Induced by Cationic Porphyrin
MACROMOLECULAR SYMPOSIA, 335:51-57, JAN 2014
abstract, full text, DOI:10.1002/masy.201200121

Li, Chen; Hua, Xue-Liang
Towards Positive Unlabeled Learning for Parallel Data Mining: A Random Forest Framework
ADVANCED DATA MINING AND APPLICATIONS, ADMA 2014, 8933:573-587, 2014
abstract, full text

Shamloo, Amir; Nikbin, Ehsan; Mehboudi, Nastaran; Damirchi, Behzad
HOMO-OLIGOMERIZATION OF TRANSMEMBRANE alpha-DOMAIN OF INTEGRIN
2014 36TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 1162-1165, 2014
abstract, full text

Macwan, Isaac; Zhao, Zihe; Sobh, Omar; Patra, Prabir
A FLAGELLUM BASED STUDY OF SEMICONDUCTOR NANOFABRICATION THROUGH MAGNETOTAXIS
2014 36TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 2777-2780, 2014
abstract, full text

Reeves, Melissa S.; Whitnell, Robert M.
New Computational Physical Chemistry Experiments: Using POGIL Techniques with ab Initio and Molecular Dynamics Calculations
ADDRESSING THE MILLENNIAL STUDENT IN UNDERGRADUATE CHEMISTRY, 1180:71-90, 2014
abstract, full text

Langmead, Christopher James
Generative Models of Conformational Dynamics
PROTEIN CONFORMATIONAL DYNAMICS, 805:87-105, 2014
abstract, full text, DOI:10.1007/978-3-319-02970-2_4

Kuyucak, Serdar; Norton, Raymond S.
Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics
FUTURE MEDICINAL CHEMISTRY, 6:1645-1658, 2014
abstract, full text, DOI:10.4155/FMC.14.98

Yim, Keun Soo
Characterization of Impact of Transient Faults and Detection of Data Corruption Errors in Large-Scale N-Body Programs Using Graphics Processing Units
2014 IEEE 28TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM, DOI:10.1109/IPDPS.2014.55, 2014
abstract, full text, DOI:10.1109/IPDPS.2014.55

Badu, Shyam R.; Melnik, Roderik; Paliy, Maxim; Prabhakar, Sanjay; Sebetci, Ali; Shapiro, Bruce A.
High Performance Computing Studies of RNA Nanotubes
PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, 601-607, 2014
abstract, full text

LeVine, Michael; Perez-Aguilar, Jose Manuel; Weinstein, Harel
N-body Information Theory (NbIT) Analysis of Rigid-Body Dynamics in Intracellular Loop 2 of the 5-HT2A Receptor
PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, 1190-1201, 2014
abstract, full text

Katagiri, Satoshi; Hayashi, Takaaki; Akahori, Masakazu; Itabashi, Takeshi; Nishino, Jo; Yoshitake, Kazutoshi; Furuno, Masaaki; Ikeo, Kazuho; Okada, Tetsuji; Tsuneoka, Hiroshi; Iwata, Takeshi
RHO Mutations (p.W126L and p.A346P) in Two Japanese Families with Autosomal Dominant Retinitis Pigmentosa
JOURNAL OF OPHTHALMOLOGY, Art. No. 210947, 2014
abstract, full text, DOI:10.1155/2014/210947

Azamat, J.; Sardroodi, J. J.; Rastkar, A.
Water desalination through armchair carbon nanotubes: a molecular dynamics study
RSC ADVANCES, 4:63712-63718, 2014
abstract, full text, DOI:10.1039/c4ra08249d

Luan, Binquan; Zhou, Bo; Tien Huynh; Zhou, Ruhong
Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane
NANOSCALE, 6:11479-11483, 2014
abstract, full text, DOI:10.1039/c4nr02754j

Ou, Shu-Ching; Cui, Di; Patel, Sandeep
Association of alkanes with the aqueous liquid-vapor interface: a reference system for interpreting hydrophobicity generally through interfacial fluctuations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26779-26785, 2014
abstract, full text, DOI:10.1039/c4cp03170a

Saharay, Moumita; Kirkpatrick, R. James
Ab initio and metadynamics studies on the role of essential functional groups in biomineralization of calcium carbonate and environmental situations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26843-26854, 2014
abstract, full text, DOI:10.1039/c4cp03904a

Zhao, Yuan; Chen, Nanhao; Mo, Yirong; Cao, Zexing
A full picture of enzymatic catalysis by hydroxynitrile lyases from Hevea brasiliensis: protonation dependent reaction steps and residue-gated movement of the substrate and the product
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26864-26875, 2014
abstract, full text, DOI:10.1039/c4cp04032e

Meneksedag-Erol, Deniz; Sun, Chongbo; Tang, Tian; Uludag, Hasan
Molecular Dynamics Simulations of Polyplexes and Lipoplexes Employed in Gene Delivery
INTRACELLULAR DELIVERY II: FUNDAMENTALS AND APPLICATIONS, 7:277-311, 2014
abstract, full text, DOI:10.1007/978-94-017-8896-0_15

Kutalkova, Eva; Hrncirik, Josef; Ingr, Marek
Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:25906-25915, 2014
abstract, full text, DOI:10.1039/c4cp03676j

Dutta, Debodyuti; Mishra, Sabyashachi
The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM method
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26348-26358, 2014
abstract, full text, DOI:10.1039/c4cp03986f

Kukkurainen, Sampo; Maatta, Juha A.; Saeger, John; Valjakka, Jarkko; Vogel, Viola; Hytonen, Vesa P.
The talin-integrin interface under mechanical stress
MOLECULAR BIOSYSTEMS, 10:3217-3228, 2014
abstract, full text, DOI:10.1039/c4mb00341a

Sikdar, Samapan; Chakrabarti, J.; Ghosh, Mahua
A microscopic insight from conformational thermodynamics to functional ligand binding in proteins
MOLECULAR BIOSYSTEMS, 10:3280-3289, 2014
abstract, full text, DOI:10.1039/c4mb00434e

Moreau, Pascale; Dezhenkova, Lyubov G.; Anizon, Fabrice; Nauton, Lionel; Thery, Vincent; Liang, Shuguang; Kaluzhny, Dmitry N.; Shtil, Alexander A.
New Potent and Selective Inhibitor of Pim-1/3 Protein Kinases Sensitizes Human Colon Carcinoma Cells to Doxorubicin
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY, 14:1228-1236, 2014
abstract, full text

Mielecki, Marcin; Milner-Krawczyk, Malgorzata; Grzelak, Krystyna; Mielecki, Damian; Krzysko, Krystiana A.; Lesyng, Bogdan; Priebe, Waldemar
Analogs of Cinnamic Acid Benzyl Amide As Nonclassical Inhibitors of Activated JAK2 Kinase
CURRENT CANCER DRUG TARGETS, 14:638-651, 2014
abstract, full text

Pontecchiani, Fabio; Simonovsky, Eyal; Wieczorek, Robert; Barbosa, Nuno; Rowinska-Zyrek, Magdalena; Potocki, Slawomir; Remelli, Maurizio; Miller, Yifat; Kozlowski, Henryk
The unusual binding mechanism of Cu(II) ions to the poly-histidyl domain of a peptide found in the venom of an African viper
DALTON TRANSACTIONS, 43:16680-16689, 2014
abstract, full text, DOI:10.1039/c4dt02257b

Hirst, Jonathan D.; Glowacki, David R.; Baaden, Marc
Molecular simulations and visualization: introduction and overview
FARADAY DISCUSSIONS, 169:9-22, 2014
abstract, full text, DOI:10.1039/c4fd90024c

Dreher, Matthieu; Prevoteau-Jonquet, Jessica; Trellet, Mikael; Piuzzi, Marc; Baaden, Marc; Raffin, Bruno; Ferey, Nicolas; Robert, Sophie; Limet, Sebastien
ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations
FARADAY DISCUSSIONS, 169:119-142, 2014
abstract, full text, DOI:10.1039/c3fd00142c

Stone, John E.; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
FARADAY DISCUSSIONS, 169:265-283, 2014
abstract, full text, TCBG publications, DOI:10.1039/c4fd00005f

Liu, Peng; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:24169-24172, 2014
abstract, full text, DOI:10.1039/c4cp04200j

Bai, Qifeng; Zhang, Yang; Li, Xiaomeng; Chen, Wenbo; Liu, Huanxiang; Yao, Xiaojun
Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:24332-24338, 2014
abstract, full text, DOI:10.1039/c4cp03331k

Turpin, Eleanor R.; Mulholland, Sam; Teale, Andrew M.; Bonev, Boyan B.; Hirst, Jonathan D.
New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations
RSC ADVANCES, 4:48621-48631, 2014
abstract, full text, DOI:10.1039/c4ra09897h

Khan, Rashid Ahmed; Liu, Jiyuan; Zhang, Yalin
Catalytic inactivation of alkaline phosphatase by cantharidin, an inhibitor of protein phosphatase
RSC ADVANCES, 4:49987-49994, 2014
abstract, full text, DOI:10.1039/c4ra09285f

Gajula, Kiran S.; Huwe, Peter J.; Mo, Charlie Y.; Crawford, Daniel J.; Stivers, James T.; Radhakrishnan, Ravi; Kohli, Rahul M.
High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase
NUCLEIC ACIDS RESEARCH, 42:9964-9975, 2014
abstract, full text, DOI:10.1093/nar/gku689

Lionta, Evanthia; Spyrou, George; Vassilatis, Demetrios K.; Cournia, Zoe
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:1923-1938, 2014
abstract, full text, DOI:10.2174/1568026614666140929124445

D'Annessa, Ilda; Coletta, Andrea; Sutthibutpong, Thana; Mitchell, Jonathan; Chillemi, Giovanni; Harris, Sarah; Desideri, Alessandro
Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site
NUCLEIC ACIDS RESEARCH, 42:9304-9312, 2014
abstract, full text, DOI:10.1093/nar/gku654

del Valle, Luis J.; Bertran, Oscar; Chaves, Gustavo; Revilla-Lopez, Guillermo; Rivas, Manuel; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
DNA adsorbed on hydroxyapatite surfaces
JOURNAL OF MATERIALS CHEMISTRY B, 2:6953-6966, 2014
abstract, full text, DOI:10.1039/c4tb01184h

Segura-Cabrera, A.; Garcia-Perez, C. A.; Cipres-Flores, F. J.; Cuevas-Hernandez, R. I.; Trujillo-Ferrara, J. G.; Correa-Basurto, J.; Soriano-Ursua, M. A.
Molecular dynamics simulations to explore the active/inactive conformers of guinea pig beta(2) adrenoceptor for the selective design of agonists or antagonists
MOLECULAR SIMULATION, 40:1244-1254, 2014
abstract, full text, DOI:10.1080/08927022.2013.857771

Luna-Palencia, Gabriela R.; Martinez-Ramos, Federico; Vasquez-Moctezuma, Ismael; Jonathan Fragoso-Vazquez, Manuel; Elena Mendieta-Wejebe, Jessica; Padilla-Martinez, Itzia I.; Sixto-Lopez, Yudibeth; Mendez-Luna, David; Trujillo-Ferrara, Jose; Meraz-Rios, Marco A.; Fonseca-Sabater, Yadira; Correa-Basurto, Jose
Three Amino Acid Derivatives of Valproic Acid: Design, Synthesis, Theoretical and Experimental Evaluation as Anticancer Agents
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY, 14:984-993, 2014
abstract, full text

Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs
CHEMICAL SOCIETY REVIEWS, 43:6750-6764, 2014
abstract, full text, DOI:10.1039/c3cs60459d

Mendes, Celso L.; Bode, Brett; Bauer, Gregory H.; Enos, Jeremy; Beldica, Cristina; Kramer, William T.
Deploying a Large Petascale System: the Blue Waters Experience
2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29:198-209, 2014
abstract, full text, DOI:10.1016/j.procs.2014.05.018

Ieong, Pek U.; Sorensen, Jesper; Vemu, Prasantha L.; Wong, Celia W.; Demir, Oezlem; Williams, Nadya P.; Wang, Jianwu; Crawl, Daniel; Swift, Robert V.; Malmstrom, Robert D.; Altintas, Ilkay; Amaro, Rommie E.
Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations
2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29:1745-1755, 2014
abstract, full text, DOI:10.1016/j.procs.2014.05.159

Kamath, Ganesh; Narayanan, Badri; Sankaranarayanan, Subramanian K. R. S.
Atomistic origin of superior performance of ionic liquid electrolytes for Al-ion batteries
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:20387-20391, 2014
abstract, full text, DOI:10.1039/c4cp02840f

Bhattacharya, R.; Kanchi, Subbarao; Roobala, C.; Lakshminarayanan, A.; Seeck, Oliver H.; Maiti, Prabal K.; Ayappa, K. G.; Jayaraman, N.; Basu, J. K.
A new microscopic insight into membrane penetration and reorganization by PETIM dendrimers
SOFT MATTER, 10:7577-7587, 2014
abstract, full text, DOI:10.1039/c4sm01112k

Kostopoulou, Ourania N.; Kouvela, Ekaterini C.; Magoulas, George E.; Garnelis, Thomas; Panagoulias, Ioannis; Rodi, Maria; Papadopoulos, Georgios; Mouzaki, Athanasia; Dinos, George P.; Papaioannou, Dionissios; Kalpaxis, Dimitrios L.
Conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol
NUCLEIC ACIDS RESEARCH, 42:8621-8634, 2014
abstract, full text, DOI:10.1093/nar/gku539

Espinoza-Fonseca, L. Michel; Colson, Brett A.; Thomas, David D.
Effects of pseudophosphorylation mutants on the structural dynamics of smooth muscle myosin regulatory light chain
MOLECULAR BIOSYSTEMS, 10:2693-2698, 2014
abstract, full text, DOI:10.1039/c4mb00364k

Lo, Kin Cheung; Li, Sheung Yin; Chan, Wai Kin
Photoconductivity enhancement and charge transport properties in a conjugated polyelectrolyte/carbon nanotube hybrid studied by scanning probe microscopy
JOURNAL OF MATERIALS CHEMISTRY C, 2:7739-7751, 2014
abstract, full text, DOI:10.1039/c4tc00819g

Martinez-Archundia, Marlet; Correa-Basurto, Jose
Molecular dynamics simulations reveal initial structural and dynamic features for the A(2)AR as a result of ligand binding
MOLECULAR SIMULATION, 40:996-1014, 2014
abstract, full text, DOI:10.1080/08927022.2013.835485

Dixit, Anshuman; Verkhivker, Gennady M.
Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 653487, 2014
abstract, full text, DOI:10.1155/2014/653487

Chen, Qile; Kong, Xian; Li, Jipeng; Lu, Diannan; Liu, Zheng
Electrokinetic desalination using honeycomb carbon nanotubes (HC-CNTs): a conceptual study by molecular simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18941-18948, 2014
abstract, full text, DOI:10.1039/c4cp02679a

Walczewska-Szewc, Katarzyna; Corry, Ben
Do bifunctional labels solve the problem of dye diffusion in FRET analysis?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18949-18954, 2014
abstract, full text, DOI:10.1039/c4cp02110j

Ilizaliturri-Flores, Ian; Correa-Basurto, Jose; Benitez-Cardoza, Claudia G.; Zamorano-Carrillo, Absalom
A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1707-1719, 2014
abstract, full text, DOI:10.1080/07391102.2013.833858

Kondratyev, Maxim S.; Lunin, Sergey M.; Kabanov, Artem V.; Samchenko, Alexandr A.; Komarov, Vladislav M.; Fesenko, Evgeny E.; Novoselova, Elena G.
Structural and dynamic properties of thymopoietin mimetics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1793-1801, 2014
abstract, full text, DOI:10.1080/07391102.2013.834851

Chapron, Yves; Charlet, Laurent; Sahai, Nita
Fate of pathological prion (PrP(sc)92-138) in soil and water: prion-clay nanoparticle molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1802-1816, 2014
abstract, full text, DOI:10.1080/07391102.2013.836461

Hudiyanti, Dwi; Radifar, Muhammad; Raharjo, Tri Joko; Narsito, Narsito; Noegrohati, Sri
A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water
JOURNAL OF CHEMISTRY, Art. No. 273084, 2014
abstract, full text, DOI:10.1155/2014/273084

Mura, Cameron; McAnany, Charles E.
An introduction to biomolecular simulations and docking
MOLECULAR SIMULATION, 40:732-764, 2014
abstract, full text, DOI:10.1080/08927022.2014.935372

LeBard, David N.
Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware
MOLECULAR SIMULATION, 40:802-820, 2014
abstract, full text, DOI:10.1080/08927022.2014.899700

des Georges, Amedee; Hashem, Yaser; Buss, Sarah N.; Jossinet, Fabrice; Zhang, Qin; Liao, Hstau Y.; Fu, Jie; Jobe, Amy; Grassucci, Robert A.; Langlois, Robert; Bajaj, Chandrajit; Westhof, Eric; Madison-Antenucci, Susan; Frank, Joachim
High-resolution Cryo-EM Structure of the Trypanosoma brucei Ribosome: A Case Study
COMPUTATIONAL METHODS FOR THREE-DIMENSIONAL MICROSCOPY RECONSTRUCTION, 97-132, 2014
abstract, full text, DOI:10.1007/978-1-4614-9521-5_5

Bai, Qifeng; Perez-Sanchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun
Ligand induced change of beta(2) adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:15874-15885, 2014
abstract, full text, DOI:10.1039/c4cp01185f

MacDonald, Corey A.; Bushnell, Eric A. C.; Gauld, James W.; Boyd, Russell J.
The catalytic formation of leukotriene C-4: a critical step in inflammatory processes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:16284-16289, 2014
abstract, full text, DOI:10.1039/c4cp01984a

Kumar, Amit; Melis, Paola; Genna, Vito; Cocco, Eleonora; Marrosu, Maria Giovanna; Pieroni, Enrico
Antigenic peptide molecular recognition by the DRB1-DQB1 haplotype modulates multiple sclerosis susceptibility
MOLECULAR BIOSYSTEMS, 10:2043-2054, 2014
abstract, full text, DOI:10.1039/c4mb00203b

Zorzini, Valentina; Buts, Lieven; Sleutel, Mike; Garcia-Pino, Abel; Talavera, Ariel; Haesaerts, Sarah; De Greve, Henri; Cheung, Ambrose; van Nuland, Nico A. J.; Loris, Remy
Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics
NUCLEIC ACIDS RESEARCH, 42:6709-6725, 2014
abstract, full text, DOI:10.1093/nar/gku266

Orozco, Modesto
A theoretical view of protein dynamics
CHEMICAL SOCIETY REVIEWS, 43:5051-5066, 2014
abstract, full text, DOI:10.1039/c3cs60474h

Jin, Lu; Ye, Fei; Zhao, Dan; Chen, Shijie; Zhu, Kongkai; Zheng, Mingyue; Jiang, Ren-Wang; Jiang, Hualiang; Luo, Cheng
Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis
BIOMED RESEARCH INTERNATIONAL, Art. No. 304563, 2014
abstract, full text, DOI:10.1155/2014/304563

Kumar, Vikash; Chandra, Sharat; Siddiqi, Mohammad Imran
Recent Advances in the Development of Antiviral Agents Using Computer-aided Structure Based Approaches
CURRENT PHARMACEUTICAL DESIGN, 20:3488-3499, 2014
abstract, full text

Abeyrathne, Chathurika D.; Halgamuge, Malka N.; Farrell, Peter M.; Skafidas, Efstratios
Dielectric properties of liquid phase molecular clusters using the external field method: molecular dynamics study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:13943-13947, 2014
abstract, full text, DOI:10.1039/c4cp00716f

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Liu, Yafang
Dynamics study on the stability of animal prion proteins
TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI, 39:188-195, 2014
abstract, full text, DOI:10.5505/tjb.2014.21033

Liu, Yingting; Radhakrishnan, Ravi
Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain
MOLECULAR BIOSYSTEMS, 10:1890-1904, 2014
abstract, full text, DOI:10.1039/c3mb70620f

Bai, Qifeng; Shi, Danfeng; Zhang, Yang; Liu, Huanxiang; Yao, Xiaojun
Exploration of the antagonist CP-376395 escape pathway for the corticotropin-releasing factor receptor 1 by random acceleration molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 10:1958-1967, 2014
abstract, full text, DOI:10.1039/c4mb00037d

Xu, Jia-Jia; Yi, Hai-Bo; Li, Hui-Ji; Chen, Yun
Ionic solvation and association in LiCl aqueous solution: a density functional theory, polarised continuum model and molecular dynamics investigation
MOLECULAR PHYSICS, 112:1710-1723, 2014
abstract, full text, DOI:10.1080/00268976.2013.860244

Plehn, Thomas; Megow, Joerg; May, Volkhard
Concerted charge and energy transfer processes in a highly flexible fullerene-dye system: a mixed quantum-classical study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:12949-12958, 2014
abstract, full text, DOI:10.1039/c4cp01081g

Murase, Sara K.; Haspel, Nurit; del Valle, Luis J.; Perpete, Eric A.; Michaux, Catherine; Nussinov, Ruth; Puiggali, Jordi; Aleman, Carlos
Molecular characterization of L-phenylalanine terminated poly(L-lactide) conjugates
RSC ADVANCES, 4:23231-23241, 2014
abstract, full text, DOI:10.1039/c4ra01534g

Wineman-Fisher, Vered; Simkovitch, Ron; Shomer, Shay; Gepshtein, Rinat; Huppert, Dan; Saif, Mari; Kallio, Karen; Remington, S. James; Miller, Yifat
Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:11196-11208, 2014
abstract, full text, DOI:10.1039/c4cp00311j

Weng, Lindong; Elliott, Gloria D.
Dynamic and thermodynamic characteristics associated with the glass transition of amorphous trehalose-water mixtures
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:11555-11565, 2014
abstract, full text, DOI:10.1039/c3cp55418j

Walczewska-Szewc, Katarzyna; Corry, Ben
Accounting for dye diffusion and orientation when relating FRET measurements to distances: three simple computational methods
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:12317-12326, 2014
abstract, full text, DOI:10.1039/c4cp01222d

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A.; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John
The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations
SOFT MATTER, 10:3716-3725, 2014
abstract, full text, DOI:10.1039/c4sm00066h

Di Leva, Francesco Saverio; Novellino, Ettore; Cavalli, Andrea; Parrinello, Michele; Limongelli, Vittorio
Mechanistic insight into ligand binding to G-quadruplex DNA
NUCLEIC ACIDS RESEARCH, 42:5447-5455, 2014
abstract, full text, DOI:10.1093/nar/gku247

Seitz, Patrick; Modarres, Hassan Pezeshgi; Borgeaud, Sandrine; Bulushev, Roman D.; Steinbock, Lorenz J.; Radenovic, Aleksandra; Dal Peraro, Matteo; Blokesch, Melanie
ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLOS GENETICS, 10 Art. No. e1004066, JAN 2014
abstract, full text, DOI:10.1371/journal.pgen.1004066

Binkowski, T. Andrew; Jiang, Wei; Roux, Benoit; Anderson, Wayne F.; Joachimiak, Andrzej
Virtual High-Throughput Ligand Screening
STRUCTURAL GENOMICS AND DRUG DISCOVERY: METHODS AND PROTOCOLS, 1140:251-261, 2014
abstract, full text, DOI:10.1007/978-1-4939-0354-2_19

Cardamone, Salvatore; Hughes, Timothy J.; Popelier, Paul L. A.
Multipolar electrostatics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:10367-10387, 2014
abstract, full text, DOI:10.1039/c3cp54829e

Nayar, Divya; Chakravarty, Charusita
Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:10199-10213, 2014
abstract, full text, DOI:10.1039/c3cp55147d

Doss, C. George Priya; Chakraborty, Chiranjib; Narayan, Vaishnavi; Kumar, D. Thirumal
Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 94, 94:365-423, 2014
abstract, full text, DOI:10.1016/B978-0-12-800168-4.00010-X

Chen, Yi; Liu, Logan
Low cost, high sensitivity SERS nano-bio-chip for kinase profiling, drug monitoring and environmental detection: a translational platform technology
PLASMONICS IN BIOLOGY AND MEDICINE XI, 8957 Art. No. 895702, 2014
abstract, full text, DOI:10.1117/12.2062790

Vitorovic, Aleksandar; Tomasevic, Milo V.; Milutinovic, Veljko M.
Manual Parallelization Versus State-of-the-Art Parallelization Techniques: The SPEC CPU2006 as a Case Study
ADVANCES IN COMPUTERS, VOL 92, 92:203-251, 2014
abstract, full text, DOI:10.1016/B978-0-12-420232-0.00005-2

Frankevich, Vladimir; Chagovets, Vitaliy; Widjaja, Fanny; Barylyuk, Konstantin; Yang, Zhiyi; Zenobi, Renato
Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:8911-8920, 2014
abstract, full text, DOI:10.1039/c3cp54521k

Raz, Yoav; Adler, Juliane; Vogel, Alexander; Scheidt, Holger A.; Haeupl, Tilmann; Abel, Bernd; Huster, Daniel; Miller, Yifat
The influence of the triangle K280 mutation and N- or C-terminal extensions on the structure, dynamics, and fibril morphology of the tau R2 repeat
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:7710-7717, 2014
abstract, full text, DOI:10.1039/c3cp54890b

Johnston, Jennifer M.; Filizola, Marta
Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods
G PROTEIN-COUPLED RECEPTORS - MODELING AND SIMULATION, 796:95-125, 2014
abstract, full text, DOI:10.1007/978-94-007-7423-0_6

Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D.
Sequence-dependent folding landscapes of adenine riboswitch aptamers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:6376-6382, 2014
abstract, full text, DOI:10.1039/c3cp53932f

Miao, Yinglong; Nichols, Sara E.; McCammon, J. Andrew
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:6398-6406, 2014
abstract, full text, DOI:10.1039/c3cp53962h

He, Jia; Wu, Ming; Feng, Xizeng; Shao, Xueguang; Cai, Wensheng
Immobilization of papain on nanoporous silica
RSC ADVANCES, 4:13304-13312, 2014
abstract, full text, DOI:10.1039/c3ra47346e

Caruso, Mario; Gatto, Emanuela; Placidi, Ernesto; Ballano, Gema; Formaggio, Fernando; Toniolo, Claudio; Zanuy, David; Aleman, Carlos; Venanzi, Mariano
A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation
SOFT MATTER, 10:2508-2519, 2014
abstract, full text, DOI:10.1039/c3sm52831f

Zhang, Kai; Zhao, Wei-Jie; Leng, Xiao-Yao; Wang, Sha; Yao, Ke; Yan, Yong-Bin
The importance of the last strand at the C-terminus in beta B2-crystallin stability and assembly
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842:44-55, JAN 2014
abstract, full text, DOI:10.1016/j.bbadis.2013.10.001

Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolfgang; Gonzalez, Tania; Desplats, Paula; Michael, Sarah E.; Trejo-Morales, Margarita; Overk, Cassia R.; Masliah, Eliezer
Structural Diversity of Alzheimer's Disease Amyloid-beta Dimers and Their Role in Oligomerization and Fibril Formation
JOURNAL OF ALZHEIMERS DISEASE, 39:583-600, 2014
abstract, full text, DOI:10.3233/JAD-131589

Martin, Lewis J.; Chao, Rebecca; Corry, Ben
Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer
BIOPHYSICAL CHEMISTRY, 185:98-107, JAN 2014
abstract, full text, DOI:10.1016/j.bpc.2013.12.003

Telpoukhovskaia, Maria A.; Rodriguez-Rodriguez, Cristina; Cawthray, Jacqueline F.; Scott, Lauren E.; Page, Brent D. G.; Ali-Torres, Jorge; Sodupe, Mariona; Bailey, Gwendolyn A.; Patrick, Brian O.; Orvig, Chris
3-Hydroxy-4-pyridinone derivatives as metal ion and amyloid binding agents
METALLOMICS, 6:249-262, 2014
abstract, full text, DOI:10.1039/c3mt00135k

Das, Amit; Chakrabarti, Jaydeb; Ghosh, Mahua
Thermodynamics of interfacial changes in a protein-protein complex
MOLECULAR BIOSYSTEMS, 10:437-445, 2014
abstract, full text, DOI:10.1039/c3mb70249a

Juntadech, Thanate; Kanintronkul, Yodsoi; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan
Importance of polarity of the alpha 4-alpha 5 loop residue-Asn(166) in the pore-forming domain of the Bacillus thuringiensis Cry4Ba toxin: Implications for ion permeation and pore opening
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:319-327, JAN 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.10.002

Basu, Ipsita; Chattopadhyay, Amitabha; Mukhopadhyay, Chaitali
Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:328-338, JAN 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.10.005

Sun, Tian-Yang; Liang, Li-Jun; Wang, Qi; Laaksonen, Aatto; Wu, Tao
A molecular dynamics study on pH response of protein adsorbed on peptide-modified polyvinyl alcohol hydrogel
BIOMATERIALS SCIENCE, 2:419-426, 2014
abstract, full text, DOI:10.1039/c3bm60213c

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
A steered molecular dynamics mediated hit discovery for histone deacetylases
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:3777-3791, 2014
abstract, full text, DOI:10.1039/c3cp53511h

Alsharif, Shada A.; Chen, Liao Y.; Tlahuice-Flores, Alfredo; Whetten, Robert L.; Yacaman, Miguel Jose
Interaction between functionalized gold nanoparticles in physiological saline
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:3909-3913, 2014
abstract, full text, DOI:10.1039/c3cp54503b

Chen, Xuebo; Fang, Weihai; Wang, Haobin
Slow deactivation channels in UV-photoexcited adenine DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:4210-4219, 2014
abstract, full text, DOI:10.1039/c3cp55020f

Hinsen, Konrad
MOSAIC: A Data Model and File Formats for Molecular Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:131-137, JAN 2014
abstract, full text, DOI:10.1021/ci400599y

Koukos, Panagiotis I.; Glykos, Nicholas M.
On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:209-217, JAN 2014
abstract, full text, DOI:10.1021/ci4005817

Shams, Hengameh; Holt, Brian D.; Mahboobi, Seyed Hanif; Jahed, Zeinab; Islam, Mohammad F.; Dahl, Kris Noel; Mofrad, Mohammad R. K.
Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes
ACS NANO, 8:188-197, JAN 2014
abstract, full text, DOI:10.1021/nn402865e

Abrams, Cameron; Bussi, Giovanni
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
ENTROPY, 16:163-199, JAN 2014
abstract, full text, DOI:10.3390/e16010163

Ban, Ehsan; Picu, Catalin R.
Strength of DNA Sticky End Links
BIOMACROMOLECULES, 15:143-149, JAN 2014
abstract, full text, DOI:10.1021/bm401425k

Carlotto, Silvia; Zerbetto, Mirco
Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N '-methyl-L-alanylamide Dipeptide
JOURNAL OF CHEMICAL EDUCATION, 91:96-102, JAN 2014
abstract, full text, DOI:10.1021/ed400346v

Lee, Tai-Sung; Radak, Brian K.; Huang, Ming; Wong, Kin-Yiu; York, Darrin M.
Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:24-34, JAN 2014
abstract, full text, DOI:10.1021/ct400691f

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian
Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:122-133, JAN 2014
abstract, full text, DOI:10.1021/ct400713t

Doemer, Manuel; Maurer, Patrick; Campomanes, Pablo; Tavernelli, Ivano; Rothlisberger, Ursula
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:412-422, JAN 2014
abstract, full text, DOI:10.1021/ct400697n

Grime, John. M. A.; Voth, Gregory A.
Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:423-431, JAN 2014
abstract, full text, DOI:10.1021/ct400727q

Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang
Spontaneous nanoinjection with carbon nanotubes: a molecular dynamics simulation study
JOURNAL OF MATERIALS CHEMISTRY B, 2:859-867, 2014
abstract, full text, DOI:10.1039/c3tb21468k

Yang, Zaixing; Xia, Zhen; Tien Huynh; King, Jonathan A.; Zhou, Ruhong
Dissecting the contributions of beta-hairpin tyrosine pairs to the folding and stability of long-lived human gamma-crystallins
NANOSCALE, 6:1797-1807, 2014
abstract, full text, DOI:10.1039/c3nr03782g

Cordova-Mateo, Esther; Bertran, Oscar; Zhang, Baozhong; Vlassopoulos, Dimitris; Pasquino, Rossana; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Interactions in dendronized polymers: intramolecular dominates intermolecular
SOFT MATTER, 10:1032-1044, 2014
abstract, full text, DOI:10.1039/c3sm52343h

Xiao, Shiyan; Zhu, Hong; Wang, Lei; Liang, Haojun
DNA conformational flexibility study using phosphate backbone neutralization model
SOFT MATTER, 10:1045-1055, 2014
abstract, full text, DOI:10.1039/c3sm52345d

Myat, Darli T.; Stewart, Matthew B.; Mergen, Max; Zhao, Oliver; Orbell, John D.; Gray, Stephen
Experimental and computational investigations of the interactions between model organic compounds and subsequent membrane fouling
WATER RESEARCH, 48:108-118, JAN 1 2014
abstract, full text, DOI:10.1016/j.watres.2013.09.020

Nishino, Noriko; Hollingsworth, Scott A.; Stern, Abraham C.; Roeselova, Martina; Tobias, Douglas J.; Finlayson-Pitts, Barbara J.
Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2358-2367, 2014
abstract, full text, DOI:10.1039/c3cp54118e

Zhao, Jun; Hu, Rundong; Sciacca, Michele F. M.; Brender, Jeffrey R.; Chen, Hong; Ramamoorthy, Ayyalusamy; Zheng, Jie
Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2368-2377, 2014
abstract, full text, DOI:10.1039/c3cp53345j

Cheng, Chang-Li; Zhang, Ming-Zhen; Zhao, Guang-Jiu
Mechanical stability and thermal conductivity of beta-barrel in green fluorescent protein by steered molecular dynamics
RSC ADVANCES, 4:6513-6516, 2014
abstract, full text, DOI:10.1039/c3ra42679c

Gillespie, C. M.; Asthagiri, D.; Lenhoff, A. M.
Polymorphic Protein Crystal Growth: Influence of Hydration and Ions in Glucose Isomerase
CRYSTAL GROWTH & DESIGN, 14:46-57, JAN 2014
abstract, full text, DOI:10.1021/cg401063b

Du, Kun; Liu, Zhongmei; Cui, Wenjing; Zhou, Li; Liu, Yi; Du, Guocheng; Chen, Jian; Zhou, Zhemin
pH-Dependent Activation of Streptomyces hygroscopicus Transglutaminase Mediated by Inteinle
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:723-729, JAN 2014
abstract, full text, DOI:10.1128/AEM.02820-13

Koseki, Yuji; Aoki, Shunsuke
Computational Medicinal Chemistry for Rational Drug Design: Identification of Novel Chemical Structures with Potential Anti-Tuberculosis Activity
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:176-188, JAN 2014
abstract, full text

Unlu, Ayhan
Computational prediction of actin-actin interaction
MOLECULAR BIOLOGY REPORTS, 41:355-364, JAN 2014
abstract, full text, DOI:10.1007/s11033-013-2869-8

Andersson, Magnus; Mattle, Daniel; Sitsel, Oleg; Klymchuk, Tetyana; Nielsen, Anna Marie; Moller, Lisbeth Birk; White, Stephen H.; Nissen, Poul; Gourdon, Pontus
Copper-transporting P-type ATPases use a unique ion-release pathway
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:43-+, JAN 2014
abstract, full text, DOI:10.1038/nsmb.2721

Loison, Claire; Nasir, Mehmet Nail; Benichou, Emmanuel; Besson, Francoise; Brevet, Pierre-Francois
Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2136-2148, 2014
abstract, full text, DOI:10.1039/c3cp53101e

Gorny, Krzysztof; Dendzik, Zbigniew; Sawicki, Bogdan; Dawid, Aleksander; Gburski, Zygmunt
Thermal activation of ethylene glycol embedded in carbon nanotubes - Computer simulation study
SOLID STATE COMMUNICATIONS, 177:117-122, JAN 2014
abstract, full text, DOI:10.1016/j.ssc.2013.10.013

Chylek, Lily A.; Harris, Leonard A.; Tung, Chang-Shung; Faeder, James R.; Lopez, Carlos F.; Hlavacek, William S.
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE, 6:13-36, JAN 2014
abstract, full text, DOI:10.1002/wsbm.1245

Schramm, Oana G.; Lopez-Cortes, Xaviera; Santos, Leonardo S.; Felipe Laurie, V.; Gonzalez Nilo, Fernando Danilo; Krolik, Michal; Fischer, Rainer; Di Fiore, Stefano
pH-dependent nano-capturing of tartaric acid using dendrimers
SOFT MATTER, 10:600-608, 2014
abstract, full text, DOI:10.1039/c3sm52255e

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.; Cheng, Yuhui; Dupuis, Michel; Raugei, Simone; Shaw, Wendy J.
Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:131-138, JAN 2014
abstract, full text, DOI:10.1016/j.bbabio.2013.08.004

Chaudhry, Jehanzeb Hameed; Comer, Jeffrey; Aksimentiev, Aleksei; Olson, Luke N.
A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 15:93-125, JAN 2014
abstract, full text, DOI:10.4208/cicp.101112.100413a

Banks, David C.; Huff, Israel J.
Halo Water: Ensemble Visualization Distinguishes Configurations Near Nanotubes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:8-14, JAN 2014
abstract, full text, DOI:10.1166/jctn.2014.3310

Bertran, Oscar; del Valle, Luis J.; Revilla-Lopez, Guillermo; Chaves, Gustavo; Cardus, Lluis; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Mineralization of DNA into nanoparticles of hydroxyapatite
DALTON TRANSACTIONS, 43:317-327, 2014
abstract, full text, DOI:10.1039/c3dt52112e

Bouvier, Benjamin
Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:48-60, 2014
abstract, full text, DOI:10.1039/c3cp52436a

Timucin, Emel; Sezerman, O. Ugur
The Conserved Lid Tryptophan, W211, Potentiates Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases
PLOS ONE, 8 Art. No. e85186, DEC 31 2013
abstract, full text, DOI:10.1371/journal.pone.0085186

Denning, Elizabeth J.; Thirumalai, D.; MacKerell, Alexander D., Jr.
Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure
BIOPHYSICAL CHEMISTRY, 184:8-16, DEC 31 2013
abstract, full text, DOI:10.1016/j.bpc.2013.08.002

Jana, Asis K.; Sengupta, Neelanjana
Surface induced collapse of A beta(1-42) with the F19A replacement following adsorption on a single walled carbon nanotube
BIOPHYSICAL CHEMISTRY, 184:108-115, DEC 31 2013
abstract, full text, DOI:10.1016/j.bpc.2013.09.008

Noskov, Sergei Yu.; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.
ATP Transport through VDAC and the VDAC-Tubulin Complex Probed by Equilibrium and Nonequilibrium MD Simulations
BIOCHEMISTRY, 52:9246-9256, DEC 24 2013
abstract, full text, DOI:10.1021/bi4011495

Vukovic, Lela; Madriaga, Antonett; Kuzmis, Antonina; Banerjee, Amrita; Tang, Alan; Tao, Kevin; Shah, Neil; Kral, Petr; Onyuksel, Hayat
Solubilization of Therapeutic Agents in Micellar Nanomedicines
LANGMUIR, 29:15747-15754, DEC 24 2013
abstract, full text, DOI:10.1021/la403264w

Liu, Jian; Wang, Chunlei; Guo, Pan; Shi, Guosheng; Fang, Haiping
Linear relationship between water wetting behavior and microscopic interactions of super-hydrophilic surfaces
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 234703, DEC 21 2013
abstract, full text, DOI:10.1063/1.4841815

Pal, Somedatta; Bandyopadhyay, Sanjoy
Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 235101, DEC 21 2013
abstract, full text, DOI:10.1063/1.4844255

Song, Jianing; Ji, Changge; Zhang, John Z. H.
Unveiling the gating mechanism of ECF Transporter RibU
SCIENTIFIC REPORTS, 3 Art. No. 3566, DEC 20 2013
abstract, full text, DOI:10.1038/srep03566

Xue, Minmin; Qiu, Hu; Guo, Wanlin
Exceptionally fast water desalination at complete salt rejection by pristine graphyne monolayers
NANOTECHNOLOGY, 24 Art. No. 505720, DEC 20 2013
abstract, full text, DOI:10.1088/0957-4484/24/50/505720

Lu, Jing; Modi, Niraj; Kleinekathoefer, Ulrich
Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering
JOURNAL OF PHYSICAL CHEMISTRY B, 117:15966-15975, DEC 19 2013
abstract, full text, DOI:10.1021/jp408495v

Profantova, Barbora; Profant, Vaclav; Zima, Vlastimil; Kopecky, Vladimir, Jr.; Bednarova, Lucie; Zentz, Christian; Baumruk, Vladimir; Turpin, Pierre-Yves; Stepanek, Josef
Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 117:16086-16095, DEC 19 2013
abstract, full text, DOI:10.1021/jp4099864

Comer, Jeffrey; Dehez, Francois; Cai, Wensheng; Chipot, Christophe
Water Conduction through a Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY C, 117:26797-26803, DEC 19 2013
abstract, full text, DOI:10.1021/jp4088223

Arnold, Axel; Fahrenberger, Florian; Holm, Christian; Lenz, Olaf; Bolten, Matthias; Dachsel, Holger; Halver, Rene; Kabadshow, Ivo; Gaehler, Franz; Heber, Frederik; Iseringhausen, Julian; Hofmann, Michael; Pippig, Michael; Potts, Daniel; Sutmann, Godehard
Comparison of scalable fast methods for long-range interactions
PHYSICAL REVIEW E, 88 Art. No. 063308, DEC 19 2013
abstract, full text, DOI:10.1103/PhysRevE.88.063308

Payne, Christina M.; Jiang, Wei; Shirts, Michael R.; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.
Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:18831-18839, DEC 18 2013
abstract, full text, DOI:10.1021/ja407287f

Lv, Xiaoying; Liu, Huihui; Ke, Meng; Gong, Haipeng
Exploring the pH-Dependent Substrate Transport Mechanism of FocA Using Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 105:2714-2723, DEC 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.11.006

Singh, Raghvendra Pratap; Blossey, Ralf; Cleri, Fabrizio
Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 105:2820-2831, DEC 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.10.021

Pessoa-Mahana, Hernan; Gonzalez-Lira, Christian; Fierro, Angelica; Zapata-Torres, Gerald; David Pessoa-Mahana, C.; Ortiz-Severin, Javiera; Iturriaga-Vasquez, Patricio; Reyes-Parada, Miguel; Silva-Matus, Paul; Saitz-Barria, Claudio; Araya-Maturana, Ramiro
Synthesis, docking and pharmacological evaluation of novel homo- and hetero-bis 3-piperazinylpropylindole derivatives at SERT and 5-HT1A receptor
BIOORGANIC & MEDICINAL CHEMISTRY, 21:7604-7611, DEC 15 2013
abstract, full text, DOI:10.1016/j.bmc.2013.10.036

Whiteley, Chris G.; Lee, Duu-Jong
Enzymes for energy. Structural computational analysis, substrate association and product dissociation from the thermophilic esterase of Alicyclobacillus acidocaldarius: Implications in biodiesel production
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 97:156-168, DEC 15 2013
abstract, full text, DOI:10.1016/j.molcatb.2013.08.008

Mayne, Christopher G.; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C.
Rapid Parameterization of Small Molecules Using the Force Field Toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2757-2770, DEC 15 2013
abstract, full text, TCBG publications, DOI:10.1002/jcc.23422

Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan
Molecular insight into conformational transmission of human P-glycoprotein
JOURNAL OF CHEMICAL PHYSICS, 139, DEC 14 2013
abstract, full text, DOI:10.1063/1.4832740

Lam, A. R.; Moran, S. D.; Preketes, N. K.; Zhang, T. O.; Zanni, M. T.; Mukamel, S.
Study of the gamma D-Crystallin Protein Using Two-Dimensional Infrared (2DIR) Spectroscopy: Experiment and Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 117:15436-15443, DEC 12 2013
abstract, full text, DOI:10.1021/jp405159v

Singharoy, Abhishek; Polavarapu, Abhigna; Joshi, Harshad; Baik, Mu-Hyun; Ortoleva, Peter
Epitope Fluctuations in the Human Papillomavirus Are Under Dynamic Allosteric Control: A Computational Evaluation of a New Vaccine Design Strategy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:18458-18468, DEC 11 2013
abstract, full text, DOI:10.1021/ja407489r

Jha, Narendra Nath; Anoop, A.; Ranganathan, Srivastav; Mohite, Ganesh M.; Padinhateeri, Ranjith; Maji, Samir K.
Characterization of Amyloid Formation by Glucagon-Like Peptides: Role of Basic Residues in Heparin-Mediated Aggregation
BIOCHEMISTRY, 52:8800-8810, DEC 10 2013
abstract, full text, DOI:10.1021/bi401398k

Yoo, Jejoong; Aksimentiev, Aleksei
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:20099-20104, DEC 10 2013
abstract, full text, DOI:10.1073/pnas.1316521110

Hashemian, Behrooz; Millan, Daniel; Arroyo, Marino
Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 214101, DEC 7 2013
abstract, full text, DOI:10.1063/1.4830403

Ikeda, Atsushi; Hirata, Akiko; Ishikawa, Michiko; Kikuchi, Jun-ichi; Mieda, Shunsuke; Shinoda, Wataru
Effect of different substituents on the water-solubility and stability properties of 1: 2 [60]fullerene derivative-gamma-cyclodextrin complexes
ORGANIC & BIOMOLECULAR CHEMISTRY, 11:7843-7851, DEC 7 2013
abstract, full text, DOI:10.1039/c3ob41513a

Shi, Guosheng; Liu, Jian; Wang, Chunlei; Song, Bo; Tu, Yusong; Hu, Jun; Fang, Haiping
Ion Enrichment on the Hydrophobic Carbon-based Surface in Aqueous Salt Solutions due to Cation-pi Interactions
SCIENTIFIC REPORTS, 3 Art. No. 3436, DEC 6 2013
abstract, full text, DOI:10.1038/srep03436

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi
Exploring the Dynamic Behaviors and Transport Properties of Gas Molecules in a Transmembrane Cyclic Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14916-14927, DEC 5 2013
abstract, full text, DOI:10.1021/jp408769u

Grigoryan, Gevorg
Absolute Free Energies of Biomolecules from Unperturbed Ensembles
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2726-2741, DEC 5 2013
abstract, full text, DOI:10.1002/jcc.23448

Smith, Jeremy C.; Roux, Benoit
Eppur Si Muove! The 2013 Nobel Prize in Chemistry
STRUCTURE, 21:2102-2105, DEC 3 2013
full text, DOI:10.1016/j.str.2013.11.005

Benitez, Benedetta Sampoli; Barbati, Zachary R.; Arora, Karunesh; Bogdanovic, Jasmina; Schlick, Tamar
How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8-Oxoguanine on the Template
BIOPHYSICAL JOURNAL, 105:2559-2568, DEC 3 2013
abstract, full text, DOI:10.1016/j.bpj.2013.10.014

Bonaiuto, Emanuela; Milelli, Andrea; Cozza, Giorgio; Tumiatti, Vincenzo; Marchetti, Chiara; Agostinelli, Enzo; Fimognari, Carmela; Hrelia, Patrizia; Minarini, Anna; Di Paolo, Maria Luisa
Novel polyamine analogues: From substrates towards potential inhibitors of monoamine oxidases
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 70:88-101, DEC 2013
abstract, full text, DOI:10.1016/j.ejmech.2013.07.005

Tan, Xiao; Bertonati, Claudia; Qin, Lixian; Furio, Laetitia; El Amri, Chahrazade; Hovnanian, Alain; Reboud-Ravaux, Michele; Villoutreix, Bruno O.
Identification by in silico and in vitro screenings of small organic molecules acting as reversible inhibitors of kallikreins
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 70:661-668, DEC 2013
abstract, full text, DOI:10.1016/j.ejmech.2013.10.040

Gursky, Olga; Jones, Martin K.; Mei, Xiaohu; Segrest, Jere P.; Atkinson, David
Structural basis for distinct functions of the naturally occurring Cys mutants of human apolipoprotein A-I
JOURNAL OF LIPID RESEARCH, 54:3244-3257, DEC 2013
abstract, full text, DOI:10.1194/jlr.R037911

Roy, Sophie; Boiteux, Celine; Alijevic, Omar; Liang, Chungwen; Berneche, Simon; Kellenberger, Stephan
Molecular determinants of desensitization in an ENaC/degenerin channel
FASEB JOURNAL, 27:5034-5045, DEC 2013
abstract, full text, DOI:10.1096/fj.13-230680

Xu, Xiaojun; Guardiani, Carlo; Yan, Chunli; Ivanov, Ivaylo
Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1
NUCLEIC ACIDS RESEARCH, 41:10020-10031, DEC 2013
abstract, full text, DOI:10.1093/nar/gkt810

Bossis, Fabrizio; Palese, Luigi L.
Amyloid beta(1-42) in aqueous environments: Effects of ionic strength and E22Q (Dutch) mutation
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2486-2493, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.08.010

Gupta, Arun A.; Chou, Ruey-Hwang; Li, Hongchun; Yang, Lee-Wei; Yu, Chin
Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2606-2619, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.09.012

Underhaug, Jan; Koldso, Heidi; Runager, Kasper; Nielsen, Jakob Toudahl; Sorensen, Charlotte S.; Kristensen, Torsten; Otzen, Daniel E.; Karring, Henrik; Malmendal, Anders; Schiott, Birgit; Enghild, Jan J.; Nielsen, Niels Chr.
Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2812-2822, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.10.008

Iakhiaev, Mikhail A.; Iakhiaev, Alexei V.
Mapping the intramolecular signal propagation pathways in protein using Bayesian change point analysis of atomic motions
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 47:89-95, DEC 2013
abstract, full text, DOI:10.1016/j.compbiolchem.2013.08.004

Borozan, Suncica Z.; Dimitrijevic, Blagoje P.; Stojanovic, Srdan D.
Cation-pi interactions in high resolution protein-RNA complex crystal structures
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 47:105-112, DEC 2013
abstract, full text, DOI:10.1016/j.compbiolchem.2013.08.005

Aykut, Ayse Ozlem; Atilgan, Ali Rana; Atilgan, Canan
Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003366, DEC 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003366

Candotti, Michela; Perez, Alberto; Ferrer-Costa, Carles; Rueda, Manuel; Meyer, Tim; Lluis Gelpi, Josep; Orozco, Modesto
Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003393, DEC 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003393

Vashisth, Harish; Storaska, Andrew J.; Neubig, Richard R.; Brooks, Charles L., I.I.I.
Conformational Dynamics of a Regulator of G-Protein Signaling Protein Reveals a Mechanism of Allosteric Inhibition by a Small Molecule
ACS CHEMICAL BIOLOGY, 8:2778-2784, DEC 2013
abstract, full text, DOI:10.1021/cb400568g

Bellucci, Luca; Angeli, Lucilla; Tafi, Andrea; Radi, Marco; Botta, Maurizio
Unconventional Plasticity of HIV-1 Reverse Transcriptase: How Inhibitors Could Open a Connection "Gate" between Allosteric and Catalytic Sites
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3117-3122, DEC 2013
abstract, full text, DOI:10.1021/ci400414s

Chen, Qi; Buolamwini, John K.; Smith, Jeremy C.; Li, Aixiu; Xu, Qin; Cheng, Xiaolin; Wei, Dongqing
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3297-3307, DEC 2013
abstract, full text, DOI:10.1021/ci400537n

Sun, Hui-Yong; Ji, Feng-Qin; Fu, Liang-Yu; Wang, Zhong-Yi; Zhang, Hong-Yu
Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3343-3351, DEC 2013
abstract, full text, DOI:10.1021/ci400457v

Telesco, Shannon E.; Vadigepalli, Rajanikanth; Radhakrishnan, Ravi
Molecular modeling of ErbB4/HER4 kinase in the context of the HER4 signaling network helps rationalize the effects of clinically identified HER4 somatic mutations on the cell phenotype
BIOTECHNOLOGY JOURNAL, 8:1452-1464, DEC 2013
abstract, full text, DOI:10.1002/biot.201300022

Riley, Julie M.; Kim, Hyunjin; Averch, Timothy D.; Kim, Hyung J.
Effect of Magnesium on Calcium and Oxalate Ion Binding
JOURNAL OF ENDOUROLOGY, 27:1487-1492, DEC 1 2013
abstract, full text, DOI:10.1089/end.2013.0173

Straatsma, T. P.; Chavarria-Miranda, Daniel G.
On eliminating synchronous communication in molecular simulations to improve scalability
COMPUTER PHYSICS COMMUNICATIONS, 184:2634-2640, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.01.009

Pall, Szilard; Hess, Berk
A flexible algorithm for calculating pair interactions on SIMD architectures
COMPUTER PHYSICS COMMUNICATIONS, 184:2641-2650, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.06.003

Mick, Jason; Hailat, Eyad; Russo, Vincent; Rushaidat, Kamel; Schwiehert, Loren; Potoff, Jeffrey
GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium
COMPUTER PHYSICS COMMUNICATIONS, 184:2662-2669, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.06.020

Zhang, Ji-Long; Zheng, Qing-Chuan; Chu, Wen-Ting; Zhang, Hong-Xing
Drug Design Benefits from Molecular Dynamics: Some Examples
CURRENT COMPUTER-AIDED DRUG DESIGN, 9:532-546, DEC 2013
abstract, full text

Immadisetty, Kalyan; Madura, Jeffry D.
A Review of Monoamine Transporter-Ligand Interactions
CURRENT COMPUTER-AIDED DRUG DESIGN, 9:556-568, DEC 2013
abstract, full text

Nunes, Alexandro Silva; Campos, Vicente Paulo; Mascarello, Alessandra; Stumpf, Taisa Regina; Chiaradia-Delatorre, Louise Domenghini; Teixeira Machado, Alan Rodrigues; Santos Junior, Helvecio Martins; Yunes, Rosendo Augusto; Nunes, Ricardo Jose; Oliveira, Denilson Ferreira
Activity of chalcones derived from 2,4,5-trimethoxybenzaldehyde against Meloidogyne exigua and in silico interaction of one chalcone with a putative caffeic acid 3-O-methyltransferase from Meloidogyne incognita
EXPERIMENTAL PARASITOLOGY, 135:661-668, DEC 2013
abstract, full text, DOI:10.1016/j.exppara.2013.10.003

Toy, Weiyi; Shen, Yang; Won, Helen; Green, Bradley; Sakr, Rita A.; Will, Marie; Li, Zhiqiang; Gala, Kinisha; Fanning, Sean; King, Tari A.; Hudis, Clifford; Chen, David; Taran, Tetiana; Hortobagyi, Gabriel; Greene, Geoffrey; Berger, Michael; Baselga, Jose; Chandarlapaty, Sarat
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
NATURE GENETICS, 45:1439-U189, DEC 2013
abstract, full text, DOI:10.1038/ng.2822

Cui, Guanglei; Swails, Jason M.; Manas, Eric S.
SPAM: A Simple Approach for Profiling Bound Water Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5539-5549, DEC 2013
abstract, full text, DOI:10.1021/ct400711g

Bulo, Rosa E.; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe
Multiscale Modeling of Chemistry in Water: Are We There Yet?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5567-5577, DEC 2013
abstract, full text, DOI:10.1021/ct4005596

Fugebakk, Edvin; Reuter, Nathalie; Hinsen, Konrad
Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5618-5628, DEC 2013
abstract, full text, DOI:10.1021/ct400399x

Bonhenry, Daniel; Tarek, Mounir; Dehez, Francois
Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5675-5684, DEC 2013
abstract, full text, DOI:10.1021/ct400576e

Palmer, David S.; Sorensen, Jesper; Schiott, Birgit; Fedorov, Maxim V.
Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin-Bovine kappa-Casein Complex Using Molecular Integral Equation Theory
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5706-5717, DEC 2013
abstract, full text, DOI:10.1021/ct400605x

Biocca, Silvia; Arcangeli, Tania; Tagliaferri, Elisa; Testa, Barbara; Vindigni, Giulia; Oteri, Francesco; Giorgi, Alessandra; Iacovelli, Federico; Novelli, Giuseppe; Desideri, Alessandro; Falconi, Mattia
Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 540:9-18, DEC 2013
abstract, full text, DOI:10.1016/j.abb.2013.10.001

Cristina Ravanal, Maria; Alegria-Arcos, Melissa; Danilo Gonzalez-Nilo, Fernando; Eyzaguirre, Jaime
Penicillium purpurogenum produces two GH family 43 enzymes with beta-xylosidase activity, one monofunctional and the other bifunctional: Biochemical and structural analyses explain the difference
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 540:117-124, DEC 2013
abstract, full text, DOI:10.1016/j.abb.2013.10.017

Barakat, Khaled H.; Huzil, J. Torin; Jordan, Kirk E.; Evangelinos, Constantinos; Houghton, Michael; Tuszynski, Jack
A Computational Model for Overcoming Drug Resistance Using Selective Dual-Inhibitors for Aurora Kinase A and Its T217D Variant
MOLECULAR PHARMACEUTICS, 10:4572-4589, DEC 2013
abstract, full text, DOI:10.1021/mp4003893

Chen, Xin; Zhu, Shuyan; Duan, Danhui; Wu, Tao; Wang, Qi
Investigation of the binding network of IGF-I on the cavity surface of IGFBP4
JOURNAL OF MOLECULAR MODELING, 19:5257-5266, DEC 2013
abstract, full text, DOI:10.1007/s00894-013-2020-8

Fiorin, Giacomo; Klein, Michael L.; Henin, Jerome
Using collective variables to drive molecular dynamics simulations
MOLECULAR PHYSICS, 111:3345-3362, DEC 1 2013
abstract, full text, DOI:10.1080/00268976.2013.813594

Bellesia, Giovanni; Gnanakaran, S.
Sodium chloride interaction with solvated and crystalline cellulose: sodium ion affects the cellotetraose molecule and the cellulose fibril in aqueous solution
CELLULOSE, 20:2695-2702, DEC 2013
abstract, full text, DOI:10.1007/s10570-013-0063-8

Wood, Irene; Pickholz, Monica
Concentration effects of sumatriptan on the properties of model membranes by molecular dynamics simulations
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:833-841, DEC 2013
abstract, full text, DOI:10.1007/s00249-013-0932-y

Dewdney, Tamaria G.; Wang, Yong; Liu, Zhigang; Sharma, Shiv K.; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Woster, Patrick M.; Kovari, Ladislau C.
Ligand modifications to reduce the relative resistance of multi-drug resistant HIV-1 protease
BIOORGANIC & MEDICINAL CHEMISTRY, 21:7430-7434, DEC 1 2013
abstract, full text, DOI:10.1016/j.bmc.2013.09.045

Wu, Qing-Yun; Guo, Hua-Yan; Li, Feng; Li, Zhen-Yu; Zeng, Ling-Yu; Xu, Kai-Lin
Disruption of E627 and R683 interaction is responsible for B-cell acute lymphoblastic leukemia caused by JAK2 R683G(S) mutations
LEUKEMIA & LYMPHOMA, 54:2693-2700, DEC 2013
abstract, full text, DOI:10.3109/10428194.2013.781171

Guemral, Devrim; Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Giorgetti, Sofia; Stoppini, Monica; Bellotti, Vittorio; Esposito, Gennaro
Reduction of conformational mobility and aggregation in W60G beta(2)-microglobulin: assessment by N-15 NMR relaxation
MAGNETIC RESONANCE IN CHEMISTRY, 51:795-807, DEC 2013
abstract, full text, DOI:10.1002/mrc.4018

Chempath, Shaji; Dueren, Tina; Sarkisov, Lev; Snurr, Randall Q.
Experiences with the publicly available multipurpose simulation code, Music
MOLECULAR SIMULATION, 39:1195-1204, DEC 1 2013
abstract, full text, DOI:10.1080/08927022.2013.819103

Unno, Masaki; Ardevol, Albert; Rovira, Carme; Ikeda-Saito, Masao
Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae X-RAY CRYSTALLOGRAPHY AND MOLECULAR DYNAMICS INVESTIGATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:34443-34458, NOV 29 2013
abstract, full text, DOI:10.1074/jbc.M113.486936

Politis, Argyris; Park, Ah Young; Hall, Zoe; Ruotolo, Brandon T.; Robinson, Carol V.
Integrative Modelling Coupled with Ion Mobility Mass Spectrometry Reveals Structural Features of the Clamp Loader in Complex with Single-Stranded DNA Binding Protein
JOURNAL OF MOLECULAR BIOLOGY, 425:4790-4801, NOV 29 2013
abstract, full text, DOI:10.1016/j.jmb.2013.04.006

De Luna, Phil; Bushnell, Eric A. C.; Gauld, James W.
A Molecular Dynamics Examination on Mutation-Induced Catalase Activity in Coral Allene Oxide Synthase
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14635-14641, NOV 28 2013
abstract, full text, DOI:10.1021/jp408486n

Kubiak-Ossowska, Karina; Burley, Glenn; Patwardhan, Siddharth V.; Mulheran, Paul A.
Spontaneous Membrane-Translocating Peptide Adsorption at Silica Surfaces: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14666-14675, NOV 28 2013
abstract, full text, DOI:10.1021/jp409130s

Markiewicz, Beatrice N.; Jo, Hyunil; Culik, Robert M.; DeGrado, William F.; Gai, Feng
Assessment of Local Friction in Protein Folding Dynamics Using a Helix Cross-Linker
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14688-14696, NOV 28 2013
abstract, full text, DOI:10.1021/jp409334h

Nichols, Matthew; Kuljanin, Miljan; Nategholeslam, Mostafa; Hoang, Tuan; Vafaei, Shaghayegh; Tomberli, Bruno; Gray, C. G.; DeBruin, Lillian; Jelokhani-Niaraki, Masoud
Dynamic Turn Conformation of a Short Tryptophan-Rich Cationic Antimicrobial Peptide and Its Interaction with Phospholipid Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14697-14708, NOV 28 2013
abstract, full text, DOI:10.1021/jp4096985

Shonberg, Jeremy; Herenbrink, Carmen Klein; Lopez, Laura; Christopoulos, Arthur; Scammells, Peter J.; Capuano, Ben; Lane, J. Robert
A Structure-Activity Analysis of Biased Agonism at the Dopamine D2 Receptor
JOURNAL OF MEDICINAL CHEMISTRY, 56:9199-9221, NOV 28 2013
abstract, full text, DOI:10.1021/jm401318w

Reale, Riccardo; English, Niall J.; Garate, Jose-Antonio; Marracino, Paolo; Liberti, Micaela; Apollonio, Francesca
Human aquaporin 4 gating dynamics under and after nanosecond-scale static and alternating electric-field impulses: A molecular dynamics study of field effects and relaxation
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 205101, NOV 28 2013
abstract, full text, DOI:10.1063/1.4832383

Hashem, Yaser; des Georges, Amedee; Dhote, Vidya; Langlois, Robert; Liao, Hstau Y.; Grassucci, Robert A.; Pestova, Tatyana V.; Hellen, Christopher U. T.; Frank, Joachim
Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit
NATURE, 503:539-+, NOV 28 2013
abstract, full text, DOI:10.1038/nature12658

Li, Minghui; Zheng, Wenjun
All-Atom Molecular Dynamics Simulations of Actin-Myosin Interactions: A Comparative Study of Cardiac alpha Myosin, beta Myosin, and Fast Skeletal Muscle Myosin
BIOCHEMISTRY, 52:8393-8405, NOV 26 2013
abstract, full text, DOI:10.1021/bi4006896

Goh, Boon Chong; Rynkiewicz, Michael J.; Cafarella, Tanya R.; White, Mitchell R.; Hartshorn, Kevan L.; Allen, Kimberly; Crouch, Erika C.; Calin, Oliviana; Seeberger, Peter H.; Schulten, Klaus; Seaton, Barbara A.
Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation
BIOCHEMISTRY, 52:8527-8538, NOV 26 2013
abstract, full text, TCBG publications, DOI:10.1021/bi4010683

Diaz, Natalia; Suarez, Dimas; Valdes, Haydee
Unraveling the Molecular Structure of the Catalytic Domain of Matrix Metalloproteinase-2 in Complex with a Triple-Helical Peptide by Means of Molecular Dynamics Simulations
BIOCHEMISTRY, 52:8556-8569, NOV 26 2013
abstract, full text, DOI:10.1021/bi401144p

Wicky, Basile I. M.; Stenta, Marco; Dal Peraro, Matteo
TAL Effectors Specificity Stems from Negative Discrimination
PLOS ONE, 8 Art. No. e80261, NOV 25 2013
abstract, full text, DOI:10.1371/journal.pone.0080261

Abad, Enrique; Zenn, Roland K.; Kaestner, Johannes
Reaction Mechanism of Monoamine Oxidase from QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14238-14246, NOV 21 2013
abstract, full text, DOI:10.1021/jp4061522

Jiang, Jun; Golchert, Kory J.; Kingsley, Carolyn N.; Brubaker, William D.; Martin, Rachel W.; Mukamel, Shaul
Exploring the Aggregation Propensity of gamma S-Crystallin Protein Variants Using Two-Dimensional Spectroscopic Tools
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14294-14301, NOV 21 2013
abstract, full text, DOI:10.1021/jp408000k

Akimov, Alexey V.; Prezhdo, Oleg V.
Persistent Electronic Coherence Despite Rapid Loss of Electron-Nuclear Correlation
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:3857-3864, NOV 21 2013
abstract, full text, DOI:10.1021/jz402035z

Boynton, P.; Di Ventra, M.
Probing Water Structures in Nanopores Using Tunneling Currents
PHYSICAL REVIEW LETTERS, 111 Art. No. 216804, NOV 20 2013
abstract, full text, DOI:10.1103/PhysRevLett.111.216804

Villanueva, Diana Y.; Lim, Joseph B.; Klauda, Jeffery B.
Influence of Ester-Modified Lipids on Bilayer Structure
LANGMUIR, 29:14196-14203, NOV 19 2013
abstract, full text, DOI:10.1021/la403919h

Zhang, Liqun; Buck, Matthias
Molecular Simulations of a Dynamic Protein Complex: Role of Salt-Bridges and Polar Interactions in Configurational Transitions
BIOPHYSICAL JOURNAL, 105:2412-2417, NOV 19 2013
abstract, full text, DOI:10.1016/j.bpj.2013.09.052

Demirci, Erhan; Junne, Tina; Baday, Sefer; Berneche, Simon; Spiess, Martin
Functional asymmetry within the Sec61p translocon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:18856-18861, NOV 19 2013
abstract, full text, DOI:10.1073/pnas.1318432110

Lima, Marisa A.; Oliveira-Neto, Mario; Kadowaki, Marco Antonio S.; Rosseto, Flavio R.; Prates, Erica T.; Squina, Fabio M.; Leme, Adriana F. P.; Skaf, Munir S.; Polikarpov, Igor
Aspergillus niger beta-Glucosidase Has a Cellulase-like Tadpole Molecular Shape INSIGHTS INTO GLYCOSIDE HYDROLASE FAMILY 3 (GH3) beta-GLUCOSIDASE STRUCTURE AND FUNCTION
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32991-33005, NOV 15 2013
abstract, full text, DOI:10.1074/jbc.M113.479279

Wu, Miao; Bu, Lintao; Vuong, Thu V.; Wilson, David B.; Crowley, Michael F.; Sandgren, Mats; Stahlberg, Jerry; Beckham, Gregg T.; Hansson, Henrik
Loop Motions Important to Product Expulsion in the Thermobifida fusca Glycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:33107-33117, NOV 15 2013
abstract, full text, DOI:10.1074/jbc.M113.502765

Hsin, Jen; Fu, Rui; Huang, Kerwyn Casey
Dimer Dynamics and Filament Organization of the Bacterial Cell Division Protein FtsA
JOURNAL OF MOLECULAR BIOLOGY, 425:4415-4426, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.07.016

Rathore, Anurag; Carpenter, Michael A.; Demir, Oeziem; Ikeda, Terumasa; Li, Ming; Shaban, Nadine M.; Law, Emily K.; Anokhin, Dmitry; Brown, William L.; Amaro, Rommie E.; Harris, Reuben S.
The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5 '-CC to 5 '-TC by a Single Amino Acid Substitution
JOURNAL OF MOLECULAR BIOLOGY, 425:4442-4454, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.07.040

Sousa, Duncan R.; Stagg, Scott M.; Stroupe, M. Elizabeth
Cryo-EM Structures of the Actin:Tropomyosin Filament Reveal the Mechanism for the Transition from C- to M-State
JOURNAL OF MOLECULAR BIOLOGY, 425:4544-4555, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.08.020

Turecek, Frantisek; Moss, Christopher L.; Pikalov, Ioannis; Pepin, Robert; Gulyuz, Kerim; Polfer, Nicolas C.; Bush, Matthew F.; Brown, Jeffery; Williams, Jonathan; Richardson, Keith
Gas-phase structures of phosphopeptide ions: A difficult case
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 354:249-256, NOV 15 2013
abstract, full text, DOI:10.1016/j.ijms.2013.06.021

Ningshen, Thuirei Jacob; Aparoy, Polamarasetty; Ventaku, Venkat Rao; Dutta-Gupta, Aparna
Functional Interpretation of a Non-Gut Hemocoelic Tissue Aminopeptidase N (APN) in a Lepidopteran Insect Pest Achaea janata
PLOS ONE, 8 Art. No. e79468, NOV 14 2013
abstract, full text, DOI:10.1371/journal.pone.0079468

Clark, Nicholas J.; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R.; Kerwin, Bruce; Kanapuram, Sekhar R.; Treuheit, Michael J.; McAuley, Arnold; Curtis, Joseph E.
Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14029-14038, NOV 14 2013
abstract, full text, DOI:10.1021/jp408710r

Zhao, Junjie; Srajer, Vukica; Franzen, Stefan
Functional Consequences of the Open Distal Pocket of Dehaloperoxidase-Hemoglobin Observed by Time-Resolved X-ray Crystallography
BIOCHEMISTRY, 52:7943-7950, NOV 12 2013
abstract, full text, DOI:10.1021/bi401118q

Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan
Visual cavity analysis in molecular simulations
BMC BIOINFORMATICS, 14 Art. No. S4, NOV 12 2013
abstract, full text, DOI:10.1186/1471-2105-14-S19-S4

Mandal, Manoj; Mukhopadhyay, Chaitali
Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation
PHYSICAL REVIEW E, 88 Art. No. 052708, NOV 11 2013
abstract, full text, DOI:10.1103/PhysRevE.88.052708

Ozcan, Ozer; Uyar, Arzu; Doruker, Pemra; Akten, Ebru Demet
Effect of intracellular loop 3 on intrinsic dynamics of human beta(2)-adrenergic receptor
BMC STRUCTURAL BIOLOGY, 13 Art. No. 29, NOV 9 2013
abstract, full text, DOI:10.1186/1472-6807-13-29

Akbal-Delibas, Bahar; Haspel, Nurit
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins
BMC STRUCTURAL BIOLOGY, 13 Art. No. S7, NOV 8 2013
abstract, full text, DOI:10.1186/1472-6807-13-S1-S7

Sabit, Hairat; Mallajosyula, Sairam S.; MacKerell, Alexander D., Jr.; Swaan, Peter W.
Transmembrane Domain II of the Human Bile Acid Transporter SLC10A2 Coordinates Sodium Translocation
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32394-32404, NOV 8 2013
abstract, full text, DOI:10.1074/jbc.M113.518555

Shim, Joong-Youn; Ahn, Kwang H.; Kendall, Debra A.
Molecular Basis of Cannabinoid CB1 Receptor Coupling to the G Protein Heterotrimer G alpha(i)beta gamma IDENTIFICATION OF KEY CB1 CONTACTS WITH THE C-TERMINAL HELIX alpha(5) OF G alpha(i)
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32449-32465, NOV 8 2013
abstract, full text, DOI:10.1074/jbc.M113.489153

Rashid, M. Harunur; Heinzelmann, Germano; Huq, Redwan; Tajhya, Rajeev B.; Chang, Shih Chieh; Chhabra, Sandeep; Pennington, Michael W.; Beeton, Christine; Norton, Raymond S.; Kuyucak, Serdar
A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation
PLOS ONE, 8 Art. No. e78712, NOV 7 2013
abstract, full text, DOI:10.1371/journal.pone.0078712

Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noe, Frank; Smith, Jeremy C.
Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 175102, NOV 7 2013
abstract, full text, DOI:10.1063/1.4824071

Kalimeri, Maria; Rahaman, Obaidur; Melchionna, Simone; Sterpone, Fabio
How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13775-13785, NOV 7 2013
abstract, full text, DOI:10.1021/jp407078z

Bidon-Chanal, Axel; Krammer, Eva-Maria; Bolt, Delphine; Pebay-Peyroula, Eva; Chipot, Christophe; Ravaud, Stephanie; Dehez, Francois
How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP-ATP Carrier
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:3787-3791, NOV 7 2013
abstract, full text, DOI:10.1021/jz401847d

Dhakshnamoorthy, Balasundaresan; Ziervogel, Brigitte K.; Blachowicz, Lydia; Roux, Benoit
A Structural Study of Ion Permeation in OmpF Porin from Anomalous X-ray Diffraction and Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:16561-16568, NOV 6 2013
abstract, full text, DOI:10.1021/ja407783a

Wei, Chenyu; Pohorille, Andrew
Activation and Proton Transport Mechanism in Influenza A M2 Channel
BIOPHYSICAL JOURNAL, 105:2036-2045, NOV 5 2013
abstract, full text, DOI:10.1016/j.bpj.2013.08.030

Gupta, Kshitij; Jang, Hyunbum; Harlen, Kevin; Puri, Anu; Nussinov, Ruth; Schneider, Joel P.; Blumenthal, Robert
Mechanism of Membrane Permeation Induced by Synthetic beta-Hairpin Peptides
BIOPHYSICAL JOURNAL, 105:2093-2103, NOV 5 2013
abstract, full text, DOI:10.1016/j.bpj.2013.09.040

Ma, Chunlong; Fiorin, Giacomo; Carnevale, Vincenzo; Wang, Jun; Lamb, Robert A.; Klein, Michael L.; Wu, Yibing; Pinto, Lawrence H.; DeGrado, William F.
Asp44 Stabilizes the Trp41 Gate of the M2 Proton Channel of Influenza A Virus
STRUCTURE, 21:2033-2041, NOV 5 2013
abstract, full text, DOI:10.1016/j.str.2013.08.029

Giudice, Emmanuel; Molza, Anne-Elisabeth; Laurin, Yoann; Nicolas, Aurelie; Le Rumeur, Elisabeth; Delalande, Olivier
Molecular Clues about the Dystrophin-Neuronal Nitric Oxide Synthase Interaction: A Theoretical Approach
BIOCHEMISTRY, 52:7777-7784, NOV 5 2013
abstract, full text, DOI:10.1021/bi400794p

Dolores Elola, M.; Rodriguez, Javier
Structure and Dynamics of Nonionic Surfactants Adsorbed at Vacuum/Ionic Liquid Interfaces
LANGMUIR, 29:13379-13387, NOV 5 2013
abstract, full text, DOI:10.1021/la402683j

Li, Yangmei; Bionda, Nina; Yongye, Austin; Geer, Phaedra; Stawikowski, Maciej; Cudic, Predrag; Martinez, Karina; Houghten, Richard A.
Dissociation of Antimicrobial and Hemolytic Activities of Gramicidin S through N-Methylation Modification
CHEMMEDCHEM, 8:1865-1872, NOV 2013
abstract, full text, DOI:10.1002/cmdc.201300232

Lushchekina, S. V.; Polomskikh, V. S.; Varfolomeev, S. D.; Masson, P.
Molecular modeling of butyrylcholinesterase inhibition by cresyl saligenin phosphate
RUSSIAN CHEMICAL BULLETIN, 62:2527-2537, NOV 2013
abstract, full text

Ortega, Davi R.; Mo, Guoya; Lee, Kwangwoon; Zhou, Hongjun; Baudry, Jerome; Dahlquist, Frederick W.; Zhulin, Igor B.
Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003337, NOV 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003337

Ganoth, Assaf; Tsfadia, Yossi; Wiener, Reuven
Ubiquitin: Molecular modeling and simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 46:29-40, NOV 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.09.006

Chen, Xin; Yu, Xiaohan; Liu, Yafang; Zhang, Jinglai
Stepwise design of non-covalent wrapping of large diameter carbon nanotubes by peptides
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 46:83-92, NOV 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.09.012

Arias, Hugo R.; Lopez, Jhon J.; Feuerbach, Dominik; Fierro, Angelica; Ortells, Marcelo O.; Perez, Edwin G.
Novel 2-(substituted benzyl)quinuclidines inhibit human alpha 7 and alpha 4 beta 2 nicotinic receptors by different mechanisms
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 45:2420-2430, NOV 2013
abstract, full text, DOI:10.1016/j.biocel.2013.08.003

Vasu, Kommireddy; Nagamalleswari, Easa; Zahran, Mai; Imhof, Petra; Xu, Shuang-yong; Zhu, Zhenyu; Chan, Siu-Hong; Nagaraja, Valakunja
Increasing cleavage specificity and activity of restriction endonuclease KpnI
NUCLEIC ACIDS RESEARCH, 41:9812-9824, NOV 2013
abstract, full text, DOI:10.1093/nar/gkt734

Juul, Sissel; Iacovelli, Federico; Falconi, Mattia; Kragh, Sofie L.; Christensen, Brian; Frohlich, Rikke; Franch, Oskar; Kristoffersen, Emil L.; Stougaard, Magnus; Leong, Kam W.; Ho, Yi-Ping; Sorensen, Esben S.; Birkedal, Victoria; Desideri, Alessandro; Knudsen, Birgitta R.
Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage
ACS NANO, 7:9724-9734, NOV 2013
abstract, full text, DOI:10.1021/nn4030543

Blacklock, Kristin; Verkhivker, Gennady M.
Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90-p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2962-2978, NOV 2013
abstract, full text, DOI:10.1021/ci400434g

Tarcsay, Akos; Paragi, Gabor; Vass, Marton; Jojart, Balazs; Bogar, Ferenc; Keseru, Gyoergy M.
The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2990-2999, NOV 2013
abstract, full text, DOI:10.1021/ci400087b

Barakat, Khaled H.; Law, John; Prunotto, Alessio; Magee, Wendy C.; Evans, David H.; Tyrrell, D. Lorne; Tuszynski, Jack; Houghton, Michael
Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3031-3043, NOV 2013
abstract, full text, DOI:10.1021/ci4003969

Hobbs, Joanne K.; Jiao, Wanting; Easter, Ashley D.; Parker, Emily J.; Schipper, Louis A.; Arcus, Vickery L.
Change in Heat Capacity for Enzyme Catalysis Determines Temperature Dependence of Enzyme Catalyzed Rates
ACS CHEMICAL BIOLOGY, 8:2388-2393, NOV 2013
abstract, full text, DOI:10.1021/cb4005029

Hajjoul, Houssam; Mathon, Julien; Ranchon, Hubert; Goiffon, Isabelle; Mozziconacci, Julien; Albert, Benjamin; Carrivain, Pascal; Victor, Jean-Marc; Gadal, Olivier; Bystricky, Kerstin; Bancaud, Aurelien
High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
GENOME RESEARCH, 23:1829-1838, NOV 2013
abstract, full text, DOI:10.1101/gr.157008.113

Dewdney, Tamaria G.; Wang, Yong; Kovari, Iulia A.; Reiter, Samuel J.; Kovari, Ladislau C.
Reduced HIV-1 integrase flexibility as a mechanism resistance
JOURNAL OF STRUCTURAL BIOLOGY, 184:245-250, NOV 2013
abstract, full text, DOI:10.1016/j.jsb.2013.07.008

Buck, Patrick M.; Kumar, Sandeep; Singh, Satish K.
Consequences of glycan truncation on Fc structural integrity
MABS, 5:904-916, NOV 1 2013
abstract, full text, DOI:10.4161/mabs.26453

Leonarski, Filip; Trovato, Fabio; Tozzini, Valentina; Les, Andrzej; Trylska, Joanna
Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:4874-4889, NOV 2013
abstract, full text, DOI:10.1021/ct4005036

Calero, C.; Marti, J.; Guardia, E.; Masia, Marco
Characterization of the Methane-Graphene Hydrophobic Interaction in Aqueous Solution from Ab Initio Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5070-5075, NOV 2013
abstract, full text, DOI:10.1021/ct400554q

Damas, Joao M.; Filipe, Luis C. S.; Campos, Sara R. R.; Lousa, Diana; Victor, Bruno L.; Baptista, Antonio M.; Soares, Claudio M.
Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5148-5157, NOV 2013
abstract, full text, DOI:10.1021/ct400529k

Fowler, Philip W.; Abad, Enrique; Beckstein, Oliver; Sansom, Mark S. P.
Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5176-5189, NOV 2013
abstract, full text, DOI:10.1021/ct4005933

Bagatin, Mariane C.; Candido, Augusto A.; Pinheiro, Glaucia M. S.; Hoeehr, Nelci F.; Machinski, Miguel, Jr.; Mossini, Simone A. G.; Basso, Ernani A.; Gauze, Gisele F.
Molecular Modeling and Anticholinesterasic Activity of Novel 2-Arylaminocyclohexyl N,N-Dimethylcarbamates
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 24:1798-1807, NOV 2013
abstract, full text, DOI:10.5935/0103-5053.20130225

Gun'ko, Vladimir M.
MODELING OF INTERFACIAL BEHAVIOR OF WATER AND ORGANICS
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 12 Art. No. 1350059, NOV 2013
abstract, full text, DOI:10.1142/S0219633613500594

Hamed, Elham; Xu, Ting; Keten, Sinan
Poly(ethylene glycol) Conjugation Stabilizes the Secondary Structure of alpha-Helices by Reducing Peptide Solvent Accessible Surface Area
BIOMACROMOLECULES, 14:4053-4060, NOV 2013
abstract, full text, DOI:10.1021/bm401164t

Arias, Hugo R.; Ortells, Marcelo O.; Feuerbach, Dominik
(-)-Reboxetine inhibits muscle nicotinic acetylcholine receptors by interacting with luminal and non-luminal sites
NEUROCHEMISTRY INTERNATIONAL, 63:423-431, NOV 2013
abstract, full text, DOI:10.1016/j.neuint.2013.07.009

Chiang, Harry; Robinson, Lucy C.; Brame, Cynthia J.; Messina, Troy C.
Molecular Mechanics and Dynamics Characterization of an In Silico Mutated Protein: A Stand-Alone Lab Module or Support Activity for In Vivo and In Vitro Analyses of Targeted Proteins
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 41:402-408, NOV 2013
abstract, full text, DOI:10.1002/bmb.20737

Istadeh, K. Hosseini; Kalantarinejad, R.; Aghaei, M. J.; Yazdi, M. R. Soleymani
Computational Investigation on H2S Adsorption on the CNT Channel of Conductometric Gas Sensor
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 10:2708-2713, NOV 2013
abstract, full text, DOI:10.1166/jctn.2013.3270

Platania, Chiara Bianca Maria; Leggio, Gian Marco; Drago, Filippo; Salomone, Salvatore; Bucolo, Claudio
Regulation of intraocular pressure in mice: Structural analysis of dopaminergic and serotonergic systems in response to cabergoline
BIOCHEMICAL PHARMACOLOGY, 86:1347-1356, NOV 1 2013
abstract, full text, DOI:10.1016/j.bcp.2013.08.010

Ramelot, Theresa A.; Yang, Yunhuang; Sahu, Indra D.; Lee, Hsiau-Wei; Xiao, Rong; Lorigan, Gary A.; Montelione, Gaetano T.; Kennedy, Michael A.
NMR structure and MD simulations of the AAA protease intermembrane space domain indicates peripheral membrane localization within the hexaoligomer
FEBS LETTERS, 587:3522-3528, NOV 1 2013
abstract, full text, DOI:10.1016/j.febslet.2013.09.009

Petruk, Ariel Alcides; Varriale, Sonia; Coscia, Maria Rosaria; Mazzarella, Lelio; Merlino, Antonello; Oreste, Umberto
The structure of the CD3 zeta zeta transmembrane dimer in POPC and raft-like lipid bilayer: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:2637-2645, NOV 2013
abstract, full text, DOI:10.1016/j.bbamem.2013.07.019

Tsai, Hui-Hsu Gavin; Juang, Wei-Fu; Chang, Che-Ming; Hou, Tsai-Yi; Lee, Jian-Bin
Molecular mechanism of Ca2+-catalyzed fusion of phospholipid micelles
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:2729-2738, NOV 2013
abstract, full text, DOI:10.1016/j.bbamem.2013.07.022

Huang, Wei; Greene, Geoffrey L.; Ravikumar, Krishnakumar M.; Yang, Sichun
Cross-talk between the ligand- and DNA-binding domains of estrogen receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1900-1909, NOV 2013
abstract, full text, DOI:10.1002/prot.24331

Loeffler, Hannes H.; Winn, Martyn D.
Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1931-1943, NOV 2013
abstract, full text, DOI:10.1002/prot.24339

Shook, Eric; Wang, Shaowen; Tang, Wenwu
A communication-aware framework for parallel spatially explicit agent-based models
INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE, 27:2160-2181, NOV 1 2013
abstract, full text, DOI:10.1080/13658816.2013.771740

Gogolinska, Anna; Nowak, Wieslaw
Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody
JOURNAL OF MOLECULAR MODELING, 19:4773-4780, NOV 2013
abstract, full text, DOI:10.1007/s00894-013-1972-z

Wang, Yu; Zhu, Guo-Fei; Ren, Si-Yan; Han, Yong-Guang; Luo, Yue; Du, Lin-Fang
Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 19:4865-4875, NOV 2013
abstract, full text, DOI:10.1007/s00894-013-1930-9

Negureanu, Lacramioara; Salsbury, Freddie R., Jr.
Destabilization of the MutS alpha's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 19:4969-4989, NOV 2013
abstract, full text, DOI:10.1007/s00894-013-1998-2

Mironov, Vladimir A.; Khrenova, Maria G.; Grigorenko, Bella L.; Savitsky, Alexander P.; Nemukhin, Alexander V.
Thermal Isomerization of the Chromoprotein asFP595 and Its Kindling Mutant A143G: QM/MM Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13507-13514, OCT 31 2013
abstract, full text, DOI:10.1021/jp407406k

Albareda, Marta; Palacios, Jose-Manuel; Imperial, Juan; Pacios, Luis F.
Computational Study of the Fe(CN)(2)CO Cofactor and Its Binding to HypC Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13523-13533, OCT 31 2013
abstract, full text, DOI:10.1021/jp407574n

Deria, Pravas; Von Bargen, Christopher D.; Olivier, Jean-Hubert; Kumbhar, Arnar S.; Saven, Jeffery G.; Therien, Michael J.
Single-Handed Helical Wrapping of Single-Walled Carbon Nanotubes by Chiral, Ionic, Semiconducting Polymers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:16220-16234, OCT 30 2013
abstract, full text, DOI:10.1021/ja408430v

Jung, Jaewoon; Mori, Takaharu; Sugita, Yuji
Efficient Lookup Table Using a Linear Function of Inverse Distance Squared
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2412-2420, OCT 30 2013
abstract, full text, DOI:10.1002/jcc.23404

Rosenhouse-Dantsker, Avia; Noskov, Sergei; Durdagi, Serdar; Logothetis, Diomedes E.; Levitan, Irena
Identification of Novel Cholesterol-binding Regions in Kir2 Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:31154-31164, OCT 25 2013
abstract, full text, DOI:10.1074/jbc.M113.496117

Li, Rongzhong; Ge, Heming W.; Cho, Samuel S.
Sequence-Dependent Base-Stacking Stabilities Guide tRNA Folding Energy Landscapes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12943-12952, OCT 24 2013
abstract, full text, DOI:10.1021/jp402114p

Von Bargen, Christopher D.; MacDermaid, Christopher M.; Lee, One-Sun; Deria, Pravas; Therien, Michael J.; Saven, Jeffery G.
Origins of the Helical Wrapping of Phenyleneethynylene Polymers about Single-Walled Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12953-12965, OCT 24 2013
abstract, full text, DOI:10.1021/jp402140t

Nilsson, Lina; Aden, Joergen; Niemiec, Moritz S.; Nam, Kwangho; Wittung-Stafshede, Pernilla
Small pH and Salt Variations Radically Alter the Thermal Stability of Metal-Binding Domains in the Copper Transporter, Wilson Disease Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13038-13050, OCT 24 2013
abstract, full text, DOI:10.1021/jp402415y

Li, Minghui; Shoemaker, Benjamin A.; Thangudu, Ratna R.; Ferraris, Joan D.; Burg, Maurice B.; Panchenko, Anna R.
Mutations in DNA-Binding Loop of NFAT5 Transcription Factor Produce Unique Outcomes on Protein-DNA Binding and Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13226-13234, OCT 24 2013
abstract, full text, DOI:10.1021/jp403310a

Lai, Jonathan; Chen, Ke; Luthey-Schulten, Zaida
Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13335-13345, OCT 24 2013
abstract, full text, DOI:10.1021/jp404106r

Han, Wei; Schulten, Klaus
Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model
JOURNAL OF PHYSICAL CHEMISTRY B, 117:13367-13377, OCT 24 2013
abstract, full text, TCBG publications, DOI:10.1021/jp404331d

Li, Zhenhua; He, Ying; Liu, Qian; Zhao, Liang; Wong, Limsoon; Kwoh, Chee Keong; Hung Nguyen; Li, Jinyan
Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding
BMC BIOINFORMATICS, 14 Art. No. S11, OCT 22 2013
abstract, full text, DOI:10.1186/1471-2105-14-S16-S11

Prakash, Priyanka; Gorfe, Alemayehu A.
Phosphatidylcholine Attenuates Aggregation of Nonsteroidal Anti-Inflammatory Drugs with Bile Acid
BIOCHEMISTRY, 52:7461-7469, OCT 22 2013
abstract, full text, DOI:10.1021/bi400723r

Tucker, Matthew J.; Abdo, Mohannad; Courter, Joel R.; Chen, Jianxin; Brown, Stephen P.; Smith, Amos B., I.I.I.; Hochstrasser, Robin M.
Nonequilibrium dynamics of helix reorganization observed by transient 2D IR spectroscopy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:17314-17319, OCT 22 2013
abstract, full text, DOI:10.1073/pnas.1311876110

Takahashi, Toshimasa; Shibasaki, Tadao; Takahashi, Harumi; Sugawara, Kenji; Ono, Aika; Inoue, Naoko; Furuya, Toshio; Seino, Susumu
Antidiabetic Sulfonylureas and cAMP Cooperatively Activate Epac2A
SCIENCE SIGNALING, 6 Art. No. ra94, OCT 22 2013
abstract, full text, DOI:10.1126/scisignal.2004581

Wilson, James; Di Ventra, M.
Single-base DNA discrimination via transverse ionic transport
NANOTECHNOLOGY, 24 Art. No. 415101, OCT 18 2013
abstract, full text, DOI:10.1088/0957-4484/24/41/415101

Wallace, Samuel J.; Kee, Tak W.; Huang, David M.
Molecular Basis of Binding and Stability of Curcumin in Diamide-Linked gamma-Cyclodextrin Dimers
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12375-12382, OCT 17 2013
abstract, full text, DOI:10.1021/jp406125x

Woelke, Anna Lena; Galstyan, Gegham; Galstyan, Artur; Meyer, Tim; Heberle, Joachim; Knapp, Ernst-Walter
Exploring the Possible Role of Glu286 in CcO by Electrostatic Energy Computations Combined with Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12432-12441, OCT 17 2013
abstract, full text, DOI:10.1021/jp407250d

Yee, Patrick; Shah, Jindal K.; Maginn, Edward J.
State of Hydrophobic and Hydrophilic Ionic Liquids in Aqueous Solutions: Are the Ions Fully Dissociated?
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12556-12566, OCT 17 2013
abstract, full text, DOI:10.1021/jp405341m

Eilmes, Andrzej; Kubisiak, Piotr
Quantum-Chemical and Molecular Dynamics Study of M+[TOTO](-) (M = Li, Na, K) Ionic Liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12583-12592, OCT 17 2013
abstract, full text, DOI:10.1021/jp4070449

Paciaroni, A.; Nibali, V. Conti; Orecchini, A.; Petrillo, C.; Haertlein, M.; Moulin, M.; Tarek, M.; D'Angelo, G.; Sacchetti, F.
Vibrational excitations of proteins and their hydration water in the far-infrared range
CHEMICAL PHYSICS, 424:80-83, OCT 16 2013
abstract, full text, DOI:10.1016/j.chemphys.2013.05.013

Chen, Rong; Chung, Shin-Ho
Molecular Dynamics Simulations of Scorpion Toxin Recognition by the Ca2+-Activated Potassium Channel K(Ca)3.1
BIOPHYSICAL JOURNAL, 105:1829-1837, OCT 15 2013
abstract, full text, DOI:10.1016/j.bpj.2013.08.046

Zheng, Wenjun; Barua, Bipasha; Hitchcock-DeGregori, Sarah E.
Probing the Flexibility of Tropomyosin and Its Binding to Filamentous Actin Using Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 105:1882-1892, OCT 15 2013
abstract, full text, DOI:10.1016/j.bpj.2013.09.003

Sassaki, Guilherme L.; Elli, Stefano; Rudd, Timothy R.; Macchi, Eleonora; Yates, Edwin A.; Naggi, Annamaria; Shriver, Zachary; Raman, Rahul; Sasisekharan, R.; Torri, Giangiacomo; Guerrini, Marco
Human (alpha 2 -> 6) and Avian (alpha 2 -> 3) Sialylated Receptors of Influenza A Virus Show Distinct Conformations and Dynamics in Solution
BIOCHEMISTRY, 52:7217-7230, OCT 15 2013
abstract, full text, DOI:10.1021/bi400677n

Calimet, Nicolas; Simoes, Manuel; Changeux, Jean-Pierre; Karplus, Martin; Taly, Antoine; Cecchini, Marco
A gating mechanism of pentameric ligand-gated ion channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:E3987-E3996, OCT 15 2013
abstract, full text, DOI:10.1073/pnas.1313785110

Heymann, Gabriel; Dai, Jian; Li, Mufeng; Silberberg, Shai D.; Zhou, Huan-Xiang; Swartz, Kenton J.
Inter- and intrasubunit interactions between transmembrane helices in the open state of P2X receptor channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:E4045-E4054, OCT 15 2013
abstract, full text, DOI:10.1073/pnas.1311071110

Megow, Joerg; Plehn, Thomas; Steffen, Ronald; Roeder, Beate; May, Volkhard
Photoinduced excitation energy transfer in hexapyropheophorbide a
CHEMICAL PHYSICS LETTERS, 585:178-183, OCT 14 2013
abstract, full text, DOI:10.1016/j.cplett.2013.08.076

Wang, Jing; Xing, Xueqing; Fang, Xiaocui; Zhou, Chang; Huang, Feng; Wu, Zhonghua; Lou, Jizhong; Liang, Wei
Cationic amphiphilic drugs self-assemble to the core-shell interface of PEGylated phospholipid micelles and stabilize micellar structure
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 371 Art. No. 20120309, OCT 13 2013
abstract, full text, DOI:10.1098/rsta.2012.0309

Pester, Oxana; Goetz, Alexander; Multhaup, Gerd; Scharnagl, Christina; Langosch, Dieter
The Cleavage Domain of the Amyloid Precursor Protein Transmembrane Helix Does Not Exhibit Above-Average Backbone Dynamics
CHEMBIOCHEM, 14:1943-1948, OCT 11 2013
full text, DOI:10.1002/cbic.201300322

Krishnan, Marimuthu; Saharay, Moumita; Kirkpatrick, R. James
Molecular Dynamics Modeling of CO2 and Poly(ethylene glycol) in Montmorillonite: The Structure of Clay-Polymer Composites and the Incorporation of CO2
JOURNAL OF PHYSICAL CHEMISTRY C, 117:20592-20609, OCT 10 2013
abstract, full text, DOI:10.1021/jp405321t

Simkovitch, Ron; Huppert, Amit; Huppert, Dan; Remington, S. James; Miller, Yifat
Proton Transfer in Wild-Type GFP and S205V Mutant Is Reduced by Conformational Changes of Residues in the Proton Wire
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11921-11931, OCT 10 2013
abstract, full text, DOI:10.1021/jp405698g

Elder, Robert M.; Jayaraman, Arthi
Molecular Simulations of Polycation-DNA Binding Exploring the Effect of Peptide Chemistry and Sequence in Nuclear Localization Sequence Based Polycations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11988-11999, OCT 10 2013
abstract, full text, DOI:10.1021/jp406875a

Lockhart, Christopher; Klimov, Dmitri K.
Revealing Hidden Helix Propensity in A beta Peptides by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12030-12038, OCT 10 2013
abstract, full text, DOI:10.1021/jp407705j

Balamurugan, D.; Aquino, Adelia J. A.; de Dios, Francis; Flores, Lionel, Jr.; Lischka, Hans; Cheung, Margaret S.
Multiscale Simulation of the Ground and Photo-Induced Charge-Separated States of a Molecular Triad in Polar Organic Solvent: Exploring the Conformations, Fluctuations, and Free Energy Landscapes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:12065-12075, OCT 10 2013
abstract, full text, DOI:10.1021/jp4026927

Wan, Hua; Hu, Jian-ping; Li, Kang-shun; Tian, Xu-hong; Chang, Shan
Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors
PLOS ONE, 8 Art. No. e76045, OCT 10 2013
abstract, full text, DOI:10.1371/journal.pone.0076045

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua
Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:15092-15100, OCT 9 2013
abstract, full text, DOI:10.1021/ja405200u

Skeby, Katrine Kirkeby; Sorensen, Jesper; Schiott, Birgit
Identification of a Common Binding Mode for Imaging Agents to Amyloid Fibrils from Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:15114-15128, OCT 9 2013
abstract, full text, DOI:10.1021/ja405530p

Zoonens, Manuela; Comer, Jeffrey; Masscheleyn, Sandrine; Pebay-Peyroula, Eva; Chipot, Christophe; Miroux, Bruno; Dehez, Francois
Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:15174-15182, OCT 9 2013
abstract, full text, DOI:10.1021/ja407424v

Baday, Sefer; Wang, Shihao; Lamoureux, Guillaume; Berneche, Simon
Different Hydration Patterns in the Pores of AmtB and RhCG Could Determine Their Transport Mechanisms
BIOCHEMISTRY, 52:7091-7098, OCT 8 2013
abstract, full text, DOI:10.1021/bi400015f

Heidarsson, Petur O.; Otazo, Mariela R.; Bellucci, Luca; Mossa, Alessandro; Imparato, Alberto; Paci, Emanuele; Corni, Stefano; Di Felice, Rosa; Kragelund, Birthe B.; Cecconi, Ciro
Single-Molecule Folding Mechanism of an EF-Hand Neuronal Calcium Sensor
STRUCTURE, 21:1812-1821, OCT 8 2013
abstract, full text, DOI:10.1016/j.str.2013.07.022

Schmidt, Chris; Irausquin, Stephanie J.; Valafar, Homayoun
Advances in the REDCAT software package
BMC BIOINFORMATICS, 14 Art. No. 302, OCT 7 2013
abstract, full text, DOI:10.1186/1471-2105-14-302

Lanza, Giuseppe; Chiacchio, Maria A.
Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides
CHEMPHYSCHEM, 14:3284-3293, OCT 7 2013
abstract, full text, DOI:10.1002/cphc.201300445

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
Ligand release mechanisms and channels in histone deacetylases
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2270-2283, OCT 5 2013
abstract, full text, DOI:10.1002/jcc.23390

Koukos, Panagiotis I.; Glykos, Nicholas M.
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2310-2312, OCT 5 2013
abstract, full text, DOI:10.1002/jcc.23381

Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Familial Alzheimer's Disease Osaka Mutant (Delta E22) beta-Barrels Suggest an Explanation for the Different A beta(1-40/42) Preferred Conformational States Observed by Experiment
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11518-11529, OCT 3 2013
abstract, full text, DOI:10.1021/jp405389n

Hu, Yuan; Ou, Shuching; Patel, Sandeep
Free Energetics of Arginine Permeation into Model DMPC Lipid Bilayers: Coupling of Effective Counterion Concentration and Lateral Bilayer Dimensions
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11641-11653, OCT 3 2013
abstract, full text, DOI:10.1021/jp404829y

Ou, Shuching; Hu, Yuan; Patel, Sandeep; Wan, Hongbin
Spherical Monovalent Ions at Aqueous Liquid-Vapor Interfaces: Interfacial Stability and Induced Interface Fluctuations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11732-11742, OCT 3 2013
abstract, full text, DOI:10.1021/jp406001b

Tong, Yujin; Verde, Ana Vila; Campen, R. Kramer
The Free OD at the Air/D2O Interface Is Structurally and Dynamically Heterogeneous
JOURNAL OF PHYSICAL CHEMISTRY B, 117:11753-11764, OCT 3 2013
abstract, full text, DOI:10.1021/jp406577v

Zhang, Hailiang; Khodadadi, Sheila; Fiedler, Steven L.; Curtis, Joseph E.
Role of Water and Ions on the Dynamical Transition of RNA
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:3325-3329, OCT 3 2013
abstract, full text, DOI:10.1021/jz401406c

Lin, Yen-Lin; Roux, Benoit
Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:14741-14753, OCT 2 2013
abstract, full text, DOI:10.1021/ja405939x

Wright, David W.; Deuzing, Ilona P.; Flandre, Philippe; van den Eede, Peter; Govaert, Micheline; Setiawan, Laurentia; Coveney, Peter V.; Marcelin, Anne-Genevieve; Calvez, Vincent; Boucher, Charles A. B.; Beerens, Nancy
A Polymorphism at Position 400 in the Connection Subdomain of HIV-1 Reverse Transcriptase Affects Sensitivity to NNRTIs and RNaseH Activity
PLOS ONE, 8 Art. No. e74078, OCT 2 2013
abstract, full text, DOI:10.1371/journal.pone.0074078

Segrest, Jere P.; Jones, Martin K.; Catte, Andrea
MD simulations suggest important surface differences between reconstituted and circulating spherical HDL
JOURNAL OF LIPID RESEARCH, 54:2718-2732, OCT 2013
abstract, full text, DOI:10.1194/jlr.M039206

Bhat, Hema Balakrishna; Kishimoto, Takuma; Abe, Mitsuhiro; Makino, Asami; Inaba, Takehiko; Murate, Motohide; Dohmae, Naoshi; Kurahashi, Atsushi; Nishibori, Kozo; Fujimori, Fumihiro; Greimel, Peter; Ishitsuka, Reiko; Kobayashi, Toshihide
Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains
JOURNAL OF LIPID RESEARCH, 54:2933-2943, OCT 2013
abstract, full text, DOI:10.1194/jlr.D041731

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A.; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F.; Feldmann, Heinz
Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure
PLOS PATHOGENS, 9 Art. No. e1003677, OCT 2013
abstract, full text, DOI:10.1371/journal.ppat.1003677

Fu, Iris W.; Markegard, Cade B.; Chu, Brian K.; Nguyen, Hung D.
The Role of Electrostatics and Temperature on Morphological Transitions of Hydrogel Nanostructures Self-Assembled by Peptide Amphiphiles Via Molecular Dynamics Simulations
ADVANCED HEALTHCARE MATERIALS, 2:1388-1400, OCT 2013
abstract, full text, DOI:10.1002/adhm.201200400

Joshi, Harshad; Lewis, Kristen; Singharoy, Abhishek; Ortoleva, Peter J.
Epitope engineering and molecular metrics of immunogenicity: A computational approach to VLP-based vaccine design
VACCINE, 31:4841-4847, OCT 1 2013
abstract, full text, DOI:10.1016/j.vaccine.2013.07.075

Gentili, D.; Chinappi, M.; Bolognesi, G.; Giacomello, A.; Casciola, C. M.
Water slippage on hydrophobic nanostructured surfaces: molecular dynamics results for different filling levels
MECCANICA, 48:1853-1861, OCT 2013
abstract, full text, DOI:10.1007/s11012-013-9717-8

Ylilauri, Mikko; Pentikainen, Olli T.
MMGBSA As a Tool To Understand the Binding Affinities of Filamin-Peptide Interactions
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2626-2633, OCT 2013
abstract, full text, DOI:10.1021/ci4002475

Morales-Quintana, Luis; Ximena Nunez-Tobar, Maria; Alejandra Moya-Leon, Maria; Herrera, Raul
Molecular Dynamics Simulation and Site-Directed Mutagenesis of Alcohol Acyltransferase: A Proposed Mechanism of Catalysis
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2689-2700, OCT 2013
abstract, full text, DOI:10.1021/ci400409s

Ge, Hu; Wang, Yu; Li, Chanjuan; Chen, Nanhao; Xie, Yufang; Xu, Mengyan; He, Yingyan; Gu, Xinchun; Wu, Ruibo; Gu, Qiong; Zeng, Liang; Xu, Jun
Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2757-2764, OCT 2013
abstract, full text, DOI:10.1021/ci400391s

Carpenter, Timothy S.; Lau, Edmond Y.; Lightstone, Felice C.
Identification of a Possible Secondary Picrotoxin-Binding Site on the GABA(A) Receptor
CHEMICAL RESEARCH IN TOXICOLOGY, 26:1444-1454, OCT 2013
abstract, full text, DOI:10.1021/tx400167b

Preller, Matthias; Holmes, Kenneth C.
The Myosin Start-of-Power Stroke State and How Actin Binding Drives the Power Stroke
CYTOSKELETON, 70:651-660, OCT 2013
abstract, full text, DOI:10.1002/cm.21125

Barollo, S.; Pezzani, R.; Cristiani, A.; Bertazza, L.; Rubin, B.; Bulfone, A.; Pelizzo, M. R.; Torresan, F.; Mantero, F.; Pennelli, G.; Moro, S.; Mian, C.
Functional Significance of the Novel H-RAS Gene Mutation M72I in a Patient with Medullary Thyroid Cancer
EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES, 121:546-550, OCT 2013
abstract, full text, DOI:10.1055/s-0033-1351299

Cosseddu, S. M.; Khovanov, I. A.; Allen, M. P.; Rodger, P. M.; Luchinsky, D. G.; McClintock, P. V. E.
Dynamics of ions in the selectivity filter of the KcsA channel
EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS, 222:2595-2605, OCT 2013
abstract, full text, DOI:10.1140/epjst/e2013-02040-9

Chen, Calvin Yu-Chian; Tou, Weng Leong
How to design a drug for the disordered proteins
DRUG DISCOVERY TODAY, 18:910-915, OCT 2013
abstract, full text, DOI:10.1016/j.drudis.2013.04.008

Nguyen, Thuy Hien T.; Liu, Zhiwei; Moore, Preston B.
Molecular Dynamics Simulations of Homo-oligomeric Bundles Embedded Within a Lipid Bilayer
BIOPHYSICAL JOURNAL, 105:1569-1580, OCT 1 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.053

Baker, Joseph L.; Voth, Gregory A.
Effects of ATP and Actin-Filament Binding on the Dynamics of the Myosin II S1 Domain
BIOPHYSICAL JOURNAL, 105:1624-1634, OCT 1 2013
abstract, full text, DOI:10.1016/j.bpj.2013.08.023

Gur, Mert; Madura, Jeffry D.; Bahar, Ivet
Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase
BIOPHYSICAL JOURNAL, 105:1643-1652, OCT 1 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.058

Batista, Mariana R. B.; Martinez, Leandro
Dynamics of Nuclear Receptor Helix-12 Switch of Transcription Activation by Modeling Time-Resolved Fluorescence Anisotropy Decays
BIOPHYSICAL JOURNAL, 105:1670-1680, OCT 1 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.032

Artali, R.; Bombieri, G.; Giovenzana, G. B.; Galli, M.; Lattuada, L.; Meneghetti, F.
Preparation, crystallographic and theoretical study on a bifunctional Gd-AAZTA derivative as potential MRI contrast agent precursor
INORGANICA CHIMICA ACTA, 407:306-312, OCT 1 2013
abstract, full text, DOI:10.1016/j.ica.2013.08.004

Khalili-Araghi, Fatemeh; Ziervogel, Brigitte; Gumbart, James C.; Roux, Benoit
Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations
JOURNAL OF GENERAL PHYSIOLOGY, 142:465-475, OCT 2013
abstract, full text, DOI:10.1085/jgp.201311014

Hernandez-Rodriguez, Maricarmen; Correa-Basurto, Jose; Benitez-Cardoza, Claudia G.; Arturo Resendiz-Albor, Aldo; Rosales-Hernandez, Martha C.
In silico and in vitro studies to elucidate the role of Cu2+ and galanthamine as the limiting step in the amyloid beta (1-42) fibrillation process
PROTEIN SCIENCE, 22:1320-1335, OCT 2013
abstract, full text, DOI:10.1002/pro.2319

Ylilauri, Mikko; Mattila, Elina; Nurminen, Elisa M.; Kapyla, Jarmo; Niinivehmas, Sanna P.; Maatta, Juha A.; Pentikainen, Ulla; Ivaska, Johanna; Pentikainen, Olli T.
Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:1988-1997, OCT 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.07.001

Grozdanovic, Milica M.; Drakulic, Branko J.; Gavrovic-Jankulovic, Marija
Conformational mobility of active and E-64-inhibited actinidin
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1830:4790-4799, OCT 2013
abstract, full text, DOI:10.1016/j.bbagen.2013.06.015

Chan, Albert H.; Wereszczynski, Jeff; Amer, Brendan R.; Yi, Sung Wook; Jung, Michael E.; McCammon, J. Andrew; Clubb, Robert T.
Discovery of Staphylococcus aureus Sortase A Inhibitors Using Virtual Screening and the Relaxed Complex Scheme
CHEMICAL BIOLOGY & DRUG DESIGN, 82:418-428, OCT 2013
abstract, full text, DOI:10.1111/cbdd.12167

Tanaka, Takeshi Q.; Deu, Edgar; Molina-Cruz, Alvaro; Ashburne, Michael J.; Ali, Omar; Suri, Amreena; Kortagere, Sandhya; Bogyo, Matthew; Williamsona, Kim C.
Plasmodium Dipeptidyl Aminopeptidases as Malaria Transmission-Blocking Drug Targets
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 57:4645-4652, OCT 2013
abstract, full text, DOI:10.1128/AAC.02495-12

Xie, Hong-Bo; Wang, Jian; Sha, Yu; Cheng, Mao-Sheng
Molecular dynamics investigation of Cl- transport through the closed and open states of the 2 alpha(1)2 beta(2)gamma(2) GABA(A) receptor
BIOPHYSICAL CHEMISTRY, 180:1-9, OCT-NOV 2013
abstract, full text, DOI:10.1016/j.bpc.2013.05.004

Stachowicz, Anna; Rogalski, Marek; Korchowiec, Jacek
Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective
JOURNAL OF MOLECULAR MODELING, 19:4163-4172, OCT 2013
abstract, full text, DOI:10.1007/s00894-013-1757-4

Song, Xuezeng; Fan, Jianfen; Liu, Dongyan; Li, Hui; Li, Rui
Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube
JOURNAL OF MOLECULAR MODELING, 19:4271-4282, OCT 2013
abstract, full text, DOI:10.1007/s00894-013-1899-4

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Zhang, Jinglai
Molecular dynamics simulation of temperature induced unfolding of animal prion protein
JOURNAL OF MOLECULAR MODELING, 19:4433-4441, OCT 2013
abstract, full text, DOI:10.1007/s00894-013-1955-0

Balaraju, Tuniki; Kumar, Amit; Bal, Chandralata; Chattopadhyay, Debprasad; Jena, Nivedita; Bal, Naresh Chandra; Sharon, Ashoke
Aromatic interaction profile to understand the molecular basis of raltegravir resistance
STRUCTURAL CHEMISTRY, 24:1499-1512, OCT 2013
abstract, full text, DOI:10.1007/s11224-012-0181-1

Liu, Ruchuan; Wu, Fei; Thiery, Jean Paul
Remarkable disparity in mechanical response among the extracellular domains of type I and II cadherins
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:1137-1149, OCT 1 2013
abstract, full text, DOI:10.1080/07391102.2012.726530

Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.
Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 24:1573-1583, OCT 2013
abstract, full text, DOI:10.1007/s13361-013-0712-z

Zhan, Yingqian Ada; Wu, Hongwei; Powell, Anne T.; Daughdrill, Gary W.; Ytreberg, F. Marty
Impact of the K24N mutation on the transactivation domain of p53 and its binding to murine double-minute clone 2
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1738-1747, OCT 2013
abstract, full text, DOI:10.1002/prot.24310

Tanis, I.; Karatasos, K.; Posocco, P.; Laurini, E.; Pricl, S.
Complexes between Poly(amido amine) Dendrimers and Poly(methacrlyic acid): Insight from Molecular Dynamics Simulations
MACROMOLECULAR SYMPOSIA, 331:34-42, OCT 2013
abstract, full text, DOI:10.1002/masy.201300036

Vassiliev, Serguei; Zaraiskaya, Tatiana; Bruce, Doug
Molecular dynamics simulations reveal highly permeable oxygen exit channels shared with water uptake channels in photosystem II
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1827:1148-1155, OCT 2013
abstract, full text, DOI:10.1016/j.bbabio.2013.06.008

Hadi-Alijanvand, Hamid; Moosavi-Movahedi, Ali A.; Goliaei, Bahram
Unfolding mechanism of PHD2 as a vital protein: all-atom simulation approach
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 10:907-914, OCT 2013
abstract, full text, DOI:10.1007/s13738-013-0227-3

Ambrosia, Matthew Stanley; Ha, Man Yeong; Balachandar, S.
The effect of pillar surface fraction and pillar height on contact angles using molecular dynamics
APPLIED SURFACE SCIENCE, 282:211-216, OCT 1 2013
abstract, full text, DOI:10.1016/j.apsusc.2013.05.104

Yang, Dengfeng; Liu, Qingzhi; Li, Hongman; Gao, Congjie
Molecular simulation of carbon nanotube membrane for Li+ and Mg2+ separation
JOURNAL OF MEMBRANE SCIENCE, 444:327-331, OCT 1 2013
abstract, full text, DOI:10.1016/j.memsci.2013.05.019

Liu, Dongyan; Fan, Jianfen; Song, Xuezeng; Li, Rui; Li, Hui
MD simulations on the influences of an external force on the water transportation behavior through a cyclic peptide nanotube
COMPUTATIONAL MATERIALS SCIENCE, 78:47-54, OCT 2013
abstract, full text, DOI:10.1016/j.commatsci.2013.05.013

Bellucci, Luca; Corni, Stefano; Di Felice, Rosa; Paci, Emanuele
The Structure of Neuronal Calcium Sensor-1 in Solution Revealed by Molecular Dynamics Simulations
PLOS ONE, 8 Art. No. e74383, SEP 30 2013
abstract, full text, DOI:10.1371/journal.pone.0074383

Huang, Jing; MacKerell, Alexander D., Jr.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2135-2145, SEP 30 2013
abstract, full text, DOI:10.1002/jcc.23354

Zhu, You-Liang; Liu, Hong; Li, Zhan-Wei; Qian, Hu-Jun; Milano, Giuseppe; Lu, Zhong-Yuan
GALAMOST: GPU-accelerated large-scale molecular simulation toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2197-2211, SEP 30 2013
abstract, full text, DOI:10.1002/jcc.23365

Haas, Kevin R.; Yang, Haw; Chu, Jhih-Wei
Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 121931, SEP 28 2013
abstract, full text, DOI:10.1063/1.4820491

Teo, Ivan; Schulten, Klaus
A computational kinetic model of diffusion for molecular systems
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 121929, SEP 28 2013
abstract, full text, TCBG publications, DOI:10.1063/1.4820876

Rahman, Kazi S.; Cui, Guiying; Harvey, Stephen C.; McCarty, Nael A.
Modeling the Conformational Changes Underlying Channel Opening in CFTR
PLOS ONE, 8 Art. No. UNSP e74574, SEP 27 2013
abstract, full text, DOI:10.1371/journal.pone.0074574

Pan, Lurong; Patterson, James C.
Molecular Dynamics Study of Zn(A beta) and Zn(A beta)(2)
PLOS ONE, 8 Art. No. e70681, SEP 27 2013
abstract, full text, DOI:10.1371/journal.pone.0070681

Khelashvili, George; LeVine, Michael V.; Shi, Lei; Quick, Matthias; Javitch, Jonathan A.; Weinstein, Harel
The Membrane Protein LeuT in Micellar Systems: Aggregation Dynamics and Detergent Binding to the S2 Site
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:14266-14275, SEP 25 2013
abstract, full text, DOI:10.1021/ja405984v

Dibenedetto, Domenica; Rossetti, Giulia; Caliandro, Rocco; Carloni, Paolo
A Molecular Dynamics Simulation-Based Interpretation of Nuclear Magnetic Resonance Multidimensional Heteronuclear Spectra of alpha-Synuclein.Dopamine Adducts
BIOCHEMISTRY, 52:6672-6683, SEP 24 2013
abstract, full text, DOI:10.1021/bi400367r

Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong
Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 34:2711-2719, SEP 20 2013
abstract, full text, DOI:10.5012/bkcs.2013.34.9.2711

Helbling, Rachel E.; Bolze, Christin S.; Golczak, Marcin; Palczewski, Krzysztof; Stocker, Achim; Cascella, Michele
Cellular Retinaldehyde Binding Protein-Different Binding Modes and Micro-Solvation Patterns for High-Affinity 9-cis- and 11-cis-Retinal Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10719-10729, SEP 19 2013
abstract, full text, DOI:10.1021/jp405410t

Lin, Yuchun; Beckham, Gregg T.; Himmel, Michael E.; Crowley, Michael F.; Chu, Jhih-Wei
Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10750-10758, SEP 19 2013
abstract, full text, DOI:10.1021/jp405897q

Li, Fee; Bravo-Rodriguez, Kenny; Fernandez-Oliva, Miguel; Ramirez-Anguita, Juan M.; Merz, Klaus; Winter, Manuela; Lehmann, Christian W.; Sander, Wolfram; Sanchez-Garcia, Elsa
Stereochemistry Rules: A Single Stereocenter Changes the Conformation of a Cyclic Tetrapeptide
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10785-10791, SEP 19 2013
abstract, full text, DOI:10.1021/jp406497r

Noinaj, Nicholas; Kuszak, Adam J.; Gumbart, James C.; Lukacik, Petra; Chang, Hoshing; Easley, Nicole C.; Lithgow, Trevor; Buchanan, Susan K.
Structural insight into the biogenesis of beta-barrel membrane proteins
NATURE, 501:385-+, SEP 19 2013
abstract, full text, DOI:10.1038/nature12521

Venerando, Andrea; Franchin, Cinzia; Cant, Natasha; Cozza, Giorgio; Pagano, Mario A.; Tosoni, Kendra; Al-Zahrani, Ateeq; Arrigoni, Giorgio; Ford, Robert C.; Mehta, Anil; Pinna, Lorenzo A.
Detection of Phospho- Sites Generated by Protein Kinase CK2 in CFTR: Mechanistic Aspects of Thr1471 Phosphorylation
PLOS ONE, 8 Art. No. e74232, SEP 18 2013
abstract, full text, DOI:10.1371/journal.pone.0074232

Pruitt, Margaret M.; Lamm, Monica H.; Coffman, Clark R.
Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure
BMC STRUCTURAL BIOLOGY, 13 Art. No. 15, SEP 18 2013
abstract, full text, DOI:10.1186/1472-6807-13-15

Mehrbod, Mehrdad; Trisno, Stephen; Mofrad, Mohammad R. K.
On the Activation of Integrin alpha IIb beta 3: Outside-in and Inside-out Pathways
BIOPHYSICAL JOURNAL, 105:1304-1315, SEP 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.055

Yilmaz, Neval; Yamada, Taro; Greimel, Peter; Uchihashi, Takayuki; Ando, Toshio; Kobayashi, Toshihide
Real-Time Visualization of Assembling of a Sphingomyelin-Specific Toxin on Planar Lipid Membranes
BIOPHYSICAL JOURNAL, 105:1397-1405, SEP 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.052

Wu, Emilia L.; Engstrom, Olof; Jo, Sunhwan; Stuhlsatz, Danielle; Yeom, Min Sun; Klauda, Jeffery B.; Widmalm, Goran; Im, Wonpil
Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
BIOPHYSICAL JOURNAL, 105:1444-1455, SEP 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.08.002

Liang, Li-Jun; Wang, Qi; Wu, Tao; Sun, Tian-Yang; Kang, Yu
Contribution of Water Molecules in the Spontaneous Release of Protein by Graphene Sheets
CHEMPHYSCHEM, 14:2902-2909, SEP 16 2013
abstract, full text, DOI:10.1002/cphc.201300414

Ilgu, Muslum; Wang, Tianjiao; Lamm, Monica H.; Nilsen-Hamilton, Marit
Investigating the malleability of RNA aptamers
METHODS, 63:178-187, SEP 15 2013
abstract, full text, DOI:10.1016/j.ymeth.2013.03.016

Kabasakal, Burak V.; Gae, David D.; Li, Jie; Lagarias, J. Clark; Koehl, Patrice; Fisher, Andrew J.
His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 537:233-242, SEP 15 2013
abstract, full text, DOI:10.1016/j.abb.2013.07.021

Liu, Guangjian; Fang, Ying; Wu, Jianhua
A Mechanism for Localized Dynamics-driven Affinity Regulation of the Binding of von Willebrand Factor to Platelet Glycoprotein Ib alpha
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:26658-26667, SEP 13 2013
abstract, full text, DOI:10.1074/jbc.M113.453803

Verde, Ana Vila; Lipowsky, Reinhard
Cooperative Slowdown of Water Rotation near Densely Charged Ions Is Intense but Short-Ranged
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10556-10566, SEP 12 2013
abstract, full text, DOI:10.1021/jp4059802

Schoeneberg, Johannes; Noe, Frank
ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments
PLOS ONE, 8 Art. No. e74261, SEP 11 2013
abstract, full text, DOI:10.1371/journal.pone.0074261

Zhang, Fuming; Aguilera, Javier; Beaudet, Julie M.; Xie, Qing; Lerch, Thomas F.; Davulcu, Omar; Colon, Wilfredo; Chapman, Michael S.; Linhardt, Robert J.
Characterization of Interactions between Heparin/Glycosaminoglycan and Adeno-Associated Virus
BIOCHEMISTRY, 52:6275-6285, SEP 10 2013
abstract, full text, DOI:10.1021/bi4008676

Lai, Chun-Liang; Srivastava, Anand; Pilling, Carissa; Chase, Anna R.; Falke, Joseph J.; Voth, Gregory A.
Molecular Mechanism of Membrane Binding of the GRP1 PH Domain
JOURNAL OF MOLECULAR BIOLOGY, 425:3073-3090, SEP 9 2013
abstract, full text, DOI:10.1016/j.jmb.2013.05.026

Bloudoff, Kristjan; Rodionov, Dmitry; Schmeing, T. Martin
Crystal Structures of the First Condensation Domain of CDA Synthetase Suggest Conformational Changes during the Synthetic Cycle of Nonribosomal Peptide Synthetases
JOURNAL OF MOLECULAR BIOLOGY, 425:3137-3150, SEP 9 2013
abstract, full text, DOI:10.1016/j.jmb.2013.06.003

Noid, W. G.
Perspective: Coarse-grained models for biomolecular systems
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 090901, SEP 7 2013
abstract, full text, DOI:10.1063/1.4818908

Alvarez-Navarro, Carlos; Cragnolini, Juan J.; Dos Santos, Helena G.; Barnea, Eilon; Admon, Arie; Morreale, Antonio; Lopez de Castro, Jose A.
Novel HLA-B27-restricted Epitopes from Chlamydia trachomatis Generated upon Endogenous Processing of Bacterial Proteins Suggest a Role of Molecular Mimicry in Reactive Arthritis
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:25810-25825, SEP 6 2013
abstract, full text, DOI:10.1074/jbc.M113.493247

Adams, Bryn L.; Finch, Amethist S.; Hurley, Margaret M.; Sarkes, Deborah A.; Stratis-Cullum, Dimitra N.
Genetically Engineered Peptides for Inorganics: Study of an Unconstrained Bacterial Display Technology and Bulk Aluminum Alloy
ADVANCED MATERIALS, 25:4585-4591, SEP 6 2013
full text, DOI:10.1002/adma.201301646

Ostmeyer, Jared; Chakrapani, Sudha; Pan, Albert C.; Perozo, Eduardo; Roux, Benoit
Recovery from slow inactivation in K+ channels is controlled by water molecules
NATURE, 501, SEP 5 2013
abstract, full text, DOI:10.1038/nature12395

Li, Xiaohu; Schatz, George C.
Osmolytic Co-Solute Perturbing the Surface Enhancement of Halide Ions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:2885-2889, SEP 5 2013
abstract, full text, DOI:10.1021/jz4014695

Huntress, Mark M.; Gozem, Samer; Malley, Konstantin R.; Jailaubekov, Askat E.; Vasileiou, Chrysoula; Vengris, Mikas; Geiger, James H.; Borhan, Babak; Schapiro, Igor; Larsen, Delmar S.; Olivucci, Massimo
Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10053-10070, SEP 5 2013
abstract, full text, DOI:10.1021/jp305935t

Venable, Richard M.; Luo, Yun; Gawrisch, Klaus; Roux, Benoit; Pastor, Richard W.
Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data
JOURNAL OF PHYSICAL CHEMISTRY B, 117:10183-10192, SEP 5 2013
abstract, full text, DOI:10.1021/jp401512z

GhattyVenkataKrishna, Pavan K.; Mostofian, Barmak
Dynamics of water in the amphiphilic pore of amyloid beta fibrils
CHEMICAL PHYSICS LETTERS, 582:1-5, SEP 4 2013
abstract, full text, DOI:10.1016/j.cplett.2013.07.026

Favreau, Amanda J.; Faller, Christina E.; Guvench, Olgun
CD44 Receptor Unfolding Enhances Binding by Freeing Basic Amino Acids to Contact Carbohydrate Ligand
BIOPHYSICAL JOURNAL, 105:1217-1226, SEP 3 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.041

Liu, Yufeng; Haddadian, Esmael; Sosnick, Tobin R.; Freed, Karl F.; Gong, Haipeng
A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of RNA
BIOPHYSICAL JOURNAL, 105:1248-1257, SEP 3 2013
abstract, full text, DOI:10.1016/j.bpj.2013.07.033

Payne, Christina M.; Resch, Michael G.; Chen, Liqun; Crowley, Michael F.; Himmel, Michael E.; Taylor, Larry E., I.I.; Sandgren, Mats; Stahlberg, Jerry; Stals, Ingeborg; Tan, Zhongping; Beckham, Gregg T.
Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:14646-14651, SEP 3 2013
abstract, full text, DOI:10.1073/pnas.1309106110

Corbi-Verge, Carles; Marinelli, Fabrizio; Zafra-Ruano, Ana; Ruiz-Sanz, Javier; Luque, Irene; Faraldo-Gomez, Jose D.
Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:E3372-E3380, SEP 3 2013
abstract, full text, DOI:10.1073/pnas.1303966110

de Veer, Simon J.; Ukolova, Svetlana S.; Munro, Christopher A.; Swedberg, Joakim E.; Buckle, Ashley M.; Harris, Jonathan M.
Mechanism-Based Selection of a Potent Kallikrein-Related Peptidase 7 Inhibitor From a Versatile Library Based on the Sunflower Trypsin Inhibitor SFTI-1
BIOPOLYMERS, 100:510-518, SEP 2013
abstract, full text, DOI:10.1002/bip.22231

Ma, Christopher I.; Diraviyam, Karthikeyan; Maier, Martin E.; Sept, David; Sibley, L. David
Synthetic Chondramide A Analogues Stabilize Filamentous Actin and Block Invasion by Toxoplasma gondii
JOURNAL OF NATURAL PRODUCTS, 76:1565-1572, SEP 2013
abstract, full text, DOI:10.1021/np400196w

Caliandro, Rocco; Nico, Giovanni; Tiscia, Giovanni; Favuzzi, Giovanni; De Stefano, Valerio; Rossi, Elena; Margaglione, Maurizio; Grandone, Elvira
Structural analysis of protein Z gene variants in patients with foetal losses
THROMBOSIS AND HAEMOSTASIS, 110:534-542, SEP 2013
abstract, full text, DOI:10.1160/TH13-01-0005

Bradley, Ryan; Radhakrishnan, Ravi
Coarse-Grained Models for Protein-Cell Membrane Interactions
POLYMERS, 5:890-936, SEP 2013
abstract, full text, DOI:10.3390/polym5030890

Khelashvili, George; Kollmitzer, Benjamin; Heftberger, Peter; Pabst, Georg; Harries, Daniel
Calculating the Bending Modulus for Multicomponent Lipid Membranes in Different Thermodynamic Phases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3866-3871, SEP 2013
abstract, full text, DOI:10.1021/ct400492e

Salomon-Ferrer, Romelia; Goetz, Andreas W.; Poole, Duncan; Le Grand, Scott; Walker, Ross C.
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3878-3888, SEP 2013
abstract, full text, DOI:10.1021/ct400314y

Jakobsen, Sofie; Kristensen, Kasper; Jensen, Frank
Electrostatic Potential of Insulin: Exploring the Limitations of Density Functional Theory and Force Field Methods
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3978-3985, SEP 2013
abstract, full text, DOI:10.1021/ct400452f

Branduardi, Davide; Faraldo-Gomez, Jose D.
String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:4140-4154, SEP 2013
abstract, full text, DOI:10.1021/ct400469w

Sun, Huiyong; Li, Youyong; Li, Dan; Hou, Tingjun
Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2376-2389, SEP 2013
abstract, full text, DOI:10.1021/ci400188q

Pietra, Francesco
Gates and Binding Pockets for Nitric Oxide with Cytochrome c ', According to Molecular Dynamics
CHEMISTRY & BIODIVERSITY, 10:1574-1588, SEP 2013
abstract, full text, DOI:10.1002/cbdv.201300164

Oliveira, Bruno L.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.; Santos, Isabel; Correia, Joao D. G.
Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 45:13-25, SEP 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.07.007

Li, Jhen-Kai; Liao, Jiahn-Haur; Li, Hongchun; Kuo, C.h.i.a.o.-.I.; Huang, Kai-Fa; Yang, Lee-Wei; Wu, Shih-Hsiung; Chang, C.h.u.n.g.-.I.
The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 69:1789-1797, SEP 2013
abstract, full text, DOI:10.1107/S090744491301500X

Zhang Ning; Li Wei-Zhong; Chen Cong; Zuo Jian-Guo
Evaluation of the Application of Hydrogen Bonding Criteria to DMSO Aqueous Solution
ACTA PHYSICO-CHIMICA SINICA, 29:1891-1899, SEP 2013
abstract, full text, DOI:10.3866/PKU.WHXB201307121

Li, Feng; Guo, Hua-Yan; Wang, Man; Geng, Hong-Li; Bian, Mei-Ru; Cao, Jiang; Chen, Chong; Zeng, Ling-Yu; Wang, Xiao-Yun; Wu, Qing-Yun
The effects of R683S (G) genetic mutations on the JAK2 activity, structure and stability
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 60:186-195, SEP 2013
abstract, full text, DOI:10.1016/j.ijbiomac.2013.05.029

Wang, Lin; Xu, Xiaojun; Kumar, Ravindra; Maiti, Buddhadev; Liu, C. Tony; Ivanov, Ivaylo; Lee, Tae-Hee; Benkovic, Stephen J.
Probing DNA clamps with single-molecule force spectroscopy
NUCLEIC ACIDS RESEARCH, 41:7804-7814, SEP 2013
abstract, full text, DOI:10.1093/nar/gkt487

Radzimanowski, Jens; Dehez, Francois; Round, Adam; Bidon-Chanal, Axel; McSweeney, Sean; Timmins, Joanna
An 'open' structure of the RecOR complex supports ssDNA binding within the core of the complex
NUCLEIC ACIDS RESEARCH, 41:7972-7986, SEP 2013
abstract, full text, DOI:10.1093/nar/gkt572

Eren, Dilek; Alakent, Burak
Frequency Response of a Protein to Local Conformational Perturbations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003238, SEP 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003238

Sinnott, Susan B.
Material design and discovery with computational materials science
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A, 31 Art. No. 050812, SEP 2013
abstract, full text, DOI:10.1116/1.4813689

Rabinovich, A. L.; Lyubartsev, A. P.
Computer Simulation of Lipid Membranes: Methodology and Achievements
POLYMER SCIENCE SERIES C, 55:162-180, SEP 2013
abstract, full text, DOI:10.1134/S1811238213070060

Reichow, Steve L.; Clemens, Daniel M.; Freites, J. Alfredo; Nemeth-Cahalan, Karin L.; Heyden, Matthias; Tobias, Douglas J.; Hall, James E.; Gonen, Tamir
Allosteric mechanism of water-channel gating by Ca2+-calmodulin
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 20:1085-+, SEP 2013
abstract, full text, DOI:10.1038/nsmb.2630

Zamora, Pablo; Pardo, Ariel; Fierro, Angelica; Prieto, Humberto; Zuniga, Gustavo E.
Molecular characterization of the chalcone isomerase gene family in Deschampsia antarctica
POLAR BIOLOGY, 36:1269-1280, SEP 2013
abstract, full text, DOI:10.1007/s00300-013-1346-0

Miszta, Przemyslaw; Basak, Subhash C.; Natarajan, Ramanathan; Nowak, Wieslaw
How Computational Studies of Mosquito Repellents Contribute to the Control of Vector Borne Diseases
CURRENT COMPUTER-AIDED DRUG DESIGN, 9:300-307, SEP 2013
abstract, full text

Wozniak, Justin M.; Wilde, Michael; Katz, Daniel S.
JETS: Language and System Support for Many-Parallel-Task Workflows
JOURNAL OF GRID COMPUTING, 11:341-360, SEP 2013
abstract, full text, DOI:10.1007/s10723-013-9259-2

Oliveira, Ana; Allegri, Alessandro; Bidon-Chanal, Axel; Knipp, Markus; Roitberg, Adrian E.; Abbruzzetti, Stefania; Viappiani, Cristiano; Javier Luque, F.
Kinetics and computational studies of ligand migration in nitrophorin 7 and its Delta 1-3 mutant
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:1711-1721, SEP 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.04.009

Joram Castro, Josue; Pablo Mendez, Juan; Mauricio Coral-Vazquez, Ramon; Antonio Soriano-Ursua, Marvin; Damian-Matsumura, Pablo; Benitez-Granados, Jesus; Rosas-Vargas, Haydee; Canto, Patricia
In Vitro and Molecular Modeling Analysis of Two Mutant Desert Hedgehog Proteins Associated with 46,XY Gonadal Dysgenesis
DNA AND CELL BIOLOGY, 32:524-530, SEP 2013
abstract, full text, DOI:10.1089/dna.2013.2052

Swett, Rebecca J.; Elias, Angela; Miller, Jeffrey A.; Dyson, Gregory E.; Cisneros, G. Andres
Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S)
DNA REPAIR, 12:733-740, SEP 2013
abstract, full text, DOI:10.1016/j.dnarep.2013.06.001

Briegel, Ariane; Ames, Peter; Gumbart, James C.; Oikonomou, Catherine M.; Parkinson, John S.; Jensen, Grant J.
The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state
MOLECULAR MICROBIOLOGY, 89:831-841, SEP 2013
abstract, full text, DOI:10.1111/mmi.12309

Aleksandrov, Alexey; Field, Martin
Mechanism of activation of elongation factor Tu by ribosome: Catalytic histidine activates GTP by protonation
RNA-A PUBLICATION OF THE RNA SOCIETY, 19:1218-1225, SEP 2013
abstract, full text, DOI:10.1261/rna.040097.113

Kia, Amirali; Darve, Eric
The accuracy of the CHARMM22/CMAP and AMBER ff99SB force fields for modelling the antimicrobial peptide cecropin P1
MOLECULAR SIMULATION, 39:922-936, SEP 1 2013
abstract, full text, DOI:10.1080/08927022.2013.781599

Mino, German; Baez, Mauricio; Gutierrez, Gonzalo
Effect of mutation at the interface of Trp-repressor dimeric protein: a steered molecular dynamics simulation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:683-690, SEP 2013
abstract, full text, DOI:10.1007/s00249-013-0918-9

Kortagere, Sandhya; Fontana, Andreia Cristina Karklin; Rose, Deja Renee; Mortensen, Ole Valente
Identification of an allosteric modulator of the serotonin transporter with novel mechanism of action
NEUROPHARMACOLOGY, 72:282-290, SEP 2013
abstract, full text, DOI:10.1016/j.neuropharm.2013.04.026

DeMonte, Daniel; Drake, Eric J.; Lim, Kok Hong; Gulick, Andrew M.; Park, Sheldon
Structure-based engineering of streptavidin monomer with a reduced biotin dissociation rate
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1621-1633, SEP 2013
abstract, full text, DOI:10.1002/prot.24320

Falconi, Mattia; Iacovelli, Federico; Desideri, Alessandro
A structural modeling approach for the understanding of initiation and elongation of ALS-linked superoxide dismutase fibrils
JOURNAL OF MOLECULAR MODELING, 19:3695-3704, SEP 2013
abstract, full text, DOI:10.1007/s00894-013-1896-7

Nicolau-Junior, Nilson; Giuliatti, Silvana
Modeling and molecular dynamics of the intrinsically disordered e7 proteins from high- and low-risk types of human papillomavirus
JOURNAL OF MOLECULAR MODELING, 19:4025-4037, SEP 2013
abstract, full text, DOI:10.1007/s00894-013-1915-8

Hu, Jian-ping; He, Hong-qiu; Jiao, Xiong; Chang, Shan
Understanding the folding and stability of a designed WW domain protein with replica exchange molecular dynamics simulations
MOLECULAR SIMULATION, 39:828-836, SEP 1 2013
abstract, full text, DOI:10.1080/08927022.2013.773431

Ding, Yanrui; Cai, Yujie
Conformational dynamics of xylanase a from Streptomyces lividans: Implications for TIM-barrel enzyme thermostability
BIOPOLYMERS, 99:594-604, SEP 2013
abstract, full text, DOI:10.1002/bip.22220

Collier, Timothy S.; Diraviyam, Karthikeyan; Monsey, John; Shen, Wei; Sept, David; Bose, Ron
Carboxyl Group Footprinting Mass Spectrometry and Molecular Dynamics Identify Key Interactions in the HER2-HER3 Receptor Tyrosine Kinase Interface
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:25254-25264, AUG 30 2013
abstract, full text, DOI:10.1074/jbc.M113.474882

Chandrakesan, Muralidharan; Sarkar, Bidyut; Mithu, Venus Singh; Abhyankar, Rajiv; Bhowmik, Debanjan; Nag, Suman; Sahoo, Bankanidhi; Shah, Riddhi; Gurav, Sushma; Banerjee, Raja; Dandekar, Sucheta; Jose, Jaya C.; Sengupta, Neelanjana; Madhu, Perunthiruthy K.; Maiti, Sudipta
The basic structural motif and major biophysical properties of Amyloid-beta are encoded in the fragment 18-35
CHEMICAL PHYSICS, 422:80-87, AUG 30 2013
abstract, full text, DOI:10.1016/j.chemphys.2013.01.010

Sinitskiy, Anton V.; Voth, Gregory A.
Coarse-graining of proteins based on elastic network models
CHEMICAL PHYSICS, 422:165-174, AUG 30 2013
abstract, full text, DOI:10.1016/j.chemphys.2013.01.024

Bhatnagar, Navendu; Kamath, Ganesh; Potoff, Jeffrey J.
Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9910-9921, AUG 29 2013
abstract, full text, DOI:10.1021/jp404314k

da Silva, Luis Pinto; Simkovitch, Ron; Huppert, Dan; Esteves da Silva, Joaquim C. G.
Theoretical Photodynamic Study of the Photoprotolytic Cycle of Firefly Oxyluciferin
CHEMPHYSCHEM, 14:2711-2716, AUG 26 2013
abstract, full text, DOI:10.1002/cphc.201300330

Exposito, Roberto R.; Taboada, Guillermo L.; Ramos, Sabela; Tourino, Juan; Doallo, Ramon
General-purpose computation on GPUs for high performance cloud computing
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 25:1628-1642, AUG 25 2013
abstract, full text, DOI:10.1002/cpe.2845

Bernardes, Amanda; Souza, Paulo C. T.; Muniz, Joao R. C.; Ricci, Clarisse G.; Ayers, Stephen D.; Parekh, Nili M.; Godoy, Andre S.; Trivella, Daniela B. B.; Reinach, Peter; Webb, Paul; Skaf, Munir S.; Polikarpov, Igor
Molecular Mechanism of Peroxisome Proliferator-Activated Receptor alpha Activation by WY14643: a New Mode of Ligand Recognition and Receptor Stabilization
JOURNAL OF MOLECULAR BIOLOGY, 425:2878-2893, AUG 23 2013
abstract, full text, DOI:10.1016/j.jmb.2013.05.010

de Almeida, Hugo; Bastos, Izabela M. D.; Ribeiro, Bergmann M.; Maigret, Bernard; Santana, Jaime M.
New Binding Site Conformations of the Dengue Virus NS3 Protease Accessed by Molecular Dynamics Simulation
PLOS ONE, 8 Art. No. UNSP e72402, AUG 21 2013
abstract, full text, DOI:10.1371/journal.pone.0072402

Das, Amit; Chakrabarti, J.; Ghosh, Mahua
Conformational thermodynamics of metal-ion binding to a protein
CHEMICAL PHYSICS LETTERS, 581:91-95, AUG 21 2013
abstract, full text, DOI:10.1016/j.cplett.2013.07.022

Chakraborty, Kaushik; Mantha, Sriteja; Bandyopadhyay, Sanjoy
Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 075103, AUG 21 2013
abstract, full text, DOI:10.1063/1.4818537

Modi, Niraj; Barcena-Uribarri, Ivan; Bains, Manjeet; Benz, Roland; Hancock, Robert E. W.; Kleinekathoefer, Ulrich
Role of the Central Arginine R133 toward the Ion Selectivity of the Phosphate Specific Channel OprP: Effects of Charge and Solvation
BIOCHEMISTRY, 52:5522-5532, AUG 20 2013
abstract, full text, DOI:10.1021/bi400522b

Kalani, Mohamad R.; Moradi, Abdulvahab; Moradi, Mahmoud; Tajkhorshid, Emad
Characterizing a Histidine Switch Controlling pH-Dependent Conformational Changes of the Influenza Virus Hemagglutinin
BIOPHYSICAL JOURNAL, 105:993-1003, AUG 20 2013
abstract, full text, DOI:10.1016/j.bpj.2013.06.047

GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Cheng, Xiaolin
Effect of the amyloid beta hairpin's structure on the handedness of helices formed by its aggregates
FEBS LETTERS, 587:2649-2655, AUG 19 2013
abstract, full text, DOI:10.1016/j.febslet.2013.06.050

Blacklock, Kristin; Verkhivker, Gennady M.
Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study
PLOS ONE, 8 Art. No. e71936, AUG 19 2013
abstract, full text, DOI:10.1371/journal.pone.0071936

Varghese, Anoop; Vemparala, Satyavani; Rajesh, R.
Force fluctuations in stretching a tethered polymer
PHYSICAL REVIEW E, 88 Art. No. 022134, AUG 19 2013
abstract, full text, DOI:10.1103/PhysRevE.88.022134

Rodriguez, Victoria B.; Kidd, Brian A.; Interlandi, Gianluca; Tchesnokova, Veronika; Sokurenko, Evgeni V.; Thomas, Wendy E.
Allosteric Coupling in the Bacterial Adhesive Protein FimH
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:24128-24139, AUG 16 2013
abstract, full text, DOI:10.1074/jbc.M113.461376

Yu, Tao; Lee, One-Sun; Schatz, George C.
Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
JOURNAL OF PHYSICAL CHEMISTRY A, 117:7453-7460, AUG 15 2013
abstract, full text, DOI:10.1021/jp401508w

Guo, Wenchang; Liu, Ruiwu; Bhardwaj, Gaurav; Ma, Ai-Hong; Changou, Chun; Yang, Joy C.; Li, Yuanpei; Feng, Caihong; Luo, Yan; Mazloom, Anisha; Sanchez, Eduardo; Wang, Yan; Huang, Wenzhe; Patterson, Randen; Evans, Christopher P.; Lam, Kit S.; Kung, Hsing-Jien
CTA095, a Novel Etk and Src Dual Inhibitor, Induces Apoptosis in Prostate Cancer Cells and Overcomes Resistance to Src Inhibitors
PLOS ONE, 8 Art. No. e70910, AUG 15 2013
abstract, full text, DOI:10.1371/journal.pone.0070910

Das, Jhuma; Flenner, Elijah; Kosztin, Ioan
Anomalous diffusion of water molecules in hydrated lipid bilayers
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 065102, AUG 14 2013
abstract, full text, DOI:10.1063/1.4817322

Raz, Yoav; Miller, Yifat
Interactions between A beta and Mutated Tau Lead to Polymorphism and Induce Aggregation of A beta-Mutated Tau Oligomeric Complexes
PLOS ONE, 8 Art. No. UNSP e73303, AUG 12 2013
abstract, full text, DOI:10.1371/journal.pone.0073303

Yao, Jianzhuang; Wlodawer, Alexander; Guo, Hong
Understanding the Autocatalytic Process of Pro-kumamolisin Activation from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical (QM/MM) Free-Energy Simulations
CHEMISTRY-A EUROPEAN JOURNAL, 19:10849-10852, AUG 12 2013
full text, DOI:10.1002/chem.201301310

Jiang, Nan; Kuznetsov, Aleksey; Nocek, Judith M.; Hoffman, Brian M.; Crane, Brian R.; Hu, Xiangqian; Beratan, David N.
Distance-Independent Charge Recombination Kinetics in Cytochrome c-Cytochrome c Peroxidase Complexes: Compensating Changes in the Electronic Coupling and Reorganization Energies
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9129-9141, AUG 8 2013
abstract, full text, DOI:10.1021/jp401551t

Chowdhary, Janamejaya; Harder, Edward; Lopes, Pedro E. M.; Huang, Lei; MacKerell, Alexander D., Jr.; Roux, Benoit
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9142-9160, AUG 8 2013
abstract, full text, DOI:10.1021/jp402860e

Cashman, Derek J.; Ortega, Davi R.; Zhulin, Igor B.; Baudry, Jerome
Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
PLOS ONE, 8 Art. No. e70705, AUG 7 2013
abstract, full text, DOI:10.1371/journal.pone.0070705

Han, Jaebeom; Mazack, Michael J. M.; Zhang, Peng; Truhlar, Donald G.; Gao, Jiali
Quantum mechanical force field for water with explicit electronic polarization
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 054503, AUG 7 2013
abstract, full text, DOI:10.1063/1.4816280

Gao, Yang; Iancu, Cristina V.; Mukind, Susmith; Choe, Jun-Yong; Honzatko, Richard B.
Mechanism of Displacement of a Catalytically Essential Loop from the Active Site of Mammalian Fructose-1,6-bisphosphatase
BIOCHEMISTRY, 52:5206-5216, AUG 6 2013
abstract, full text, DOI:10.1021/bi400532n

Cook, Gabriel A.; Dawson, Lindsay A.; Tian, Ye; Opella, Stanley J.
Three-Dimensional Structure and Interaction Studies of Hepatitis C Virus p7 in 1,2-Dihexanoyl-sn-glycero-3-phosphocholine by Solution Nuclear Magnetic Resonance
BIOCHEMISTRY, 52:5295-5303, AUG 6 2013
abstract, full text, DOI:10.1021/bi4005623

Cheng, Mary Hongying; Bahar, Ivet
Coupled Global and Local Changes Direct Substrate Translocation by Neurotransmitter-Sodium Symporter Ortholog LeuT
BIOPHYSICAL JOURNAL, 105:630-639, AUG 6 2013
abstract, full text, DOI:10.1016/j.bpj.2013.06.032

Bykhovskaia, Maria; Jagota, Anand; Gonzalez, Agustin; Vasin, Alexander; Littleton, J. Troy
Interaction of the Complexin Accessory Helix with the C-Terminus of the SNARE Complex: Molecular-Dynamics Model of the Fusion Clamp
BIOPHYSICAL JOURNAL, 105:679-690, AUG 6 2013
abstract, full text, DOI:10.1016/j.bpj.2013.06.018

Wang, Beibei; Predeus, Alexander V.; Burton, Zachary F.; Feig, Michael
Energetic and Structural Details of the Trigger-Loop Closing Transition in RNA Polymerase II
BIOPHYSICAL JOURNAL, 105:767-775, AUG 6 2013
abstract, full text, DOI:10.1016/j.bpj.2013.05.060

Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2 '-O-transphosphorylation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:13002-13007, AUG 6 2013
abstract, full text, DOI:10.1073/pnas.1215086110

Farelli, Jeremiah D.; Gumbart, James C.; Akey, Ildiko V.; Hempstead, Andrew; Amyot, Whitney; Head, James F.; McKnight, C. James; Isberg, Ralph R.; Akey, Christopher W.
IcmQ in the Type 4b Secretion System Contains an NAD(+) Binding Domain
STRUCTURE, 21:1361-1373, AUG 6 2013
abstract, full text, DOI:10.1016/j.str.2013.05.017

Wood, Irene; Florencia Martini, M.; Pickholz, Monica
Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE, 1045:124-130, AUG 6 2013
abstract, full text, DOI:10.1016/j.molstruc.2013.04.011

Harris, Travis V.; Morokuma, Keiji
QM/MM Structural and Spectroscopic Analysis of the Di-iron(II) and Di-iron(III) Ferroxidase Site in M Ferritin
INORGANIC CHEMISTRY, 52:8551-8563, AUG 5 2013
abstract, full text, DOI:10.1021/ic4006168

Kononova, Olga; Litvinov, Rustem I.; Zhmurov, Artem; Alekseenko, Andrey; Cheng, Chia Ho; Agarwal, Silvi; Marx, Kenneth A.; Weisel, John W.; Barsegov, Valeri
Molecular Mechanisms, Thermodynamics, and Dissociation Kinetics of Knob-Hole Interactions in Fibrin
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:22681-22692, AUG 2 2013
abstract, full text, DOI:10.1074/jbc.M113.472365

Minassian, Natali A.; Gibbs, Alan; Shih, Amy Y.; Liu, Yi; Neff, Robert A.; Sutton, Steven W.; Mirzadegan, Tara; Connor, Judith; Fellows, Ross; Husovsky, Matthew; Nelson, Serena; Hunter, Michael J.; Flinspach, Mack; Wickenden, Alan D.
Analysis of the Structural and Molecular Basis of Voltage-sensitive Sodium Channel Inhibition by the Spider Toxin Huwentoxin-IV (mu-TRTX-Hh2a)
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:22707-22720, AUG 2 2013
abstract, full text, DOI:10.1074/jbc.M113.461392

Zhang, Yuebin; Liu, Li; Wu, Lei; Li, Shuai; Li, Fei; Li, Zhengqiang
Theoretical investigation on the diatomic ligand migration process and ligand binding properties in non-O-2-binding H-NOX domain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1363-1376, AUG 2013
abstract, full text, DOI:10.1002/prot.24279

Pang, Xueqin; Yang, Mingjun; Han, Keli
Antagonist binding and induced conformational dynamics of GPCR A(2A) adenosine receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1399-1410, AUG 2013
abstract, full text, DOI:10.1002/prot.24283

Sun, Tian-Yang; Wang, Qi; Zhang, Jin; Wu, Tao; Zhang, Fan
Trastuzumab-Peptide Interactions: Mechanism and Application in Structure-Based Ligand Design
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 14:16836-16850, AUG 2013
abstract, full text, DOI:10.3390/ijms140816836

Sawada, Daisuke; Nishiyama, Yoshiharu; Petridis, Loukas; Parthasarathi, R.; Gnanakaran, S.; Forsyth, V. Trevor; Wada, Masahisa; Langan, Paul
Structure and dynamics of a complex of cellulose with EDA: insights into the action of amines on cellulose
CELLULOSE, 20:1563-1571, AUG 2013
abstract, full text, DOI:10.1007/s10570-013-9974-7

Lima, Leonardo H. F.; Serpa, Viviane I.; Rosseto, Flavio R.; Sartori, Geraldo Rodrigues; de Oliveira Neto, Mario; Martinez, Leandro; Polikarpov, Igor
Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum
CELLULOSE, 20:1573-1585, AUG 2013
abstract, full text, DOI:10.1007/s10570-013-9933-3

Ge Zhen-Peng; Shi Yan-Chao; Li Xiao-Yi
Effects of Orthogonal Electric Field on Water Flux through a Carbon Nanotube
ACTA PHYSICO-CHIMICA SINICA, 29:1655-1660, AUG 2013
abstract, full text, DOI:10.3866/PKU.WHXB201305222

Pang, ChunLi; Cao, TianGuang; Li, JunWei; Jia, MengWen; Zhang, SuHua; Ren, ShuXi; An, HaiLong; Zhan, Yong
Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 27:697-705, AUG 2013
abstract, full text, DOI:10.1007/s10822-013-9668-0

Dimitrov, Mitko; Alattia, Jean-Rene; Lemmin, Thomas; Lehal, Rajwinder; Fligier, Andrzej; Houacine, Jemila; Hussain, Ishrut; Radtke, Freddy; Dal Peraro, Matteo; Beher, Dirk; Fraering, Patrick C.
Alzheimer's disease mutations in APP but not gamma-secretase modulators affect epsilon-cleavage-dependent AICD production
NATURE COMMUNICATIONS, 4 Art. No. 2246, AUG 2013
abstract, full text, DOI:10.1038/ncomms3246

Belkin, Maxim; Maffeo, Christopher; Wells, David B.; Aksimentiev, Aleksei
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
ACS NANO, 7:6816-6824, AUG 2013
abstract, full text, DOI:10.1021/nn403575n

Park, Jiho; Czapla, Luke; Amaro, Rommie E.
Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2047-2056, AUG 2013
abstract, full text, DOI:10.1021/ci400225w

Zhang, Qian; Wang, Junmei; Guerrero, Gines D.; Cecilia, Jose M.; Garcia, Jose M.; Li, Youyong; Perez-Sanchez, Horacio; Hou, Tingjun
Accelerated Conformational Entropy Calculations Using Graphic Processing Units
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2057-2064, AUG 2013
abstract, full text, DOI:10.1021/ci400263t

Cheng, Xi; Jo, Sunhwan; Lee, Hui Sun; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2171-2180, AUG 2013
abstract, full text, DOI:10.1021/ci4002684

Yesylevskyy, Semen O.; Kraszewski, Sebastian; Picaud, Fabien; Ramseyer, Christophe
Efficiency of the monofunctionalized C-60 fullerenes as membrane targeting agents studied by all-atom molecular dynamics simulations
MOLECULAR MEMBRANE BIOLOGY, 30:338-345, AUG-SEP 2013
abstract, full text, DOI:10.3109/09687688.2013.828856

Spiga, Enrico; Alemani, Davide; Degiacomi, Matteo T.; Cascella, Michele; Dal Peraro, Matteo
Electrostatic-Consistent Coarse-Grained Potentials for Molecular Simulations of Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3515-3526, AUG 2013
abstract, full text, DOI:10.1021/ct400137q

Huang, Lei; Roux, Benoit
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3543-3556, AUG 2013
abstract, full text, DOI:10.1021/ct4003477

Gumbart, James C.; Roux, Benoit; Chipot, Christophe
Efficient Determination of Protein-Protein Standard Binding Free Energies from First Principles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:3789-3798, AUG 2013
abstract, full text, DOI:10.1021/ct400273t

Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo
All-atom simulations of crowding effects on ubiquitin dynamics
PHYSICAL BIOLOGY, 10 Art. No. 045006, AUG 2013
abstract, full text, DOI:10.1088/1478-3975/10/4/045006

Yu, Tao; Schatz, George C.
Free Energy Profile and Mechanism of Self-Assembly of Peptide Amphiphiles Based on a Collective Assembly Coordinate
JOURNAL OF PHYSICAL CHEMISTRY B, 117:9004-9013, AUG 1 2013
abstract, full text, DOI:10.1021/jp404835q

Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo
Molecular dynamics simulation of aggregation in dimethyl sulfoxide-water binary mixture
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1017:126-135, AUG 1 2013
abstract, full text, DOI:10.1016/j.comptc.2013.05.018

Cota, Junio; Oliveira, Leandro C.; Damasio, Andre R. L.; Citadini, Ana P.; Hoffmam, Zaira B.; Alvarez, Thabata M.; Codima, Carla A.; Leite, Vitor B. P.; Pastore, Glaucia; de Oliveira-Neto, Mario; Murakami, Mario T.; Ruller, Roberto; Squina, Fabio M.
Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:1492-1500, AUG 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.02.030

Mishra, Avinash; Rao, Satyanarayan; Mittal, Aditya; Jayaram, B.
Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:1520-1531, AUG 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.04.023

Chen, Liao Y.
Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:1786-1793, AUG 2013
abstract, full text, DOI:10.1016/j.bbamem.2013.03.008

Mukherjee, Sanchita; Bhattacharyya, Dhananjay
Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:896-912, AUG 1 2013
abstract, full text, DOI:10.1080/07391102.2012.713780

Ghemtio, Leo; Muzet, Nicolas
Retrospective molecular docking study of WY-25105 ligand to beta-secretase and bias of the three-dimensional structure flexibility
JOURNAL OF MOLECULAR MODELING, 19:2971-2979, AUG 2013
abstract, full text, DOI:10.1007/s00894-013-1821-0

Dawar, Chhavi; Jain, Sunita; Kumar, Sudhir
Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.)
JOURNAL OF MOLECULAR MODELING, 19:3351-3367, AUG 2013
abstract, full text, DOI:10.1007/s00894-013-1851-7

Gonnet, Pedro
Pseudo-Verlet lists: a new, compact neighbour list representation
MOLECULAR SIMULATION, 39:721-727, AUG 1 2013
abstract, full text, DOI:10.1080/08927022.2012.762097

Lavecchia, A.; Di Giovanni, C.
Virtual Screening Strategies in Drug Discovery: A Critical Review
CURRENT MEDICINAL CHEMISTRY, 20:2839-2860, AUG 2013
abstract, full text

Friedman, Ran; Boye, Kjetil; Flatmark, Kjersti
Molecular modelling and simulations in cancer research
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER, 1836:1-14, AUG 2013
abstract, full text, DOI:10.1016/j.bbcan.2013.02.001

Chen, Bao-Dong; Yang, Chuan-Lu; Yang, Jun-Sheng; Wang, Mei-Shan; Ma, Xiao-Guang
Dynamic mechanism of HIV replication inhibitor peptide encapsulated into carbon nanotubes
CURRENT APPLIED PHYSICS, 13:1001-1007, AUG 2013
abstract, full text, DOI:10.1016/j.cap.2013.02.004

Kudryashev, Mikhail; Stenta, Marco; Schmelz, Stefan; Amstutz, Marlise; Wiesand, Ulrich; Castano-Diez, Daniel; Degiacomi, Matteo T.; Muennich, Stefan; Bleck, Christopher K. E.; Kowal, Julia; Diepold, Andreas; Heinz, Dirk W.; Dal Peraro, Matteo; Cornelis, Guy R.; Stahlberg, Henning
In situ structural analysis of the Yersinia enterocolitica injectisome
ELIFE, 2 Art. No. e00792, JUL 30 2013
abstract, full text, DOI:10.7554/eLife.00792

Madrona, Yarrow; Hollingsworth, Scott A.; Khan, Bushra; Poulos, Thomas L.
P450cin Active Site Water: Implications for Substrate Binding and Solvent Accessibility
BIOCHEMISTRY, 52:5039-5050, JUL 30 2013
abstract, full text, DOI:10.1021/bi4006946

Bai, Qifeng; Zhang, Yang; Ban, Yihe; Liu, Huanxiang; Yao, Xiaojun
Computational Study on the Different Ligands Induced Conformation Change of beta 2 Adrenergic Receptor-Gs Protein Complex
PLOS ONE, 8 Art. No. e68138, JUL 29 2013
abstract, full text, DOI:10.1371/journal.pone.0068138

Hobiger, Kirstin; Utesch, Tillmann; Mroginski, Maria Andrea; Seebohm, Guiscard; Friedrich, Thomas
The Linker Pivot in Ci-VSP: The Key to Unlock Catalysis
PLOS ONE, 8 Art. No. e70272, JUL 29 2013
abstract, full text, DOI:10.1371/journal.pone.0070272

Xu, Jun; Zhang, John Z. H.; Xiang, Yun
Molecular Dynamics Simulation and Computational Two-Dimensional Infrared Spectroscopic Study of Model Amyloid beta-Peptide Oligomers
JOURNAL OF PHYSICAL CHEMISTRY A, 117:6373-6379, JUL 25 2013
abstract, full text, DOI:10.1021/jp403748z

Abou Chaaya, Adib; Le Poitevin, Mathilde; Cabello-Aguilar, Simon; Balme, Sebastien; Bechelany, Mikhael; Kraszewski, Sebastian; Picaud, Fabien; cambedouzou, Julien; Balanzat, Emmanuel; Janot, Jean-Marc; Thami, Thierry; Miele, Philippe; Dejardin, Philippe
Enhanced Ionic Transport Mechanism by Gramicidin A Confined Inside Nanopores Tuned by Atomic Layer Deposition
JOURNAL OF PHYSICAL CHEMISTRY C, 117:15306-15315, JUL 25 2013
abstract, full text, DOI:10.1021/jp403330d

Escobar, Francisco Velazquez; Utesch, Tillmann; Narikawa, Rei; Ikeuchi, Masahiko; Mroginski, Maria Andrea; Gaertner, Wolfgang; Hildebrandt, Peter
Photoconversion Mechanism of the Second GAF Domain of Cyanobacteriochrome AnPixJ and the Cofactor Structure of Its Green-Absorbing State
BIOCHEMISTRY, 52:4871-4880, JUL 23 2013
abstract, full text, DOI:10.1021/bi400506a

Li, Yinfeng; Yuan, Hongyan; von dem Bussche, Annette; Creighton, Megan; Hurt, Robert H.; Kane, Agnes B.; Gao, Huajian
Graphene microsheets enter cells through spontaneous membrane penetration at edge asperities and corner sites
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:12295-12300, JUL 23 2013
abstract, full text, DOI:10.1073/pnas.1222276110

Gao, Jian; Chen, Jianhan
Effects of Flanking Loops on Membrane Insertion of Transmennbrane Helices: A Role for Peptide Conformational Equilibrium
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8330-8339, JUL 18 2013
abstract, full text, DOI:10.1021/jp402356c

Yu, Tao; Higashi, Masahiro; Cembran, Alessandro; Gao, Jiali; Truhlar, Donald G.
Concerted Hydrogen Atom and Electron Transfer Mechanism for Catalysis by Lysine-Specific Demethylase
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8422-8429, JUL 18 2013
abstract, full text, DOI:10.1021/jp404292t

Yoon, Donghwan; Jung, Hyun Tae; Kwon, Gyemin; Yoon, Yeoeun; Lee, Minsoo; Bae, Imhyuck; Joo, Beom Jun; Kim, Mansuk; Lee, Sun Ae; Lee, Jihye; Lee, Yeonhee; Cho, Eunseog; Shin, Kwanwoo; Sung, Bong June
Dynamics and Mechanism of Flame Retardants in Polymer Matrixes: Experiment and Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8571-8578, JUL 18 2013
abstract, full text, DOI:10.1021/jp400114x

Swett, Rebecca J.; Cisneros, G. Andres; Feig, Andrew L.
Disruption of Intrinsic Motions as a Mechanism for Enzyme Inhibition
BIOPHYSICAL JOURNAL, 105:494-501, JUL 16 2013
abstract, full text, DOI:10.1016/j.bpj.2013.05.031

Roscioni, Otello Maria; Muccioli, Luca; Della Valle, Raffaele Guido; Pizzirusso, Antonio; Ricci, Matteo; Zannoni, Claudio
Predicting the Anchoring of Liquid Crystals at a Solid Surface: 5-Cyanobiphenyl on Cristobalite and Glassy Silica Surfaces of Increasing Roughness
LANGMUIR, 29:8950-8958, JUL 16 2013
abstract, full text, DOI:10.1021/la400857s

Hilder, Tamsyn A.; Chung, Shin-Ho
Designing a C-84 fullerene as a specific voltage-gated sodium channel blocker
NANOSCALE RESEARCH LETTERS, 8 Art. No. 323, JUL 16 2013
abstract, full text, DOI:10.1186/1556-276X-8-323

Pang, Xueqin; Han, Keli; Cui, Qiang
A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:1620-1635, JUL 15 2013
abstract, full text, DOI:10.1002/jcc.23305

Nandy, Bidisha; Bindu, D. Hima; Dixit, Narendra M.; Maiti, Prabal K.
Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 024905, JUL 14 2013
abstract, full text, DOI:10.1063/1.4812801

Bullard, Zachary; Meunier, Vincent
Dynamical properties of carbon nanotube welding into X junctions
PHYSICAL REVIEW B, 88 Art. No. 035422, JUL 12 2013
abstract, full text, DOI:10.1103/PhysRevB.88.035422

Hoshino, Tyuji; Mahmood, Md. Iqbal; Mori, Kenichi; Matsuzaki, Katsumi
Binding and Aggregation Mechanism of Amyloid beta-Peptides onto the GM1 Ganglioside-Containing Lipid Membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8085-8094, JUL 11 2013
abstract, full text, DOI:10.1021/jp4029062

Lee, Wook; Engels, Bernd
Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8095-8104, JUL 11 2013
abstract, full text, DOI:10.1021/jp403067m

Huggins, David J.; Payne, Mike C.
Assessing the Accuracy of Inhomogeneous Fluid Solvation Theory in Predicting Hydration Free Energies of Simple Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8232-8244, JUL 11 2013
abstract, full text, DOI:10.1021/jp4042233

Pal, Somedatta; Bandyopadhyay, Sanjoy
Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water
CHEMICAL PHYSICS, 420:35-43, JUL 11 2013
abstract, full text, DOI:10.1016/j.chemphys.2013.04.019

Turpin, Eleanor R.; Fang, Huey-Jen; Thomas, Neil R.; Hirst, Jonathan D.
Cooperativity and Site Selectivity in the Ileal Lipid Binding Protein
BIOCHEMISTRY, 52:4723-4733, JUL 9 2013
abstract, full text, DOI:10.1021/bi400192w

Xiao, Shifeng; Patsalo, Vadim; Shan, Bing; Bi, Yuan; Green, David F.; Raleigh, Daniel P.
Rational modification of protein stability by targeting surface sites leads to complicated results
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:11337-11342, JUL 9 2013
abstract, full text, DOI:10.1073/pnas.1222245110

Doki, Shintaro; Kato, Hideaki E.; Solcan, Nicolae; Iwaki, Masayo; Koyama, Michio; Hattori, Motoyuki; Iwase, Norihiko; Tsukazaki, Tomoya; Sugita, Yuji; Kandori, Hideki; Newstead, Simon; Ishitani, Ryuichiro; Nureki, Osamu
Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:11343-11348, JUL 9 2013
abstract, full text, DOI:10.1073/pnas.1301079110

Steele, Ryan P.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 011102, JUL 7 2013
abstract, full text, DOI:10.1063/1.4812568

Garzon, Diana; Anselmi, Claudio; Bond, Peter J.; Faraldo-Gomez, Jose D.
Dynamics of the Antigen-binding Grooves in CD1 Proteins REVERSIBLE HYDROPHOBIC COLLAPSE IN THE LIPID-FREE STATE
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:19528-19536, JUL 5 2013
abstract, full text, DOI:10.1074/jbc.M113.470179

Song, Hyun Deok; Zhu, Fangqiang
Conformational Dynamics of a Ligand-Free Adenylate Kinase
PLOS ONE, 8 Art. No. e68023, JUL 5 2013
abstract, full text, DOI:10.1371/journal.pone.0068023

Shim, Jihyun; Coop, Andrew; MacKerell, Alexander D., Jr.
Molecular Details of the Activation of the mu Opioid Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 117:7907-7917, JUL 4 2013
abstract, full text, DOI:10.1021/jp404238n

Jahangiri, Soran; Mercer, Sean M.; Jessop, Philip G.; Peslherbe, Gilles H.
Computational Investigation of the Hydration of Alkyl Diammonium Chlorides and Their Effect on THF/Water Phase Separation
JOURNAL OF PHYSICAL CHEMISTRY B, 117:8010-8017, JUL 4 2013
abstract, full text, DOI:10.1021/jp403984q

Ndlovu, Hlengisizwe; Ashcroft, Alison E.; Radford, Sheena E.; Harris, Sarah A.
Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects
BEILSTEIN JOURNAL OF NANOTECHNOLOGY, 4:429-440, JUL 4 2013
abstract, full text, DOI:10.3762/bjnano.4.50

Himstedt, Heath H.; Du, Hongbo; Marshall, Kathryn M.; Wickramasinghe, S. Ranil; Qian, Xianghong
pH Responsive Nanofiltration Membranes for Sugar Separations
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 52:9259-9269, JUL 3 2013
abstract, full text, DOI:10.1021/ie400982p

Baez, Mauricio; Cabrera, Ricardo; Pereira, Humberto M.; Blanco, Alejandro; Villalobos, Pablo; Ramirez-Sarmiento, Cesar A.; Caniuguir, Andres; Guixe, Victoria; Garratt, Richard C.; Babul, Jorge
A Ribokinase Family Conserved Monovalent Cation Binding Site Enhances the MgATP-induced Inhibition in E. coli Phosphofructokinase-2
BIOPHYSICAL JOURNAL, 105:185-193, JUL 2 2013
abstract, full text, DOI:10.1016/j.bpj.2013.05.028

Leonard, Sarah R.; Cormier, Ashley R.; Pang, Xiaodong; Zimmerman, Maxwell I.; Zhou, Huan-Xiang; Paravastu, Anant K.
Solid-State NMR Evidence for beta-Hairpin Structure within MAX8 Designer Peptide Nanofibers
BIOPHYSICAL JOURNAL, 105:222-230, JUL 2 2013
abstract, full text, DOI:10.1016/j.bpj.2013.05.047

Biswas, Mithun; Langowski, Joerg; Bishop, Thomas C.
Atomistic simulations of nucleosomes
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 3:378-392, JUL 2013
abstract, full text, DOI:10.1002/wcms.1139

Rosenhouse-Dantsker, Avia; Noskov, Sergei; Logothetis, Diomedes E.; Levitan, Irena
Cholesterol sensitivity of KIR2.1 depends on functional inter-links between the N and C termini
CHANNELS, 7:303-312, JUL 1 2013
abstract, full text, DOI:10.4161/chan.25437

Tsai, Min-Yeh; Yuan, Jian-Min; Yamaki, Masahiro; Lin, Chih-Kai; Lin, Sheng Hsien
Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta-Hairpin Peptide
JOURNAL OF THE CHINESE CHEMICAL SOCIETY, 60:915-928, JUL 2013
abstract, full text, DOI:10.1002/jccs.201300173

Banerjee, Avik; Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Nandi, Tapas K.; Mishra, Deepak K.
Conserved water mediated H-bonding dynamics of Ser117 and Thr119 residues in human transthyretin-thyroxin complexation: Inhibitor modeling study through docking and molecular dynamics simulation
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 44:70-80, JUL 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.04.010

Malac, Kamil; Barvik, Ivan
Complex between Human RNase HI and the phosphonate-DNA/RNA duplex: Molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 44:81-90, JUL 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.05.004

Puiatti, Marcelo; Luis Borioni, Jose; Guadalupe Vallejo, Mariana; Luis Cabrera, Jose; Mariel Agnese, Alicia; Gabriela Ortega, Maria; Beatriz Pierini, Adriana
Study of the interaction of Huperzia saururus Lycopodium alkaloids with the acetylcholinesterase enzyme
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 44:136-144, JUL 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.05.009

Zhuang, Shulin; Bao, Lingling; Linhananta, Apichart; Liu, Weiping
Molecular modeling revealed that ligand dissociation from thyroid hormone receptors is affected by receptor heterodimerization
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 44:155-160, JUL 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.06.001

Ebejer, Jean-Paul; Fulle, Simone; Morris, Garrett M.; Finn, Paul W.
The emerging role of cloud computing in molecular modelling
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 44:177-187, JUL 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.06.002

Sun, Wei; Zhu, Ye Julia; Wang, Zhizhi; Zhong, Qiang; Gao, Feng; Lou, Jizhong; Gong, Weimin; Xu, Wenqing
Crystal structure of the yeast TSC1 core domain and implications for tuberous sclerosis pathological mutations
NATURE COMMUNICATIONS, 4 Art. No. 2135, JUL 2013
abstract, full text, DOI:10.1038/ncomms3135

Hospital, Adam; Faustino, Ignacio; Collepardo-Guevara, Rosana; Gonzalez, Carlos; Lluis Gelpi, Josep; Orozco, Modesto
NAFlex: a web server for the study of nucleic acid flexibility
NUCLEIC ACIDS RESEARCH, 41:W47-W55, JUL 2013
abstract, full text, DOI:10.1093/nar/gkt378

Santiso, Erik E.; Musolino, Nicholas; Trout, Bernhardt L.
Design of Linear Ligands for Selective Separation Using a Genetic Algorithm Applied to Molecular Architecture
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:1638-1660, JUL 2013
abstract, full text, DOI:10.1021/ci400043q

Bucher, Denis; Hsu, Yuan-Hao; Mouchlis, Varnavas D.; Dennis, Edward A.; McCammon, J. Andrew
Insertion of the Ca2+-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003156, JUL 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003156

Miao, Yinglong; Hong, Liang; Yi, Zheng; Smith, Jeremy C.
Zaccai neutron resilience and site-specific hydration dynamics in a globular protein
EUROPEAN PHYSICAL JOURNAL E, 36 Art. No. 72, JUL 2013
abstract, full text, DOI:10.1140/epje/i2013-13072-5

Hancock, Stephen P.; Ghane, Tahereh; Cascio, Duilio; Rohs, Remo; Di Felice, Rosa; Johnson, Reid C.
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group
NUCLEIC ACIDS RESEARCH, 41:6750-6760, JUL 2013
abstract, full text, DOI:10.1093/nar/gkt357

McGibbon, Robert T.; Pande, Vijay S.
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:2900-2906, JUL 2013
abstract, full text, DOI:10.1021/ct400132h

Li, Song; Zhao, Xiongce; Mo, Yiming; Cummings, Peter T.; Heller, William T.
Human serum albumin interactions with C-60 fullerene studied by spectroscopy, small-angle neutron scattering, and molecular dynamics simulations
JOURNAL OF NANOPARTICLE RESEARCH, 15 Art. No. UNSP 1769, JUL 2013
abstract, full text, DOI:10.1007/s11051-013-1769-0

Slootweg, Erik J.; Spiridon, Laurentiu N.; Roosien, Jan; Butterbach, Patrick; Pomp, Rikus; Westerhof, Lotte; Wilbers, Ruud; Bakker, Erin; Bakker, Jaap; Petrescu, Andrei-Jose; Smant, Geert; Goverse, Aska
Structural Determinants at the Interface of the ARC2 and Leucine-Rich Repeat Domains Control the Activation of the Plant Immune Receptors Rx1 and Gpa2
PLANT PHYSIOLOGY, 162:1510-1528, JUL 2013
abstract, full text, DOI:10.1104/pp.113.218842

Bello, Martiniano; Martinez-Archundia, Marlet; Correa-Basurto, Jose
Automated docking for novel drug discovery
EXPERT OPINION ON DRUG DISCOVERY, 8:821-834, JUL 2013
abstract, full text, DOI:10.1517/17460441.2013.794780

Kitova, Elena N.; Sinelnikov, Igor; Deng, Lu; Klassen, John S.
Thermal dissociation of streptavidin homotetramer in the gas phase: Subunit loss versus backbone fragmentation
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 345:97-103, JUL 1 2013
abstract, full text, DOI:10.1016/j.ijms.2012.08.025

Kostyuchenko, Victor A.; Zhang, Qian; Tan, Joanne L.; Ng, Thiam-Seng; Lok, Shee-Mei
Immature and Mature Dengue Serotype 1 Virus Structures Provide Insight into the Maturation Process
JOURNAL OF VIROLOGY, 87:7700-7707, JUL 2013
abstract, full text, DOI:10.1128/JVI.00197-13

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.
An insight to the dynamics of conserved water-mediated salt bridge interaction and interdomain recognition in hIMPDH isoforms
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:788-808, JUL 1 2013
abstract, full text, DOI:10.1080/07391102.2012.712458

Jordheim, Lars Petter; Barakat, Khaled H.; Heinrich-Balard, Laurence; Matera, Eva-Laure; Cros-Perrial, Emeline; Bouledrak, Karima; El Sabeh, Rana; Perez-Pineiro, Rolando; Wishart, David S.; Cohen, Richard; Tuszynski, Jack; Dumontet, Charles
Small Molecule Inhibitors of ERCC1-XPF Protein-Protein Interaction Synergize Alkylating Agents in Cancer Cells
MOLECULAR PHARMACOLOGY, 84:12-24, JUL 2013
abstract, full text, DOI:10.1124/mol.112.082347

Perilla, Juan R.; Leahy, Daniel J.; Woolf, Thomas B.
Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1113-1126, JUL 2013
abstract, full text, DOI:10.1002/prot.24257

Yan, Shixu E.; Lemmin, Thomas; Salvi, Suzanne; Lausch, Ekkehart; Superti-Furga, Andrea; Rokicki, Dariusz; Dal Peraro, Matteo; van der Goot, F. Gisou
In-Depth Analysis of Hyaline Fibromatosis Syndrome Frameshift Mutations at the Same Site Reveal the Necessity of Personalized Therapy
HUMAN MUTATION, 34:1005-1017, JUL 2013
abstract, full text, DOI:10.1002/humu.22324

Tapia, G.; Morales-Quintana, L.; Parra, C.; Berbel, A.; Alcorta, M.
Study of nsLTPs in Lotus japonicus genome reveal a specific epidermal cell member (LjLTP10) regulated by drought stress in aerial organs with a putative role in cutin formation
PLANT MOLECULAR BIOLOGY, 82:485-501, JUL 2013
abstract, full text, DOI:10.1007/s11103-013-0080-x

Ebro, Hannah; Kim, Young Mi; Kim, Joon Ha
Molecular dynamics simulations in membrane-based water treatment processes: A systematic overview
JOURNAL OF MEMBRANE SCIENCE, 438:112-125, JUL 1 2013
abstract, full text, DOI:10.1016/j.memsci.2013.03.027

Chintha, R.; Kaipa, P. R.; Sekhar, N.; Hasan, Q.
Mitochondria and tumors: A new perspective
INDIAN JOURNAL OF CANCER, 50:206-213, JUL-SEP 2013
abstract, full text, DOI:10.4103/0019-509X.118732

Zhao, Chao; Zhao, Jun; Li, Xiaosi; Wu, Jiang; Chen, Shenfu; Chen, Qiang; Wang, Qiuming; Gong, Xiong; Li, Lingyan; Zheng, Jie
Probing structure-antifouling activity relationships of polyacrylamides and polyacrylates
BIOMATERIALS, 34:4714-4724, JUL 2013
abstract, full text, DOI:10.1016/j.biomaterials.2013.03.028

Stoilova-McPhie, Svetla; Lynch, Gillian C.; Ludtke, Steven; Pettitt, B. Montgomery
Domain organization of membrane-bound factor VIII
BIOPOLYMERS, 99:448-459, JUL 2013
abstract, full text, DOI:10.1002/bip.22199

GhattyVenkataKrishna, Pavan K.; Chavali, Neelima; Uberbacher, Edward C.
Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase
CHEMICAL PAPERS, 67:677-681, JUL 2013
abstract, full text, DOI:10.2478/s11696-013-0354-4

He, Yi; Prieto, Lidia; Lazaridis, Themis
Modeling peptide binding to anionic membrane pores
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:1463-1475, JUN 30 2013
abstract, full text, DOI:10.1002/jcc.23282

Williamson, Danielle M.; Elferich, Johannes; Ramakrishnan, Parvathy; Thomas, Gary; Shinde, Ujwal
The Mechanism by Which a Propeptide-encoded pH Sensor Regulates Spatiotemporal Activation of Furin
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:19154-19165, JUN 28 2013
abstract, full text, DOI:10.1074/jbc.M112.442681

Mahadevan, T.; Kojic, M.; Ferrari, M.; Ziemys, A.
Mechanisms of reduced solute diffusivity at nanoconfined solid-liquid interface
CHEMICAL PHYSICS, 421:15-21, JUN 27 2013
abstract, full text, DOI:10.1016/j.chemphys.2013.05.010

D'Avino, Gabriele; Mothy, Sebastien; Muccioli, Luca; Zannoni, Claudio; Wang, Linjun; Cornil, Jerome; Beljonne, David; Castet, Frederic
Energetics of Electron-Hole Separation at P3HT/PCBM Heterojunctions
JOURNAL OF PHYSICAL CHEMISTRY C, 117:12981-12990, JUN 27 2013
abstract, full text, DOI:10.1021/jp402957g

Zhu, Shengshuang; Brown, Michael F.; Feller, Scott E.
Retinal Conformation Governs pK(a) of Protonated Schiff Base in Rhodopsin Activation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:9391-9398, JUN 26 2013
abstract, full text, DOI:10.1021/ja4002986

Grafmueller, Andrea; Noya, Eva G.; Voth, Gregory A.
Nucleotide-Dependent Lateral and Longitudinal Interactions in Microtubules
JOURNAL OF MOLECULAR BIOLOGY, 425:2232-2246, JUN 26 2013
abstract, full text, DOI:10.1016/j.jmb.2013.03.029

Johnson, James M.; Sanford, Brianne L.; Strom, Alexander M.; Tadayon, Stephanie N.; Lehman, Brent P.; Zirbes, Arrianna M.; Bhattacharyya, Sudeep; Musier-Forsyth, Karin; Hati, Sanchita
Multiple Pathways Promote Dynamical Coupling between Catalytic Domains in Escherichia coli Prolyl-tRNA Synthetase
BIOCHEMISTRY, 52:4399-4412, JUN 25 2013
abstract, full text, DOI:10.1021/bi400079h

Figueroa, Carlos M.; Kuhn, Misty L.; Falaschetti, Christine A.; Solamen, Ligin; Olsen, Kenneth W.; Ballicora, Miguel A.; Iglesias, Alberto A.
Unraveling the Activation Mechanism of the Potato Tuber ADP-Glucose Pyrophosphorylase
PLOS ONE, 8 Art. No. e66824, JUN 24 2013
abstract, full text, DOI:10.1371/journal.pone.0066824

Zhang, Qi-Lin; Jiang, Wei-Zhou; Liu, Jian; Miao, Ren-De; Sheng, Nan
Water Transport through Carbon Nanotubes with the Radial Breathing Mode
PHYSICAL REVIEW LETTERS, 110 Art. No. 254501, JUN 21 2013
abstract, full text, DOI:10.1103/PhysRevLett.110.254501

Tritzant-Martinez, Yalina; Zeng, Tao; Broom, Aron; Meiering, Elizabeth; Le Roy, Robert J.; Roy, Pierre-Nicholas
On the analytical representation of free energy profiles with a Morse/long-range model: Application to the water dimer
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 234103, JUN 21 2013
abstract, full text, DOI:10.1063/1.4810006

Mori, Yoshiharu; Okumura, Hisashi
Pressure-Induced Helical Structure of a Peptide Studied by Simulated Tempering Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:2079-2083, JUN 20 2013
abstract, full text, DOI:10.1021/jz400769w

Martinez, Anna Victoria; Dominguez, Laura; Malolepsza, Edyta; Moser, Adam; Ziegler, Zack; Straub, John E.
Probing the Structure and Dynamics of Confined Water in AOT Reverse Micelles
JOURNAL OF PHYSICAL CHEMISTRY B, 117:7345-7351, JUN 20 2013
abstract, full text, DOI:10.1021/jp402270e

O'Mahony, S.; O'Dwyer, C.; Nijhuis, C. A.; Greer, J. C.; Quinn, A. J.; Thompson, D.
Nanoscale Dynamics and Protein Adhesivity of Alkylamine Self-Assembled Mono layers on Graphene
LANGMUIR, 29:7271-7282, JUN 18 2013
abstract, full text, DOI:10.1021/la304545n

Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning
Structural Dynamics of the MecA-ClpC Complex A TYPE II AAA(+) PROTEIN UNFOLDING MACHINE
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:17597-17608, JUN 14 2013
abstract, full text, DOI:10.1074/jbc.M113.458752

Koldso, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiott, Birgit
Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations
PLOS ONE, 8 Art. No. e63635, JUN 12 2013
abstract, full text, DOI:10.1371/journal.pone.0063635

Baylon, Javier L.; Lenov, Ivan L.; Sligar, Stephen G.; Tajkhorshid, Emad
Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:8542-8551, JUN 12 2013
abstract, full text, DOI:10.1021/ja4003525

Paulus, Geraldine L. C.; Wang, Qing Hua; Ulissi, Zachary W.; McNicholas, Thomas P.; Vijayaraghavan, Aravind; Shih, Chih-Jen; Jin, Zhong; Strano, Michael S.
Charge Transfer at Junctions of a Single Layer of Graphene and a Metallic Single Walled Carbon Nanotube
SMALL, 9:1954-1963, JUN 10 2013
abstract, full text, DOI:10.1002/smll.201201034

Salewski, Johannes; Escobar, Francisco Velazquez; Kaminski, Steve; von Stetten, David; Keidel, Anke; Rippers, Yvonne; Michael, Norbert; Scheerer, Patrick; Piwowarski, Patrick; Bartl, Franz; Frankenberg-Dinkel, Nicole; Ringsdorf, Simone; Gaertner, Wolfgang; Lamparter, Tilman; Mroginski, Maria Andrea; Hildebrandt, Peter
Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:16800-16814, JUN 7 2013
abstract, full text, DOI:10.1074/jbc.M113.457531

Salama-Alber, Orly; Jobby, Maroor K.; Chitayat, Seth; Smith, Steven P.; White, Bryan A.; Shimon, Linda J. W.; Lamed, Raphael; Frolow, Felix; Bayer, Edward A.
Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components BINDING FIDELITY, PROMISCUITY, AND STRUCTURAL BUTTRESSES
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:16827-16838, JUN 7 2013
abstract, full text, DOI:10.1074/jbc.M113.466672

Calero, C.; Gordillo, M. C.; Marti, J.
Size effects on water adsorbed on hydrophobic probes at the nanometric scale
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 214702, JUN 7 2013
abstract, full text, DOI:10.1063/1.4807092

Eskici, Gozde; Gur, Mert
Computational Design of New Peptide Inhibitors for Amyloid Beta (A beta) Aggregation in Alzheimer's Disease: Application of a Novel Methodology
PLOS ONE, 8 Art. No. e66178, JUN 6 2013
abstract, full text, DOI:10.1371/journal.pone.0066178

Vergara-Jaque, Ariela; Comer, Jeffrey; Monsalve, Luis; Gonzalez-Nilo, Fernando D.; Sandoval, Claudia
Computationally Efficient Methodology for Atomic-Level Characterization of Dendrimer-Drug Complexes: A Comparison of Amine- and Acetyl-Terminated PAMAM
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6801-6813, JUN 6 2013
abstract, full text, DOI:10.1021/jp4000363

Ortiz, Aurelie U.; Boutin, Anne; Fuchs, Alain H.; Coudert, Francois-Xavier
Investigating the Pressure-Induced Amorphization of Zeolitic Imidazolate Framework ZIF-8: Mechanical Instability Due to Shear Mode Softening
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:1861-1865, JUN 6 2013
abstract, full text, DOI:10.1021/jz400880p

Moradi, Mahmoud; Tajkhorshid, Emad
Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:1882-1887, JUN 6 2013
abstract, full text, DOI:10.1021/jz400816x

He, Jia; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Cyclodextrin-Mediated Recruitment and Delivery of Amphotericin B
JOURNAL OF PHYSICAL CHEMISTRY C, 117:11750-11756, JUN 6 2013
abstract, full text, DOI:10.1021/jp3128324

Banavali, Nilesh K.
Partial Base Flipping Is Sufficient for Strand Slippage near DNA Duplex Termini
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:8274-8282, JUN 5 2013
abstract, full text, DOI:10.1021/ja401573j

Pallesen, Jesper; Hashem, Yaser; Korkmaz, Gurkan; Koripella, Ravi Kiran; Huang, Chenhui; Ehrenberg, Mans; Sanyal, Suparna; Frank, Joachim
Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1
ELIFE, 2 Art. No. e00411, JUN 4 2013
abstract, full text, DOI:10.7554/eLife.00411

Xia, Mengdie; Liu, Huihui; Li, Yang; Yan, Nieng; Gong, Haipeng
The Mechanism of Na+/K+ Selectivity in Mammalian Voltage-Gated Sodium Channels Based on Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 104:2401-2409, JUN 4 2013
abstract, full text, DOI:10.1016/j.bpj.2013.04.035

Herzog, Florian A.; Vogel, Viola
Multiple Steps to Activate FAK's Kinase Domain: Adaptation to Confined Environments?
BIOPHYSICAL JOURNAL, 104:2521-2529, JUN 4 2013
abstract, full text, DOI:10.1016/j.bpj.2013.04.021

Ferrer-Tasies, Lidia; Moreno-Calvo, Evelyn; Cano-Sarabia, Mary; Aguilella-Arzo, Marcel; Angelova, Angelina; Lesieur, Sylviane; Ricart, Susagna; Faraudo, Jordi; Ventosa, Nora; Veciana, Jaume
Quatsomes: Vesicles Formed by Self-Assembly of Sterols and Quaternary Ammonium Surfactants
LANGMUIR, 29:6519-6528, JUN 4 2013
abstract, full text, DOI:10.1021/la4003803

Muecksch, Christian; Urbassek, Herbert M.
Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics
PLOS ONE, 8 Art. No. e64883, JUN 3 2013
abstract, full text, DOI:10.1371/journal.pone.0064883

Liang, Li-Jun; Wu, Tao; Kang, Yu; Wang, Qi
Dispersion of Graphene Sheets in Aqueous Solution by Oligodeoxynucleotides
CHEMPHYSCHEM, 14:1626-1632, JUN 3 2013
abstract, full text, DOI:10.1002/cphc.201201084

Lopez-Perez, Marcos; Mirete, Salvador; Jardon-Valadez, Eduardo; Gonzalez-Pastor, Jose E.
Identification and modeling of a novel cloramphenicol resistance protein detected by functional metagenomics in a wetland of Lerma, Mexico
INTERNATIONAL MICROBIOLOGY, 16:103-111, JUN 2013
abstract, full text, DOI:10.2436/20.1501.01.xx

Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey
Dynamics simulations for engineering macromolecular interactions
CHAOS, 23 Art. No. 025110, JUN 2013
abstract, full text, DOI:10.1063/1.4810915

Jaeger, Vance W.; Pfaendtner, Jim
Structure, Dynamics, and Activity of Xylanase Solvated in Binary Mixtures of Ionic Liquid and Water
ACS CHEMICAL BIOLOGY, 8:1179-1186, JUN 2013
abstract, full text, DOI:10.1021/cb3006837

Wang, Qiuming; Yu, Xiang; Patal, Kunal; Hu, Rundong; Chuang, Steven; Zhang, Ge; Zheng, Jie
Tanshinones Inhibit Amyloid Aggregation by Amyloid-beta Peptide, Disaggregate Amyloid Fibrils, and Protect Cultured Cells
ACS CHEMICAL NEUROSCIENCE, 4:1004-1015, JUN 2013
abstract, full text, DOI:10.1021/cn400051e

Raju, S. G.; Barber, Annika F.; LeBard, David N.; Klein, Michael L.; Carnevale, Vincenzo
Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003090, JUN 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003090

Small, Meagan C.; Lopes, Pedro; Andrade, Rodrigo B.; MacKerell, Alexander D., Jr.
Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003113, JUN 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003113

Lakkaraju, Sirish Kaushik; Xue, Fengtian; Faden, Alan I.; MacKerell, Alexander D., Jr.
Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:1337-1349, JUN 2013
abstract, full text, DOI:10.1021/ci400160x

Franco, Duvan; Sgrignani, Jacopo; Bussi, Giovanni; Magistrato, Alessandra
Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:1371-1387, JUN 2013
abstract, full text, DOI:10.1021/ci4001647

Schulz, Sarah; Iglesias-Cans, Marina; Krah, Alexander; Yildiz, Oezkan; Leone, Vanessa; Matthies, Doreen; Cook, Gregory M.; Faraldo-Gomez, Jose D.; Meier, Thomas
A New Type of Na+-Driven ATP Synthase Membrane Rotor with a Two-Carboxylate Ion-Coupling Motif
PLOS BIOLOGY, 11 Art. No. e1001596, JUN 2013
abstract, full text, DOI:10.1371/journal.pbio.1001596

Liu Ming; Li Ping; Liu Bin; Su Ji-Guo; Wang Cun-Xin
Insights Into The Working Mechanism and Unfolding Property of Arthrobacter chlorophenolicus Amylosucrase
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 40:565-577, JUN 2013
abstract, full text, DOI:10.3724/SP.J.1206.2013.00044

Fei, Baojin; Xu, Hui; Zhang, Feiwei; Li, Xinran; Ma, Shuhan; Cao, Yu; Xie, Jie; Qiao, Dairong; Cao, Yi
Relationship between Escherichia coli AppA phytase's thermostability and salt bridges
JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 115:623-627, JUN 2013
abstract, full text, DOI:10.1016/j.jbiosc.2012.12.010

Erdem, Safiye Sag; Turkkan, Seyhan; Yelekci, Kemal; Gokhan-Kelekci, Nesrin
Insights into the binding mode of new N-substituted pyrazoline derivatives to MAO-A: docking and quantum chemical calculations
JOURNAL OF NEURAL TRANSMISSION, 120:859-862, JUN 2013
abstract, full text, DOI:10.1007/s00702-012-0950-4

Nam, Sangkil; Wen, Wei; Schroeder, Anne; Herrmann, Andreas; Yu, Hua; Cheng, Xinlai; Merz, Karl-Heinz; Eisenbrand, Gerhard; Li, Hongzhi; Yuan, Yate-Ching; Jove, Richard
Dual inhibition of Janus and Src family kinases by novel indirubin derivative blocks constitutively-activated Stat3 signaling associated with apoptosis of human pancreatic cancer cells
MOLECULAR ONCOLOGY, 7:369-378, JUN 2013
abstract, full text, DOI:10.1016/j.molonc.2012.10.013

Geyer, R. Ryan; Musa-Aziz, Raif; Enkavi, Giray; Mahinthichaichan, P.; Tajkhorshid, Emad; Boron, Walter F.
Movement of NH3 through the human urea transporter B: a new gas channel
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY, 304:F1447-F1457, JUN 2013
abstract, full text, DOI:10.1152/ajprenal.00609.2012

Bruno, Agostino; Amori, Laura; Costantino, Gabriele
Computational Insights into the Mechanism of Inhibition of OASS-A by a Small Molecule Inhibitor
MOLECULAR INFORMATICS, 32:447-457, JUN 2013
abstract, full text, DOI:10.1002/minf.201200174

Pietra, Francesco
From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics
CHEMISTRY & BIODIVERSITY, 10:963-975, JUN 2013
abstract, full text, DOI:10.1002/cbdv.201300060

Chen, Nanhao; Ge, Hu; Xu, Jun; Cao, Zexing; Wu, Ruibo
Loop motion and base release in purine-specific nucleoside hydrolase: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:1117-1124, JUN 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.02.005

Zhang, Kai; Wang, Li; Liu, Yanxin; Chan, Kwok-Yan; Pang, Xiaoyun; Schulten, Klaus; Dong, Zhiyang; Sun, Fei
Flexible interwoven termini determine the thermal stability of thermosomes
PROTEIN & CELL, 4:432-444, JUN 2013
abstract, full text, TCBG publications, DOI:10.1007/s13238-013-3026-9

Zheng, Fengxian; Pan, Jun; Yin, Xiaohui; Li, Jingyuan; Wang, Fei; Zhao, Lina
Simulation Study on Gold Nanoparticle-Cellular Membrane Complex in Endocytosis Process
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 13:3990-3998, JUN 2013
abstract, full text, DOI:10.1166/jnn.2013.7225

Kaszuba, Karol; Postila, Pekka A.; Cramariuc, Oana; Sarewicz, Marcin; Osyczka, Artur; Vattulainen, Ilpo; Rog, Tomasz
Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations
THEORETICAL CHEMISTRY ACCOUNTS, 132 Art. No. UNSP 1370, JUN 2013
abstract, full text, DOI:10.1007/s00214-013-1370-8

Ling, Zhenmin; Liu, Yi; Teng, Shaolei; Kang, Zhen; Zhang, Jingjing; Chen, Jian; Du, Guocheng
Rational Design of a Novel Propeptide for Improving Active Production of Streptomyces griseus Trypsin in Pichia pastoris
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79:3851-3855, JUN 2013
abstract, full text, DOI:10.1128/AEM.00376-13

Sajevic, Tamara; Leonardi, Adrijana; Kovacic, Lidija; Lang-Balija, Maja; Kurtovic, Tihana; Pungercar, Joze; Halassy, Beata; Trampus-Bakija, Alenka; Krizaj, Igor
VaH3, one of the principal hemorrhagins in Vipera ammodytes ammodytes venom, is a homodimeric P-IIIc metalloproteinase
BIOCHIMIE, 95:1158-1170, JUN 2013
abstract, full text, DOI:10.1016/j.biochi.2013.01.003

Liu, Ming; Hou, Tingjun; Feng, Zhiwei; Li, Youyong
The flexibility of P-glycoprotein for its poly-specific drug binding from molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:612-629, JUN 1 2013
abstract, full text, DOI:10.1080/07391102.2012.706079

Zander, Catherine B.; Albers, Thomas; Grewer, Christof
Voltage-dependent processes in the electroneutral amino acid exchanger ASCT2
JOURNAL OF GENERAL PHYSIOLOGY, 141:659-672, JUN 2013
abstract, full text, DOI:10.1085/jgp.201210948

Nichols, Sara E.; Hernandez, Carlos X.; Wang, Yi; McCammon, James Andrew
Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface
PROTEIN SCIENCE, 22:745-754, JUN 2013
abstract, full text, DOI:10.1002/pro.2258

Vashisth, Harish; Abrams, Cameron F.
All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1017-1030, JUN 2013
abstract, full text, DOI:10.1002/prot.24255

Laghaei, Rozita; Evans, Deborah G.; Coalson, Rob D.
Metal binding sites of human H-chain ferritin and iron transport mechanism to the ferroxidase sites: A molecular dynamics simulation study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:1042-1050, JUN 2013
abstract, full text, DOI:10.1002/prot.24251

Newhouse, E. Irene; Newhouse, James S.; Alam, Maqsudul
Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity
JOURNAL OF MOLECULAR MODELING, 19:2265-2271, JUN 2013
abstract, full text, DOI:10.1007/s00894-012-1739-y

Postila, Pekka A.; Kaszuba, Karol; Sarewicz, Marcin; Osyczka, Artur; Vattulainen, Ilpo; Rog, Tomasz
Key role of water in proton transfer at the Q(o)-site of the cytochrome bc(1) complex predicted by atomistic molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1827:761-768, JUN 2013
abstract, full text, DOI:10.1016/j.bbabio.2013.02.005

Poyry, Sanja; Cramariuc, Oana; Postila, Pekka A.; Kaszuba, Karol; Sarewicz, Marcin; Osyczka, Artur; Vattulainen, Ilpo; Rog, Tomasz
Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc(1) complex
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1827:769-778, JUN 2013
abstract, full text, DOI:10.1016/j.bbabio.2013.03.005

Jose, Jaya C.; Sengupta, Neelanjana
Molecular dynamics simulation studies of the structural response of an isolated A beta(1-42) monomer localized in the vicinity of the hydrophilic TiO2 surface
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:487-494, JUN 2013
abstract, full text, DOI:10.1007/s00249-013-0900-6

Liu, Zhongqiu; Liu, Yaolin; Guo, Yangjie; Wang, Hua
Progress in global parallel computing research: a bibliometric approach
SCIENTOMETRICS, 95:967-983, JUN 2013
abstract, full text, DOI:10.1007/s11192-012-0927-y

Sigstam, Therese; Gannon, Greg; Cascella, Michele; Pecson, Brian M.; Wigginton, Krista Rule; Kohn, Tamar
Subtle Differences in Virus Composition Affect Disinfection Kinetics and Mechanisms
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79:3455-3467, JUN 2013
abstract, full text, DOI:10.1128/AEM.00663-13

Munichandrababu, Tirumalasetty; Bhaskar, Baki Vijaya; Ravi, Sahukari; Bhuvaneswar, Cherukupalle; Rajendra, Wudayagiri
Structure based virtual screening of non-steroidal anti-inflammatory drugs (NSAIDs) against RNA-binding motif 6 (RBM6) involved in human lung cancer
MEDICINAL CHEMISTRY RESEARCH, 22:2828-2839, JUN 2013
abstract, full text, DOI:10.1007/s00044-012-0276-7

Martinez-Ramos, Federico; Fonseca-Sabater, Yadira; Soriano-Ursua, Marvin A.; Torres, Eduardo; Rosales-Hernandez, Martha C.; Trujillo-Ferrara, Jose G.; Tolentino-Lopez, Luis E.; Ian, Ilizaliturri-Flores; Correa-Basurto, Jose
o-Alkylselenenylated Benzoic Acid Accesses Several Sites in Serum Albumin According to Fluorescence Studies, Raman Spectroscopy and Theoretical Simulations
PROTEIN AND PEPTIDE LETTERS, 20:705-714, JUN 2013
abstract, full text

Polyakov, A. Yu.; Lyutyy, T. V.; Denisov, S.; Reva, V. V.; Haenggi, P.
Large-scale ferrofluid simulations on graphics processing units
COMPUTER PHYSICS COMMUNICATIONS, 184:1483-1489, JUN 2013
abstract, full text, DOI:10.1016/j.cpc.2013.01.016

Geng, Weihua; Jacob, Ferosh
A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
COMPUTER PHYSICS COMMUNICATIONS, 184:1490-1496, JUN 2013
abstract, full text, DOI:10.1016/j.cpc.2013.01.017

Zhao, Gongpu; Perilla, Juan R.; Yufenyuy, Ernest L.; Meng, Xin; Chen, Bo; Ning, Jiying; Ahn, Jinwoo; Gronenborn, Angela M.; Schulten, Klaus; Aiken, Christopher; Zhang, Peijun
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
NATURE, 497:643-646, MAY 30 2013
abstract, full text, TCBG publications, DOI:10.1038/nature12162

Palermo, Mattia Felice; Pizzirusso, Antonio; Muccioli, Luca; Zannoni, Claudio
An atomistic description of the nematic and smectic phases of 4-n-octyl-4 ' cyanobiphenyl (8CB)
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 204901, MAY 28 2013
abstract, full text, DOI:10.1063/1.4804270

Asthana, Shailendra; Shukla, Saumya; Vargiu, Attilio V.; Ceccarelli, Matteo; Ruggerone, Paolo; Paglietti, Giuseppe; Marongiu, Maria E.; Blois, Sylvain; Giliberti, Gabriele; La Colla, Paolo
Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole
BIOCHEMISTRY, 52:3752-3764, MAY 28 2013
abstract, full text, DOI:10.1021/bi400107h

Chen, Rong; Chung, Shin-Ho
Complex Structures between the N-Type Calcium Channel (Ca(V)2.2) and omega-Conotoxin GVIA Predicted via Molecular Dynamics
BIOCHEMISTRY, 52:3765-3772, MAY 28 2013
abstract, full text, DOI:10.1021/bi4003327

Tang, Ming; Nesbitt, Anna E.; Sperling, Lindsay J.; Berthold, Deborah A.; Schwieters, Charles D.; Gennis, Robert B.; Rienstra, Chad M.
Structure of the Disulfide Bond Generating Membrane Protein DsbB in the Lipid Bilayer
JOURNAL OF MOLECULAR BIOLOGY, 425:1670-1682, MAY 27 2013
abstract, full text, DOI:10.1016/j.jmb.2013.02.009

Huang, Yan-Dong; Shua, Jian-Wei
Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6138-6148, MAY 23 2013
abstract, full text, DOI:10.1021/jp4021933

Han, Yang; Raghunathan, Varun; Feng, Ran-ran; Maekawa, Hiroaki; Chung, Chao-Yu; Feng, Yuan; Potma, Eric O.; Ge, Nien-Hui
Mapping Molecular Orientation with Phase Sensitive Vibrationally Resonant Sum-Frequency Generation Microscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6149-6156, MAY 23 2013
abstract, full text, DOI:10.1021/jp4022147

Sharma, Monika; Predeus, Alexander V.; Mukherjee, Shayantani; Feig, Michael
DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6194-6205, MAY 23 2013
abstract, full text, DOI:10.1021/jp403127a

Natarajan, Kathiresan; Senapati, Sanjib
Probing the Conformational Flexibility of Monomeric FtsZ in GTP-Bound, GDP-Bound, and Nucleotide-Free States
BIOCHEMISTRY, 52:3543-3551, MAY 21 2013
abstract, full text

Kantcheva, Adriana K.; Quick, Matthias; Shi, Lei; Winther, Anne-Marie Lund; Stolzenberg, Sebastian; Weinstein, Harel; Javitch, Jonathan A.; Nissen, Poul
Chloride binding site of neurotransmitter sodium symporters
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:8489-8494, MAY 21 2013
abstract, full text, DOI:10.1073/pnas.1221279110

Dai, Bin; Kang, Seung-gu; Tien Huynh; Lei, Haozhi; Castelli, Matteo; Hu, Jun; Zhang, Yi; Zhou, Ruhong
Salts drive controllable multilayered upright assembly of amyloid-like peptides at mica/water interface
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:8543-8548, MAY 21 2013
abstract, full text, DOI:10.1073/pnas.1220711110

Dai, Jian; Zhou, Huan-Xiang
An NMDA Receptor Gating Mechanism Developed from MD Simulations Reveals Molecular Details Underlying Subunit-Specific Contributions
BIOPHYSICAL JOURNAL, 104:2170-2181, MAY 21 2013
abstract, full text, DOI:10.1016/j.bpj.2013.04.013

Sodt, Alexander J.; Pastor, Richard W.
Bending Free Energy from Simulation: Correspondence of Planar and Inverse Hexagonal Lipid Phases
BIOPHYSICAL JOURNAL, 104:2202-2211, MAY 21 2013
abstract, full text, DOI:10.1016/j.bpj.2013.03.048

Ruiz, L.; VonAchen, P.; Lazzara, T. D.; Xu, T.; Keten, S.
Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force
NANOTECHNOLOGY, 24 Art. No. 195103, MAY 17 2013
abstract, full text, DOI:10.1088/0957-4484/24/19/195103

Cao, Xiaobo; Yap, Jeremy L.; Newell-Rogers, M. Karen; Peddaboina, Chander; Jiang, Weihua; Papaconstantinou, Harry T.; Jupitor, Dan; Rai, Arun; Jung, Kwan-Young; Tubin, Richard P.; Yu, Wenbo; Vanommeslaeghe, Kenno; Wilder, Paul T.; MacKerell, Alexander D., Jr.; Fletcher, Steven; Smythe, Roy W.
The novel BH3 alpha-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak
MOLECULAR CANCER, 12 Art. No. 42, MAY 16 2013
abstract, full text, DOI:10.1186/1476-4598-12-42

Pal, Somedatta; Bandyopadhyay, Sanjoy
Effects of Protein Conformational Flexibilities and Electrostatic Interactions on the Low-Frequency Vibrational Spectrum of Hydration Water
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5848-5856, MAY 16 2013
abstract, full text, DOI:10.1021/jp402662v

Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Computer Simulation of Fifth Generation Dendronized Polymers: Impact of Charge on Internal Organization
JOURNAL OF PHYSICAL CHEMISTRY B, 117:6007-6017, MAY 16 2013
abstract, full text, DOI:10.1021/jp402695g

Prigozhin, Maxim B.; Liu, Yanxin; Wirth, Anna Jean; Kapoor, Shobhna; Winter, Roland; Schulten, Klaus; Gruebele, Martin
Misplaced helix slows down ultrafast pressure-jump protein folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:8087-8092, MAY 14 2013
abstract, full text, TCBG publications, DOI:10.1073/pnas.1219163110

Dixit, Purushottam D.
A maximum entropy thermodynamics of small systems
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 184111, MAY 14 2013
abstract, full text, DOI:10.1063/1.4804549

Dos Santos, Helena G.; Abia, David; Janowski, Robert; Mortuza, Gulnahar; Bertero, Michela G.; Boutin, Mailys; Guarin, Nayibe; Mendez-Giraldez, Raul; Nunez, Alfonso; Pedrero, Juan G.; Redondo, Pilar; Sanz, Maria; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, Jose M.; Gonzalez, Cayetano; Reina, Jose; Valpuesta, Jose M.; Vernos, Isabelle; Zabala, Juan C.; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis
Structure and Non-Structure of Centrosomal Proteins
PLOS ONE, 8 Art. No. e62633, MAY 9 2013
abstract, full text, DOI:10.1371/journal.pone.0062633

Bereau, Tristan; Kramer, Christian; Monnard, Fabien W.; Nogueira, Elisa S.; Ward, Thomas R.; Meuwly, Markus
Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5460-5471, MAY 9 2013
abstract, full text, DOI:10.1021/jp400593c

Heinzelmann, Germano; Bastug, Turgut; Kuyucak, Serdar
Mechanism and Energetics of Ligand Release in the Aspartate Transporter Glt(Ph)
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5486-5496, MAY 9 2013
abstract, full text, DOI:10.1021/jp4010423

Georgoulia, Panagiota S.; Glykos, Nicholas M.
On the Foldability of Tryptophan-Containing Tetra- and Pentapeptides: An Exhaustive Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5522-5532, MAY 9 2013
abstract, full text, DOI:10.1021/jp401239v

Suresh, Gorle; Priyakumar, U. Deva
Structures, Dynamics, and Stabilities of Fully Modified Locked Nucleic Acid (beta-D-LNA and alpha-L-LNA) Duplexes in Comparison to Pure DNA and RNA Duplexes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5556-5564, MAY 9 2013
abstract, full text, DOI:10.1021/jp4016068

Gomez, Hansel; Lluch, Jose M.; Masgrau, Laura
Substrate-Assisted and Nucleophilically Assisted Catalysis in Bovine alpha 1,3-Galactosyltransferase. Mechanistic Implications for Retaining Glycosyltransferases
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:7053-7063, MAY 8 2013
abstract, full text, DOI:10.1021/ja4024447

Balijepalli, Arvind; Robertson, Joseph W. F.; Reiner, Joseph E.; Kasianowicz, John J.; Pastor, Richard W.
Theory of Polymer-Nanopore Interactions Refined Using Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:7064-7072, MAY 8 2013
abstract, full text, DOI:10.1021/ja4026193

Abeyrathne, Chathurika D.; Halgamuge, Malka N.; Farrell, Peter M.; Skafidas, Efstratios
An ab-initio Computational Method to Determine Dielectric Properties of Biological Materials
SCIENTIFIC REPORTS, 3 Art. No. 1796, MAY 8 2013
abstract, full text, DOI:10.1038/srep01796

Li, Jing; Shaikh, Saher A.; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad
Transient formation of water-conducting states in membrane transporters
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:7696-7701, MAY 7 2013
abstract, full text, DOI:10.1073/pnas.1218986110

Hirsh, Andrew D.; Taranova, Maryna; Lionberger, Troy A.; Lillian, Todd D.; Andricioaei, Ioan; Perkins, N. C.
Structural Ensemble and Dynamics of Toroidal-like DNA Shapes in Bacteriophage phi 29 Exit Cavity
BIOPHYSICAL JOURNAL, 104:2058-2067, MAY 7 2013
abstract, full text, DOI:10.1016/j.bpj.2013.03.032

Shi, Wei; Luebke, David R.
Enhanced Gas Absorption in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]) Confined in Silica Slit Pores: A Molecular Simulation Study
LANGMUIR, 29:5563-5572, MAY 7 2013
abstract, full text, DOI:10.1021/la400226g

Honorat, Mylene; Terreux, Raphael; Falson, Pierre; Di Pietro, Attilio; Dumontet, Charles; Payen, Lea
Localization of putative binding sites for cyclic guanosine monophosphate and the anti-cancer drug 5-fluoro-2 '-deoxyuridine-5 '-monophosphate on ABCC11 in silico models
BMC STRUCTURAL BIOLOGY, 13 Art. No. 7, MAY 6 2013
abstract, full text, DOI:10.1186/1472-6807-13-7

de Gloucester, Paul Colin
Referees Often Miss Obvious Errors in Computer and Electronic Publications
ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE, 20:143-166, MAY 4 2013
abstract, full text, DOI:10.1080/08989621.2013.788379

Kundu, Achintya; Watanabe, Hidekazu; Yamaguchi, Shoichi; Tahara, Tahei
Agreement between Experimentally and Theoretically Estimated Orientational Distributions of Solutes at the Air/Water Interface
JOURNAL OF PHYSICAL CHEMISTRY C, 117:8887-8891, MAY 2 2013
abstract, full text, DOI:10.1021/jp402674u

Islam, Shahidul M.; Stein, Richard A.; Mchaourab, Hassane S.; Roux, Benoit
Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4740-4754, MAY 2 2013
abstract, full text, DOI:10.1021/jp311723a

Kyrychenko, Alexander; Tobias, Douglas J.; Ladokhin, Alexey S.
Validation of Depth-Dependent Fluorescence Quenching in Membranes by Molecular Dynamics Simulation of Tryptophan Octyl Ester in POPC Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4770-4778, MAY 2 2013
abstract, full text, DOI:10.1021/jp310638f

Taylor, Courtney B.; Payne, Christina M.; Himmel, Michael E.; Crowley, Michael F.; McCabe, Clare; Beckham, Gregg T.
Binding Site Dynamics and Aromatic-Carbohydrate Interactions in Processive and Non-Processive Family 7 Glycoside Hydrolases
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4924-4933, MAY 2 2013
abstract, full text, DOI:10.1021/jp401410h

Etienne, Thibaud; Very, Thibaut; Perpete, Eric A.; Monari, Antonio; Assfeld, Xavier
A QM/MM Study of the Absorption Spectrum of Harmane in Water Solution and Interacting with DNA: The Crucial Role of Dynamic Effects
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4973-4980, MAY 2 2013
abstract, full text, DOI:10.1021/jp4017882

Curtis, Emily M.; Hall, Carol K.
Molecular Dynamics Simulations of DPPC Bilayers Using "LIME", a New Coarse-Grained Model
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5019-5030, MAY 2 2013
abstract, full text, DOI:10.1021/jp309712b

Du, Hongbo; Wickramasinghe, Sumith Ranil; Qian, Xianghong
Specificity in Cationic Interaction with Poly(N-isopropylacrylamide)
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5090-5101, MAY 2 2013
abstract, full text, DOI:10.1021/jp401817h

Riahi, Saleh; Rowley, Christopher N.
A Drude Polarizable Model for Liquid Hydrogen Sulfide
JOURNAL OF PHYSICAL CHEMISTRY B, 117:5222-5229, MAY 2 2013
abstract, full text, DOI:10.1021/jp401847s

Amarasinghe, Priyanthi M.; Anandarajah, A.
Molecular Dynamic Study of the Swelling Behavior of Na-Montmorillonite
ENVIRONMENTAL & ENGINEERING GEOSCIENCE, 19:173-183, MAY 2013
abstract, full text

Chew, Teong Han; Joyce-Tan, Kwee Hong; Hussein, Zeti Azura Mohamed; Elizabeth-Chia, Pek Iee; Shamsir, Mohd Shahir
Improving Molecular Dynamics Simulation Performance on Low-Cost Systems
COMPUTING IN SCIENCE & ENGINEERING, 15:64-70, MAY-JUN 2013
abstract, full text

Qin, Zhao; Fabre, Andrea; Buehler, Markus J.
Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale
EUROPEAN PHYSICAL JOURNAL E, 36 Art. No. 53, MAY 2013
abstract, full text, DOI:10.1140/epje/i2013-13053-8

Kral, Petr; Wang, Boyang
Material Drag Phenomena in Nanotubes
CHEMICAL REVIEWS, 113:3372-3390, MAY 2013
full text, DOI:10.1021/cr200244h

Li, Yunlang; Schlick, Tamar
"Gate-keeper'' Residues and Active-Site Rearrangements in DNA Polymerase mu Help Discriminate Non-cognate Nucleotides
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003074, MAY 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003074

Sethi, Anurag; Tian, Jianhui; Derdeyn, Cynthia A.; Korber, Bette; Gnanakaran, S.
A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003046, MAY 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003046

Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.
Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003072, MAY 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003072

Walther, Jens H.; Ritos, Konstantinos; Cruz-Chu, Eduardo R.; Megaridis, Constantine M.; Koumoutsakos, Petros
Barriers to Superfast Water Transport in Carbon Nanotube Membranes
NANO LETTERS, 13:1910-1914, MAY 2013
abstract, full text, DOI:10.1021/nl304000k

Avdoshenko, Stanislav M.; Nozaki, Daijiro; da Rocha, Claudia Gomes; Gonzalez, Jhon W.; Lee, Myeong H.; Gutierrez, Rafael; Cuniberti, Gianaurelio
Dynamic and Electronic Transport Properties of DNA Translocation through Graphene Nanopores
NANO LETTERS, 13:1969-1976, MAY 2013
abstract, full text, DOI:10.1021/nl304735k

Robinson, David
A Polarizable Force-Field for Cholesterol and Sphingomyelin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:2498-2503, MAY 2013
abstract, full text, DOI:10.1021/ct400103e

Ahumada, O.; Perez-Madrigal, M. M.; Ramirez, J.; Curco, D.; Esteves, C.; Salvador-Matar, A.; Luongo, G.; Armelin, E.; Puiggali, J.; Aleman, C.
Sensitive thermal transitions of nanoscale polymer samples using the bimetallic effect: Application to ultra-thin polythiophene
REVIEW OF SCIENTIFIC INSTRUMENTS, 84 Art. No. UNSP 053904, MAY 2013
abstract, full text, DOI:10.1063/1.4804395

Clementi, Nicola; Mancini, Nicasio; Castelli, Matteo; Clementi, Massimo; Burioni, Roberto
Characterization of epitopes recognized by monoclonal antibodies: experimental approaches supported by freely accessible bioinformatic tools
DRUG DISCOVERY TODAY, 18:464-471, MAY 2013
abstract, full text, DOI:10.1016/j.drudis.2012.11.006

Zanuy, David; Kotla, Rohith; Nussinov, Ruth; Teesalu, Tambet; Sugahara, Kazuki N.; Aleman, Carlos; Haspel, Nurit
Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor
JOURNAL OF STRUCTURAL BIOLOGY, 182:78-86, MAY 2013
abstract, full text, DOI:10.1016/j.jsb.2013.02.006

Beeby, Morgan; Gumbart, James C.; Roux, Benoit; Jensen, Grant J.
Architecture and assembly of the Gram-positive cell wall
MOLECULAR MICROBIOLOGY, 88:664-672, MAY 2013
abstract, full text, DOI:10.1111/mmi.12203

Wang Shen; Tu Yu-Song; Wan Rong-Zheng; Fang Hai-Ping
Effects of Surface Dipole Lengths on Evaporation of Tiny Water Aggregation
COMMUNICATIONS IN THEORETICAL PHYSICS, 59:623-628, MAY 2013
abstract, full text, DOI:10.1088/0253-6102/59/5/17

Korabecny, Jan; Janovec, Ladislav; Musilek, Kamil; Zemek, Filip; Horova, Anna; Nepovimova, Eugenie; Dolezal, Rafael; Opletalova, Veronika; Hroudova, Jana; Fisar, Zdenek; Jung, Young-Sik; Kuca, Kamil
Comparison of Novel Tacrine and 7-MEOTA Derivatives with Aromatic and Alicyclic Residues: Synthesis, Biological Evaluation and Docking Studies
LETTERS IN ORGANIC CHEMISTRY, 10:291-297, MAY 2013
abstract, full text

Kim, Youngchang; Cunningham, Mark A.; Mire, Joseph; Tesar, Christine; Sacchettini, James; Joachimiak, Andrzej
NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism
FASEB JOURNAL, 27:1917-1927, MAY 2013
abstract, full text, DOI:10.1096/fj.12-224014

Durmaz, Emel; Kuyucak, Serdar; Sezerman, Ugur O.
Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex
PROTEIN ENGINEERING DESIGN & SELECTION, 26:325-333, MAY 2013
abstract, full text, DOI:10.1093/protein/gzt004

Yang Can-qun; Wu Qiang; Tang Tao; Wang Feng; Xue Jing-ling
Programming for scientific computing on peta-scale heterogeneous parallel systems
JOURNAL OF CENTRAL SOUTH UNIVERSITY, 20:1189-1203, MAY 2013
abstract, full text, DOI:10.1007/s11771-013-1602-z

Reyes Loyola, Paola Kinara; Campos-Rodriguez, R.; Bello, Martiniano; Rojas-Hernandez, S.; Zimic, Mirko; Quiliano, Miguel; Briz, Veronica; Angeles Munoz-Fernandez, M.; Tolentino-Lopez, Luis; Correa-Basurto, Jose
Theoretical analysis of the neuraminidase epitope of the Mexican A H1N1 influenza strain, and experimental studies on its interaction with rabbit and human hosts
IMMUNOLOGIC RESEARCH, 56:44-60, MAY 2013
abstract, full text, DOI:10.1007/s12026-013-8385-z

Furlani, Thomas R.; Jones, Matthew D.; Gallo, Steven M.; Bruno, Andrew E.; Lu, Charng-Da; Ghadersohi, Amin; Gentner, Ryan J.; Patra, Abani; DeLeon, Robert L.; von Laszewski, Gregor; Wang, Fugang; Zimmerman, Ann
Performance metrics and auditing framework using application kernels for high-performance computer systems
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 25:918-931, MAY 2013
abstract, full text, DOI:10.1002/cpe.2871

Vilos, Cristian; Morales, Francisco A.; Solar, Paula A.; Herrera, Natalia S.; Gonzalez-Nilo, Fernando D.; Aguayo, Daniel A.; Mendoza, Hegaly L.; Comer, Jeffrey; Bravo, Maria L.; Gonzalez, Pamela A.; Kato, Sumie; Cuello, Mauricio A.; Alonso, Catalina; Bravo, Erasmo J.; Bustamante, Eva I.; Owen, Gareth I.; Velasquez, Luis A.
Paclitaxel-PHBV nanoparticles and their toxicity to endometrial and primary ovarian cancer cells
BIOMATERIALS, 34:4098-4108, MAY 2013
abstract, full text, DOI:10.1016/j.biomaterials.2013.02.034

Ozcan, Ahmet; Olmez, Elif Ozkirimli; Alakent, Burak
Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:788-804, MAY 2013
abstract, full text, DOI:10.1002/prot.24234

Jin, Hao-Bai; Kang, Yu; Zhang, Jin; Wu, Tao; Wang, Qi
Interaction between tissue-type plasminogen activator and ligands grafted onto hydrogel
MOLECULAR SIMULATION, 39:513-520, MAY 1 2013
abstract, full text, DOI:10.1080/08927022.2012.749408

Lejal, Nathalie; Tarus, Bogdan; Bouguyon, Edwige; Chenavas, Sylvie; Bertho, Nicolas; Delmas, Bernard; Ruigrok, Rob W. H.; Di Primo, Carmelo; Slama-Schwok, Anny
Structure-Based Discovery of the Novel Antiviral Properties of Naproxen against the Nucleoprotein of Influenza A Virus
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 57:2231-2242, MAY 2013
abstract, full text, DOI:10.1128/AAC.02335-12

Ermakova, Elena; Miller, Michelle C.; Nesmelova, Irina V.; Lopez-Merino, Lara; Alvaro Berbis, Manuel; Nesmelov, Yuri; Tkachev, Yaroslav V.; Lagartera, Laura; Daragan, Vladimir A.; Andre, Sabine; Javier Canada, F.; Jimenez-Barbero, Jesus; Solis, Dolores; Gabius, Hans-Joachim; Mayo, Kevin H.
Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity
GLYCOBIOLOGY, 23:508-523, MAY 2013
abstract, full text, DOI:10.1093/glycob/cwt005

Florian, Paula E.; Macovei, Alina; Lazar, Catalin; Milac, Adina L.; Sokolowska, Izabela; Darie, Costel C.; Evans, Robert W.; Roseanu, Anca; Branza-Nichita, Norica
Characterization of the anti-HBV activity of HLP123, a human lactoferrin-derived peptide
JOURNAL OF MEDICAL VIROLOGY, 85:780-788, MAY 2013
abstract, full text, DOI:10.1002/jmv.23549

Hofmeyer, Thomas; Schmelz, Stefan; Degiacomi, Matteo T.; Dal Peraro, Matteo; Daneschdar, Matin; Scrima, Andrea; van den Heuvel, Joop; Heinz, Dirk W.; Kolmar, Harald
Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
JOURNAL OF MOLECULAR BIOLOGY, 425:1302-1317, APR 26 2013
abstract, full text, DOI:10.1016/j.jmb.2012.12.017

Li, Li; Martinis, Susan A.; Luthey-Schulten, Zaida
Capture and Quality Control Mechanisms for Adenosine-5 '-triphosphate Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:6047-6055, APR 24 2013
abstract, full text, DOI:10.1021/ja308044w

Flatt, Justin W.; Kim, Robert; Smith, Jason G.; Nemerow, Glen R.; Stewart, Phoebe L.
An Intrinsically Disordered Region of the Adenovirus Capsid Is Implicated in Neutralization by Human Alpha Defensin 5
PLOS ONE, 8 Art. No. e61571, APR 19 2013
abstract, full text, DOI:10.1371/journal.pone.0061571

Porrini, Massimiliano; Zachariae, Ulrich; Barran, Perdita E.; MacPhee, Cait E.
Effect of Protonation State on the Stability of Amyloid Oligomers Assembled from TTR(105-115)
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:1233-1238, APR 18 2013
abstract, full text, DOI:10.1021/jz400372u

McCullagh, Martin; Voth, Gregory A.
Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase: A New Application of Coarse-Graining
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4062-4071, APR 18 2013
abstract, full text, DOI:10.1021/jp402441s

Amaral, Marta; Levy, Colin; Heyes, Derren J.; Lafite, Pierre; Outeiro, Tiago F.; Giorgini, Flaviano; Leys, David; Scrutton, Nigel S.
Structural basis of kynurenine 3-monooxygenase inhibition
NATURE, 496:382-+, APR 18 2013
abstract, full text, DOI:10.1038/nature12039

Grauffel, Cedric; Yang, Boqian; He, Tao; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie
Cation-pi Interactions As Lipid-Specific Anchors for Phosphatidylinositol-Specific Phospholipase C
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:5740-5750, APR 17 2013
abstract, full text, DOI:10.1021/ja312656v

Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele
Funnel metadynamics as accurate binding free-energy method
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:6358-6363, APR 16 2013
abstract, full text, DOI:10.1073/pnas.1303186110

Fontani, Giacomo; Gaspari, Roberto; Spencer, Nicholas D.; Passerone, Daniele; Crockett, Rowena
Adsorption and Friction Behavior of Amphiphilic Polymers on Hydrophobic Surfaces
LANGMUIR, 29:4760-4771, APR 16 2013
abstract, full text, DOI:10.1021/la400263r

Li, Ning; Mao, Debin; Lu, Shouqin; Tong, Chunfang; Zhang, Yan; Long, Mian
Distinct Binding Affinities of Mac-1 and LFA-1 in Neutrophil Activation
JOURNAL OF IMMUNOLOGY, 190:4371-4381, APR 15 2013
abstract, full text, DOI:10.4049/jimmunol.1201374

Falvo, Cyril; Debnath, Arunangshu; Meier, Christoph
Vibrational ladder climbing in carboxy-hemoglobin: Effects of the protein environment
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 145101, APR 14 2013
abstract, full text, DOI:10.1063/1.4799271

Yu, Shuai; Huang, He; Iliuk, Anton; Wang, Wen-Horng; Jayasundera, Keerthi B.; Tao, W. Andy; Post, Carol B.; Geahlen, Robert L.
Syk Inhibits the Activity of Protein Kinase A by Phosphorylating Tyrosine 330 of the Catalytic Subunit
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:10870-10881, APR 12 2013
abstract, full text, DOI:10.1074/jbc.M112.426130

Fan, Jun; Saunders, Marissa G.; Haddadian, Esmael J.; Freed, Karl F.; De La Cruz, Enrique M.; Voth, Gregory A.
Molecular Origins of Cofilin-Linked Changes in Actin Filament Mechanics
JOURNAL OF MOLECULAR BIOLOGY, 425:1225-1240, APR 12 2013
abstract, full text, DOI:10.1016/j.jmb.2013.01.020

Vashisth, Harish; Skiniotis, Georgios; Brooks, Charles L., I.I.I.
Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3738-3746, APR 11 2013
abstract, full text, DOI:10.1021/jp3126297

Stock, Leticia; Delemotte, Lucie; Carnevale, Vincenzo; Treptow, Werner; Klein, Michael L.
Conduction in a Biological Sodium Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3782-3789, APR 11 2013
abstract, full text, DOI:10.1021/jp401403b

Zhao, Li; Li, Wenzhao; Tian, Pu
Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics
PLOS ONE, 8 Art. No. e60553, APR 11 2013
abstract, full text, DOI:10.1371/journal.pone.0060553

Zimbron, Jeremy M.; Heinisch, Tillmann; Schmid, Maurus; Hamels, Didier; Nogueira, Elisa S.; Schirmer, Tilman; Ward, Thomas R.
A Dual Anchoring Strategy for the Localization and Activation of Artificial Metalloenzymes Based on the Biotin-Streptavidin Technology
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:5384-5388, APR 10 2013
abstract, full text, DOI:10.1021/ja309974s

Kumar, Eric A.; Chen, Qianyi; Kizhake, Smitha; Kolar, Carol; Kang, Myungshim; Chang, Chia-en A.; Borgstahl, Gloria E. O.; Natarajan, Amarnath
The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides
SCIENTIFIC REPORTS, 3 Art. No. 1639, APR 10 2013
abstract, full text, DOI:10.1038/srep01639

Revilla-Lopez, Guillermo; Casanovas, Jordi; Bertran, Oscar; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Modeling biominerals formed by apatites and DNA
BIOINTERPHASES, 8 Art. No. 10, APR 8 2013
abstract, full text, DOI:10.1186/1559-4106-8-10

Cocco, Eleonora; Murru, Raffaele; Costa, Gianna; Kumar, Amit; Pieroni, Enrico; Melis, Cristina; Barberini, Luigi; Sardu, Claudia; Lorefice, Lorena; Fenu, Giuseppe; Frau, Jessica; Coghe, Giancarlo; Carboni, Nicola; Marrosu, Maria Giovanna
Interaction between HLA-DRB1-DQB1 Haplotypes in Sardinian Multiple Sclerosis Population
PLOS ONE, 8 Art. No. e59790, APR 8 2013
abstract, full text, DOI:10.1371/journal.pone.0059790

Musolino, Nicholas; Trout, Bernhardt L.
Insight into the molecular mechanism of water evaporation via the finite temperature string method
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 134707, APR 7 2013
abstract, full text, DOI:10.1063/1.4798458

Liu, Yang; Esser, Lothar; Interlandi, Gianluca; Kisiela, Dagmara I.; Tchesnokova, Veronika; Thomas, Wendy E.; Sokurenko, Evgeni; Xia, Di; Savarino, Stephen J.
Tight Conformational Coupling between the Domains of the Enterotoxigenic Escherichia coli Fimbrial Adhesin CfaE Regulates Binding State Transition
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:9993-10001, APR 5 2013
abstract, full text, DOI:10.1074/jbc.M112.413534

Shkurti, Ardita; Orsi, Mario; Macii, Enrico; Ficarra, Elisa; Acquaviva, Andrea
Acceleration of coarse grain molecular dynamics on GPU architectures
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:803-818, APR 5 2013
abstract, full text, DOI:10.1002/jcc.23183

Nowosielski, Marcin; Hoffmann, Marcin; Kuron, Aneta; Korycka-Machala, Malgorzata; Dziadek, Jaroslaw
The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics dagger
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:750-756, APR 5 2013
abstract, full text, DOI:10.1002/jcc.23192

Gao, Junkuo; Shi, Wu-Jun; Ye, Jun; Wang, Xiaoqing; Hirao, Hajime; Zhao, Yang
QM/MM Modeling of Environmental Effects on Electronic Transitions of the FMO Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3488-3495, APR 4 2013
abstract, full text, DOI:10.1021/jp3109418

George, Anthony M.; Jones, Peter M.
An Asymmetric Post-Hydrolysis State of the ABC Transporter ATPase Dimer
PLOS ONE, 8 Art. No. e59854, APR 3 2013
abstract, full text, DOI:10.1371/journal.pone.0059854

Neumann, Anna; Baginski, Maciej; Winczewski, Szymon; Czub, Jacek
The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
BIOPHYSICAL JOURNAL, 104:1485-1494, APR 2 2013
abstract, full text, DOI:10.1016/j.bpj.2013.02.029

Janosi, Lorant; Ceccarelli, Matteo
The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations
PLOS ONE, 8 Art. No. e59897, APR 2 2013
abstract, full text, DOI:10.1371/journal.pone.0059897

Felix, Jan; Elegheert, Jonathan; Gutsche, Irina; Shkumatov, Alexander V.; Wen, Yurong; Bracke, Nathalie; Pannecoucke, Erwin; Vandenberghe, Isabel; Devreese, Bart; Svergun, Dmitri I.; Pauwels, Ewald; Vergauwen, Bjorn; Savvides, Savvas N.
Human IL-34 and CSF-1 Establish Structurally Similar Extracellular Assemblies with Their Common Hematopoietic Receptor
STRUCTURE, 21:528-539, APR 2 2013
abstract, full text, DOI:10.1016/j.str.2013.01.018

Plummer, Ashlee; Thompson, Matthew K.; Franzen, Stefan
Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin
BIOCHEMISTRY, 52:2218-2227, APR 2 2013
abstract, full text, DOI:10.1021/bi301509r

Emileh, Ali; Tuzer, Ferit; Yeh, Herman; Umashankara, Muddegowda; Moreira, Diogo R. M.; LaLonde, Judith M.; Bewley, Carole A.; Abrams, Cameron F.; Chaiken, Irwin M.
A Model of Peptide Triazole Entry Inhibitor Binding to HIV-1 gp120 and the Mechanism of Bridging Sheet Disruption
BIOCHEMISTRY, 52:2245-2261, APR 2 2013
abstract, full text, DOI:10.1021/bi400166b

Noorbatcha, I. A.; Sultan, A. M.; Salleh, H. M.; Amid, Azura
Understanding Thermostability Factors of Aspergillus niger PhyA Phytase: A Molecular Dynamics Study
PROTEIN JOURNAL, 32:309-316, APR 2013
abstract, full text, DOI:10.1007/s10930-013-9489-y

Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong
Molecular dynamics study on water self-diffusion in aqueous mixtures of methanol, ethylene glycol and glycerol: investigations from the point of view of hydrogen bonding
MOLECULAR PHYSICS, 111:939-949, APR 1 2013
abstract, full text, DOI:10.1080/00268976.2012.760050

Malac, Kamil; Barvik, Ivan
Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 27:373-388, APR 2013
abstract, full text, DOI:10.1007/s10822-013-9652-8

Meneksedag, Deniz; Dogan, Asligul; Kanlikilicer, Pinar; Ozkirimli, Elif
Communication between the active site and the allosteric site in class A beta-lactamases
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 43:1-10, APR 2013
abstract, full text, DOI:10.1016/j.compbiolchem.2012.12.002

Mondal, Sayan; Khelashvili, George; Shi, Lei; Weinstein, Harel
The cost of living in the membrane: A case study of hydrophobic mismatch for the multi-segment protein LeuT
CHEMISTRY AND PHYSICS OF LIPIDS, 169:27-38, APR 2013
abstract, full text, DOI:10.1016/j.chemphyslip.2013.01.006

Khelashvili, George; Harries, Daniel
How sterol tilt regulates properties and organization of lipid membranes and membrane insertions
CHEMISTRY AND PHYSICS OF LIPIDS, 169:113-123, APR 2013
abstract, full text, DOI:10.1016/j.chemphyslip.2012.12.006

Baker, Joseph L.; Biais, Nicolas; Tama, Florence
Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003032, APR 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003032

Chebaro, Yassmine; Amal, Ismail; Rochel, Natacha; Rochette-Egly, Cecile; Stote, Roland H.; Dejaegere, Annick
Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003012, APR 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003012

Golji, Javad; Mofrad, Mohammad R. K.
The Interaction of Vinculin with Actin
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002995, APR 2013
abstract, full text, DOI:10.1371/journal.pcbi.1002995

Kuttner, Yosef Y.; Nagar, Tal; Engel, Stanislav
Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca2+
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003028, APR 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003028

Wojtas-Niziurski, Wojciech; Meng, Yilin; Roux, Benoit; Berneche, Simon
Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1885-1895, APR 2013
abstract, full text, DOI:10.1021/ct300978b

Pirie, Christopher M.; De Mey, Marjan; Prather, Kristala L. Jones; Ajikumar, Parayil Kumaran
Integrating the Protein and Metabolic Engineering Toolkits for Next-Generation Chemical Biosynthesis
ACS CHEMICAL BIOLOGY, 8:662-672, APR 2013
abstract, full text, DOI:10.1021/cb300634b

Longhi, Giovanna; Ceselli, Alberto; Fornili, Sandro L.; Abbate, Sergio; Ceraulo, Leopoldo; Liveri, Vincenzo Turco
Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate
JOURNAL OF MASS SPECTROMETRY, 48:478-486, APR 2013
abstract, full text, DOI:10.1002/jms.3179

Furini, Simone; Barbini, Paolo; Domene, Carmen
DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence
NUCLEIC ACIDS RESEARCH, 41:3963-3972, APR 2013
abstract, full text, DOI:10.1093/nar/gkt099

Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Huang, Jian-Ming; Juwita, Ratna
A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 14:7702-7715, APR 2013
abstract, full text, DOI:10.3390/ijms14047702

Pan, Peichen; Li, Youyong; Yu, Huidong; Sun, Huiyong; Hou, Tingjun
Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:997-1006, APR 2013
abstract, full text, DOI:10.1021/ci400066x

Patmanidis, Ilias; Glykos, Nicholas M.
As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 41:68-71, APR 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.02.004

Gordon, Dan; Chen, Rong; Chung, Shin-Ho
COMPUTATIONAL METHODS OF STUDYING THE BINDING OF TOXINS FROM VENOMOUS ANIMALS TO BIOLOGICAL ION CHANNELS: THEORY AND APPLICATIONS
PHYSIOLOGICAL REVIEWS, 93:767-802, APR 2013
abstract, full text, DOI:10.1152/physrev.00035.2012

Roberts, Michael L.; Kino, Tomoshige; Nicolaides, Nicolas C.; Hurt, Darrell E.; Katsantoni, Eleni; Sertedaki, Amalia; Komianou, Filadelfia; Kassiou, Korina; Chrousos, George P.; Charmandari, Evangelia
A Novel Point Mutation in the DNA-Binding Domain (DBD) of the Human Glucocorticoid Receptor Causes Primary Generalized Glucocorticoid Resistance by Disrupting the Hydrophobic Structure of its DBD
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 98:E790-E795, APR 2013
abstract, full text, DOI:10.1210/jc.2012-3549

Pietra, Francesco
On the Pathways of Biologically Relevant Diatomic Gases through Proteins. Dioxygen and Heme Oxygenase from the Perspective of Molecular Dynamics
CHEMISTRY & BIODIVERSITY, 10:556-568, APR 2013
abstract, full text, DOI:10.1002/cbdv.201200434

Azcune, Itxaso; Balentova, Eva; Sagartzazu-Aizpurua, Maialen; Ignacio Santos, J.; Miranda, Jose I.; Fratila, Raluca M.; Aizpurua, Jesus M.
Modulating Lectin Inhibition with N-Glycosyl-1,2,3-triazole Scaffolds
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 12, 2434-2444, APR 2013
abstract, full text, DOI:10.1002/ejoc.201201674

Shi Ji-Pei; Zhao Juan; Yang Fan; Wang Jian-Ping
Femtosecond Two-Dimensional Infrared Spectroscopy of N-Ethypropionamide
ACTA PHYSICO-CHIMICA SINICA, 29:695-700, APR 2013
abstract, full text, DOI:10.3866/PKU.WHXB201302213

Nevidimov, A. V.; Razumov, V. F.
Molecular dynamics simulation of reverse micelles: A search for the most efficient strategy
COLLOID JOURNAL, 75:191-197, APR 2013
abstract, full text, DOI:10.1134/S1061933X13010080

Krammer, Eva-Maria; Homble, Fabrice; Prevost, Martine
Molecular origin of VDAC selectivity towards inorganic ions: A combined molecular and Brownian dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:1284-1292, APR 2013
abstract, full text, DOI:10.1016/j.bbamem.2012.12.018

Pronk, Sander; Pall, Szilard; Schulz, Roland; Larsson, Per; Bjelkmar, Par; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
BIOINFORMATICS, 29:845-854, APR 1 2013
abstract, full text, DOI:10.1093/bioinformatics/btt055

Mahmood, Md. Iqbal; Liu, Xinli; Neya, Saburo; Hoshino, Tyuji
Influence of Lipid Composition on the Structural Stability of G-Protein Coupled Receptor
CHEMICAL & PHARMACEUTICAL BULLETIN, 61:426-437, APR 2013
abstract, full text

Oliveira, Bruno L.; Moreira, Irina S.; Fernandes, Pedro A.; Ramos, Maria J.; Santos, Isabel; Correia, Joao D. G.
Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
JOURNAL OF MOLECULAR MODELING, 19:1537-1551, APR 2013
abstract, full text, DOI:10.1007/s00894-012-1677-8

Randjelovic, Jelena; Eric, Slavica; Savic, Vladimir
Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex
JOURNAL OF MOLECULAR MODELING, 19:1711-1725, APR 2013
abstract, full text, DOI:10.1007/s00894-012-1735-2

Sukalovic, Vladimir; Soskic, Vukic; Sencanski, Milan; Andric, Deana; Kostic-Rajacic, Sladjana
Determination of key receptor-ligand interactions of dopaminergic arylpiperazines and the dopamine D2 receptor homology model
JOURNAL OF MOLECULAR MODELING, 19:1751-1762, APR 2013
abstract, full text, DOI:10.1007/s00894-012-1731-6

Yatawara, Achani; Wilson, Jamie L.; Taylor, Linda; Polgar, Peter; Mierke, Dale F.
C-terminus of ET A/ETB receptors regulate endothelin-1 signal transmission
JOURNAL OF PEPTIDE SCIENCE, 19:257-262, APR 2013
abstract, full text, DOI:10.1002/psc.2499

Ramirez-Duran, L. A.; Rosales-Hernandez, M. C.; Hernandez-Rodriguez, Maricarmen; Elena Mendieta-Wejebe, Jessica; Trujillo-Ferrara, Jose; Correa-Basurto, Jose
Mapping Myeloperoxidase to Identify its Promiscuity Properties Using Docking and Molecular Dynamics Simulations
CURRENT PHARMACEUTICAL DESIGN, 19:2204-2215, APR 2013
abstract, full text

Mao, Lei; Yang, Yongliang
Targeting the Nuclear Transport Machinery by Rational Drug Design
CURRENT PHARMACEUTICAL DESIGN, 19:2318-2325, APR 2013
abstract, full text

Pulawski, Wojciech; Filipek, Slawomir; Zwolinska, Anna; Debinski, Aleksander; Krzysko, Krystiana; Garduno-Juarez, Ramon; Viswanathan, Sowmya; Renugopalakrishnan, Venkatesan
Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:291-300, APR 2013
abstract, full text, DOI:10.1007/s00249-012-0874-9

Zhang, Zhiyi; Liu, Ming; Li, Beiping; Wang, Yuelan; Yue, Junjie; Liang, Long; Sun, Jianzhong
Exploring the mechanism of a regulatory SNP of KLK3 by molecular dynamics simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:426-440, APR 1 2013
abstract, full text, DOI:10.1080/07391102.2012.703067

Lai-Kee-Him, Josephine; Schellenberger, Pascale; Dumas, Christian; Richard, Eric; Trapani, Stefano; Komar, Veronique; Demangeat, Gerard; Ritzenthaler, Christophe; Bron, Patrick
The backbone model of the Arabis mosaic virus reveals new insights into functional domains of Nepovirus capsid
JOURNAL OF STRUCTURAL BIOLOGY, 182:1-9, APR 2013
abstract, full text, DOI:10.1016/j.jsb.2013.01.007

Chapman, Michael S.; Trzynka, Andrew; Chapman, Brynmor K.
Atomic modeling of cryo-electron microscopy reconstructions - Joint refinement of model and imaging parameters
JOURNAL OF STRUCTURAL BIOLOGY, 182:10-21, APR 2013
abstract, full text, DOI:10.1016/j.jsb.2013.01.003

Garate, Jose Antonio; Oostenbrink, Chris
Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:658-674, APR 2013
abstract, full text, DOI:10.1002/prot.24223

Sun, Chongbo; Tang, Tian; Uludag, Hasan
A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation
BIOMATERIALS, 34:2822-2833, APR 2013
abstract, full text, DOI:10.1016/j.biomaterials.2013.01.011

Halverson, Jonathan D.; Brandes, Thomas; Lenz, Olaf; Arnold, Axel; Bevc, Stas; Starchenko, Vitaliy; Kremer, Kurt; Stuehn, Torsten; Reith, Dirk
ESPResSo++: A modern multiscale simulation package for soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 184:1129-1149, APR 2013
abstract, full text, DOI:10.1016/j.cpc.2012.12.004

Hu, Guodong; Qi, Lisheng; Dou, Xianghua; Wang, Jihua
The influences of protonation state of histidine on aromatic/arginine region of aquaporin-1 protein
MOLECULAR SIMULATION, 39:261-269, APR 1 2013
abstract, full text, DOI:10.1080/08927022.2012.718438

Raczynski, Przemyslaw; Gorny, Krzysztof; Pabiszczak, Mateusz; Gburski, Zygmunt
Nanoindentation of biomembrane by carbon nanotubes - MD simulation
COMPUTATIONAL MATERIALS SCIENCE, 70:13-18, APR 2013
abstract, full text, DOI:10.1016/j.commatsci.2012.12.031

Qiu, Wanzhi; Nguyen, Thanh C.; Skafidas, Efstratios (Stan)
Modeling and Estimating Simulated DNA Nanopore Translocation Signals
IEEE SENSORS JOURNAL, 13:1216-1222, APR 2013
abstract, full text, DOI:10.1109/JSEN.2012.2225044

Hor, Lilian; Dobson, Renwick C. J.; Downton, Matthew T.; Wagner, John; Hutton, Craig A.; Perugini, Matthew A.
Dimerization of Bacterial Diaminopimelate Epimerase Is Essential for Catalysis
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:9238-9248, MAR 29 2013
abstract, full text, DOI:10.1074/jbc.M113.450148

Wang, Luying; Dumont, Randall S.; Dickson, James M.
Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 124701, MAR 28 2013
abstract, full text, DOI:10.1063/1.4794685

Gross, Adam S.; Bell, Alexis T.; Chu, Jhih-Wei
Preferential Interactions between Lithium Chloride and Glucan Chains in N,N-Dimethylacetamide Drive Cellulose Dissolution
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3280-3286, MAR 28 2013
abstract, full text, DOI:10.1021/jp311770u

Bernini, Caterina; Andruniow, Tadeusz; Olivucci, Massimo; Pogni, Rebecca; Basosi, Riccardo; Sinicropi, Adalgisa
Effects of the Protein Environment on the Spectral Properties of Tryptophan Radicals in Pseudomonas aeruginosa Azurin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:4822-4833, MAR 27 2013
abstract, full text, DOI:10.1021/ja400464n

Kumar, Amit; Cocco, Eleonora; Atzori, Luigi; Marrosu, Maria Giovanna; Pieroni, Enrico
Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study
PLOS ONE, 8 Art. No. e59711, MAR 26 2013
abstract, full text, DOI:10.1371/journal.pone.0059711

Mirza, I. Ahmad; Burk, David L.; Xiong, Bing; Iwaki, Hiroaki; Hasegawa, Yoshie; Grosse, Stephan; Lau, Peter C. K.; Berghuis, Albert M.
Structural Analysis of a Novel Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A
PLOS ONE, 8 Art. No. e60072, MAR 26 2013
abstract, full text, DOI:10.1371/journal.pone.0060072

Song, Yu; Peng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi
Exploring the Folding Pattern of a Polymer Chain in a Single Crystal by Combining Single-Molecule Force Spectroscopy and Steered Molecular Dynamics Simulations
LANGMUIR, 29:3853-3857, MAR 26 2013
abstract, full text, DOI:10.1021/la305157p

Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D.; Izumi, Tadahide; Arvai, Andrew S.; Mantha, Anil K.; Szczesny, Bartosz; Ivanov, Ivaylo N.; Hosfield, David J.; Maiti, Buddhadev; Pique, Mike E.; Frankel, Kenneth A.; Hitomi, Kenichi; Cunningham, Richard P.; Mitra, Sankar; Tainer, John A.
Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:8445-8455, MAR 22 2013
abstract, full text, DOI:10.1074/jbc.M112.422774

Glass, Dennis C.; Krishnan, Marimuthu; Smith, Jeremy C.; Baudry, Jerome
Three Entropic Classes of Side Chain in a Globular Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3127-3134, MAR 21 2013
abstract, full text, DOI:10.1021/jp400564q

Das, Amit; Chakrabarti, J.; Ghosh, Mahua
Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation
BIOPHYSICAL JOURNAL, 104:1274-1284, MAR 19 2013
abstract, full text, DOI:10.1016/j.bpj.2012.12.058

Genchev, Georgi Z.; Kobayashi, Tomoyoshi; Lu, Hui
Calcium Induced Regulation of Skeletal Troponin - Computational Insights from Molecular Dynamics Simulations
PLOS ONE, 8 Art. No. e58313, MAR 15 2013
abstract, full text, DOI:10.1371/journal.pone.0058313

Gorny, K.; Dendzik, Z.; Pabiszczak, M.; Gburski, Z.
Non-Debye dipolar relaxation of ethylene glycol embedded in ZSM-5 zeolite host matrix - Computer simulation study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 364:28-33, MAR 15 2013
abstract, full text, DOI:10.1016/j.jnoncrysol.2012.12.042

Ikeda, Atsushi; Ishikawa, Michiko; Aono, Ryota; Kikuchi, Jun-ichi; Akiyama, Motofusa; Shinoda, Wataru
Regioselective Recognition of a [60]Fullerene-Bisadduct by Cyclodextrin
JOURNAL OF ORGANIC CHEMISTRY, 78:2534-2541, MAR 15 2013
abstract, full text, DOI:10.1021/jo3027609

Prates, Erica T.; Stankovic, Ivana; Silveira, Rodrigo L.; Liberato, Marcelo V.; Henrique-Silva, Flavio; Pereira, Nei, Jr.; Polikarpov, Igor; Skaf, Munir S.
X-ray Structure and Molecular Dynamics Simulations of Endoglucanase 3 from Trichoderma harzianum: Structural Organization and Substrate Recognition by Endoglucanases That Lack Cellulose Binding Module
PLOS ONE, 8 Art. No. e59069, MAR 14 2013
abstract, full text, DOI:10.1371/journal.pone.0059069

Hom, Kellie; Heinzl, Geoffrey A.; Eakanunkul, Suntara; Lopes, Pedro E. M.; Xue, Fengtian; MacKerell, Alexander D., Jr.; Wilks, Angela
Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa
JOURNAL OF MEDICINAL CHEMISTRY, 56:2097-2109, MAR 14 2013
abstract, full text, DOI:10.1021/jm301819k

Komuro, Yasuaki; Miyashita, Naoyuki; Mori, Takaharu; Muneyuki, Eiro; Saitoh, Takashi; Kohda, Daisuke; Sugita, Yuji
Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2864-2871, MAR 14 2013
abstract, full text, DOI:10.1021/jp400113e

Morrow, Christin P.; Yazaydin, A. Oezguer; Krishnan, Marimuthu; Bowers, Geoffrey M.; Kalinichev, Andrey G.; Kirkpatrick, R. James
Structure, Energetics, and Dynamics of Smectite Clay Interlayer Hydration: Molecular Dynamics and Metadynamics Investigation of Na-Hectorite
JOURNAL OF PHYSICAL CHEMISTRY C, 117:5172-5187, MAR 14 2013
abstract, full text, DOI:10.1021/jp312286g

Chuev, Gennady N.; Vyalov, I.; Georgi, N.
Extraction of atom-atom bridge and direct correlation functions from molecular simulations: A test for ambient water
CHEMICAL PHYSICS LETTERS, 561:175-178, MAR 13 2013
abstract, full text, DOI:10.1016/j.cplett.2013.01.052

Lee, Cheng K.; Hua, Chi C.; Chen, Show A.
Phase Transition and Gels in Conjugated Polymer Solutions
MACROMOLECULES, 46:1932-1938, MAR 12 2013
abstract, full text, DOI:10.1021/ma302343e

Das, Atanu; Plotkin, Steven S.
Mechanical Probes of SOD1 Predict Systematic Trends in Metal and Dimer Affinity of ALS-Associated Mutants
JOURNAL OF MOLECULAR BIOLOGY, 425:850-874, MAR 11 2013
abstract, full text, DOI:10.1016/j.jmb.2012.12.022

Patel, Pryank; Clarke, Christopher; Barraclough, Dong Liu; Jowitt, Thomas Adam; Rudland, Philip Spencer; Barraclough, Roger; Lian, Lu-Yun
Metastasis-Promoting Anterior Gradient 2 Protein Has a Dimeric Thioredoxin Fold Structure and a Role in Cell Adhesion
JOURNAL OF MOLECULAR BIOLOGY, 425:929-943, MAR 11 2013
abstract, full text, DOI:10.1016/j.jmb.2012.12.009

Clavier, A.; Kraszewski, S.; Ramseyer, C.; Picaud, F.
Insertion kinetics of small nucleotides through single walled carbon nanotube
JOURNAL OF BIOTECHNOLOGY, 164:13-18, MAR 10 2013
abstract, full text, DOI:10.1016/j.jbiotec.2012.12.008

Machado, L. D.; Legoas, S. B.; Soares, J. S.; Shadmi, N.; Jorio, A.; Joselevich, E.; Galvao, D. S.
Dynamics of the Formation of Carbon Nanotube Serpentines
PHYSICAL REVIEW LETTERS, 110 Art. No. 105502, MAR 8 2013
abstract, full text, DOI:10.1103/PhysRevLett.110.105502

Karachevtsev, Maksym V.; Gladchenko, Galina O.; Plokhotnichenko, Alexander M.; Leontiev, Victor S.; Karachevtsev, Victor A.
Adsorption of Biopolymers on SWCNT: Ordered Poly(rC) and Disordered Poly(rI)
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2636-2644, MAR 7 2013
abstract, full text, DOI:10.1021/jp311005y

Burney, Patrick R.; Pfaendtner, Jim
Structural and Dynamic Features of Candida rugosa Lipase 1 in Water, Octane, Toluene, and Ionic Liquids BMIM-PF6 and BMIM-NO3
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2662-2670, MAR 7 2013
abstract, full text, DOI:10.1021/jp312299d

Harada, Ryuhei; Tochio, Naoya; Kigawa, Takanori; Sugita, Yuji; Feig, Michael
Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:3696-3701, MAR 6 2013
abstract, full text, DOI:10.1021/ja3126992

Geng, Ruishuang; Sotomayor, Marcos; Kinder, Kimberly J.; Gopal, Suhasini R.; Gerka-Stuyt, John; Chen, Daniel H. -C.; Hardisty-Hughes, Rachel E.; Ball, Greg; Parker, Andy; Gaudet, Rachelle; Furness, David; Brown, Steve D.; Corey, David P.; Alagramam, Kumar N.
Noddy, a Mouse Harboring a Missense Mutation in Protocadherin-15, Reveals the Impact of Disrupting a Critical Interaction Site between Tip-Link Cadherins in Inner Ear Hair Cells
JOURNAL OF NEUROSCIENCE, 33:4395-4404, MAR 6 2013
abstract, full text, DOI:10.1523/JNEUROSCI.4514-12.2013

Stock, Leticia; Souza, Caio; Treptow, Werner
Structural Basis for Activation of Voltage-Gated Cation Channels
BIOCHEMISTRY, 52:1501-1513, MAR 5 2013
abstract, full text, DOI:10.1021/bi3013017

Mahdavi, Somayeh; Kuyucak, Serdar
Why the Drosophila Shaker K+ Channel Is Not a Good Model for Ligand Binding to Voltage-Gated Kv1 Channels
BIOCHEMISTRY, 52:1631-1640, MAR 5 2013
abstract, full text, DOI:10.1021/bi301257p

Mijajlovic, Milan; Penna, Matthew J.; Biggs, Mark J.
Free Energy of Adsorption for a Peptide at a Liquid/Solid Interface via Nonequilibrium Molecular Dynamics
LANGMUIR, 29:2919-2926, MAR 5 2013
abstract, full text, DOI:10.1021/la3047966

de la Iglesia, Diana; Garcia-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Victor
The Impact of Computer Science in Molecular Medicine: Enabling High-Throughput Research
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 13:526-575, MAR 2013
abstract, full text

Hsiao, Chiaolong; Lenz, Timothy K.; Peters, Jessica K.; Fang, Po-Yu; Schneider, Dana M.; Anderson, Eric J.; Preeprem, Thanawadee; Bowman, Jessica C.; O'Neill, Eric B.; Lie, Lively; Athavale, Shreyas S.; Gossett, J. Jared; Trippe, Catherine; Murray, Jason; Petrov, Anton S.; Wartell, Roger M.; Harvey, Stephen C.; Hud, Nicholas V.; Williams, Loren Dean
Molecular paleontology: a biochemical model of the ancestral ribosome
NUCLEIC ACIDS RESEARCH, 41:3373-3385, MAR 2013
abstract, full text, DOI:10.1093/nar/gkt023

Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klaerner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian
Molecular tweezers modulate 14-3-3 protein-protein interactions
NATURE CHEMISTRY, 5:234-239, MAR 2013
abstract, full text, DOI:10.1038/NCHEM.1570

Jin, Albert J.; Lafer, Eileen M.; Peng, Jennifer Q.; Smith, Paul D.; Nossal, Ralph
Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy
METHODS, 59:316-327, MAR 1 2013
abstract, full text, DOI:10.1016/j.ymeth.2012.12.006

Zhang, Xu; Xia, Mengdie; Li, Yang; Liu, Huihui; Jiang, Xin; Ren, Wenlin; Wu, Jianping; DeCaen, Paul; Yu, Feng; Huang, Sheng; He, Jianhua; Clapham, David E.; Yan, Nieng; Gong, Haipeng
Analysis of the selectivity filter of the voltage-gated sodium channel NavRh
CELL RESEARCH, 23:409-422, MAR 2013
abstract, full text, DOI:10.1038/cr.2012.173

Thibault, Julien C.; Facelli, Julio C.; Cheatham, Thomas E., I.I.I.
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:726-736, MAR 2013
abstract, full text, DOI:10.1021/ci300524j

Rashid, M. Harunur; Mahdavi, Somayeh; Kuyucak, Serdar
Computational Studies of Marine Toxins Targeting Ion Channels
MARINE DRUGS, 11:848-869, MAR 2013
abstract, full text, DOI:10.3390/md11030848

Mehrbod, Mehrdad; Mofrad, Mohammad R. K.
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002948, MAR 2013
abstract, full text, DOI:10.1371/journal.pcbi.1002948

Paasche, Alexander; Schirmeister, Tanja; Engels, Bernd
Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1765-1777, MAR 2013
abstract, full text, DOI:10.1021/ct301082y

Gracia, Eduard; Farre, Daniel; Cortes, Antoni; Ferrer-Costa, Carles; Orozco, Modesto; Mallol, Josefa; Lluis, Carme; Canela, Enric I.; McCormick, Peter J.; Franco, Rafael; Fanelli, Francesca; Casado, Vicent
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors
FASEB JOURNAL, 27:1048-1061, MAR 2013
abstract, full text, DOI:10.1096/fj.12-212621

Galaz, Sebastian; Morales-Quintana, Luis; Alejandra Moya-Leon, Maria; Herrera, Raul
Structural analysis of the alcohol acyltransferase protein family from Cucumismelo shows that enzyme activity depends on an essential solvent channel
FEBS JOURNAL, 280:1344-1357, MAR 2013
abstract, full text, DOI:10.1111/febs.12127

Wu, Qing-Yun; Li, Feng; Guo, Hua-Yan; Cao, Jiang; Chen, Chong; Chen, Wei; Zeng, Ling-Yu; Li, Zhen-Yu; Wang, Xiao-Yun; Xu, Kai-Lin
Disrupting of E79 and K138 interaction is responsible for human muscle creatine kinase deficiency diseases
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 54:216-224, MAR 2013
abstract, full text, DOI:10.1016/j.ijbiomac.2012.12.034

Gao, Yi; Olsen, Kenneth W.
Molecular Dynamics of Drug Crystal Dissolution: Simulation of Acetaminophen Form I in Water
MOLECULAR PHARMACEUTICS, 10:905-917, MAR 2013
abstract, full text, DOI:10.1021/mp4000212

Chang, Chia M.; Jalbout, Abraham F.
Theoretical Design of Free Radical "Sponges" in DNA
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 10:591-593, MAR 2013
abstract, full text, DOI:10.1166/jctn.2013.2739

Atkinson, Sarah C.; Dogovski, Con; Downton, Matthew T.; Czabotar, Peter E.; Dobson, Renwick C. J.; Gerrard, Juliet A.; Wagner, John; Perugini, Matthew A.
Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition
PLANT MOLECULAR BIOLOGY, 81:431-446, MAR 2013
abstract, full text, DOI:10.1007/s11103-013-0014-7

Morris, Kyle L.; Rodger, Alison; Hicks, Matthew R.; Debulpaep, Maya; Schymkowitz, Joost; Rousseau, Frederic; Serpell, Louise C.
Exploring the sequence-structure relationship for amyloid peptides
BIOCHEMICAL JOURNAL, 450:275-283, MAR 1 2013
abstract, full text, DOI:10.1042/BJ20121773

Escaffre, Olivier; Le Nouen, Cyril; Amelot, Michel; Ambroggio, Xavier; Ogden, Kristen M.; Guionie, Olivier; Toquin, Didier; Mueller, Hermann; Islam, Mohammed R.; Eterradossi, Nicolas
Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus
JOURNAL OF VIROLOGY, 87:2767-2780, MAR 2013
abstract, full text, DOI:10.1128/JVI.02360-12

Mifsud, John; Ravaud, Stephanie; Krammer, Eva-Maria; Chipot, Chris; Kunji, Edmund R. S.; Pebay-Peyroula, Eva; Dehez, Francois
The substrate specificity of the human ADP/ATP carrier AAC1
MOLECULAR MEMBRANE BIOLOGY, 30:160-168, MAR 2013
abstract, full text, DOI:10.3109/09687688.2012.745175

Buck, Patrick M.; Kumar, Sandeep; Singh, Satish K.
Insights into the potential aggregation liabilities of the b12 Fab fragment via elevated temperature molecular dynamics
PROTEIN ENGINEERING DESIGN & SELECTION, 26:195-205, MAR 2013
abstract, full text, DOI:10.1093/protein/gzs099

Ward, Katherine E.; Bhardwaj, Nitin; Vora, Mohsin; Chalfant, Charles E.; Lu, Hui; Stahelin, Robert V.
The molecular basis of ceramide-1-phosphate recognition by C2 domains
JOURNAL OF LIPID RESEARCH, 54:636-648, MAR 2013
abstract, full text, DOI:10.1194/jlr.M031088

Xin, Yong-Ning; Zhao, Yuqi; Lin, Zhong-Hua; Jiang, Xiangjun; Xuan, Shi-Ying; Huang, Jingfei
Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:406-414, MAR 2013
abstract, full text, DOI:10.1002/prot.24199

Lei, Dongsheng; Zhang, Xing; Jiang, Shengbo; Cai, Zhaodi; Rames, Matthew J.; Zhang, Lei; Ren, Gang; Zhang, Shengli
Structural features of cholesteryl ester transfer protein: A molecular dynamics simulation study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:415-425, MAR 2013
abstract, full text, DOI:10.1002/prot.24200

Wang, Xiaoling; Kumar, Sandeep; Buck, Patrick M.; Singh, Satish K.
Impact of deglycosylation and thermal stress on conformational stability of a full length murine igG2a monoclonal antibody: Observations from molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:443-460, MAR 2013
abstract, full text, DOI:10.1002/prot.24202

Olson, Mark A.; Lee, Michael S.
Structure refinement of protein model decoys requires accurate side-chain placement
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:469-478, MAR 2013
abstract, full text, DOI:10.1002/prot.24204

Amaro, Mariana; Kubiak-Ossowska, Karina; Birch, David J. S.; Rolinski, Olaf J.
Initial stages of beta-amyloid A beta(1-40) and A beta(1-42) oligomerization observed using fluorescence decay and molecular dynamics analyses of tyrosine
METHODS AND APPLICATIONS IN FLUORESCENCE, 1, MAR 1 2013
abstract, full text, DOI:10.1088/2050-6120/1/1/015006

Song, Hyun Deok; Beck, Thomas L.
Temperature Dependence of Gramicidin Channel Transport and Structure
JOURNAL OF PHYSICAL CHEMISTRY C, 117:3701-3712, FEB 28 2013
abstract, full text, DOI:10.1021/jp305557s

Cerutti, David S.; Rice, Julia E.; Swope, William C.; Case, David A.
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2328-2338, FEB 28 2013
abstract, full text, DOI:10.1021/jp311851r

Karatasos, K.
Self-Association and Complexation of the Anti-Cancer Drug Doxorubicin with PEGylated Hyperbranched Polyesters in an Aqueous Environment
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2564-2575, FEB 28 2013
abstract, full text, DOI:10.1021/jp312125c

Kang, Seung-gu; Tien Huynh; Xia, Zhen; Zhang, Yi; Fang, Haiping; Wei, Guanghong; Zhou, Ruhong
Hydrophobic Interaction Drives Surface-Assisted Epitaxial Assembly of Amyloid-like Peptides
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:3150-3157, FEB 27 2013
abstract, full text, DOI:10.1021/ja310989u

Gonzalez, Wendy; Zuniga, Leandro; Cid, L. Pablo; Arevalo, Barbara; Niemeyer, Maria Isabel; Sepulveda, Francisco V.
An Extracellular Ion Pathway Plays a Central Role in the Cooperative Gating of a K-2P K+ Channel by Extracellular pH
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:5984-5991, FEB 22 2013
abstract, full text, DOI:10.1074/jbc.M112.445528

Takemura, Kazuhiro; Burri, Raghunadha Reddy; Ishikawa, Takeshi; Ishikura, Takakazu; Sakuraba, Shun; Matubayasi, Nobuyuki; Kuwata, Kazuo; Kitao, Akio
Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation
CHEMICAL PHYSICS LETTERS, 559:94-98, FEB 20 2013
abstract, full text, DOI:10.1016/j.cplett.2012.12.063

Ricci, Maria; Spijker, Peter; Stellacci, Francesco; Molinari, Jean-Francois; Voitchovsky, Kislon
Direct Visualization of Single Ions in the Stern Layer of Calcite
LANGMUIR, 29:2207-2216, FEB 19 2013
abstract, full text, DOI:10.1021/la3044736

Ren, Shukun; Sato, Ryoichi; Hasegawa, Koji; Ohta, Hiroyuki; Masuda, Shinji
A Predicted Structure for the PixD-PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study
BIOCHEMISTRY, 52:1272-1279, FEB 19 2013
abstract, full text, DOI:10.1021/bi301004v

GhattyVenkataKrishna, Pavan K.; Alekozai, Emal M.; Beckham, Gregg T.; Schulz, Roland; Crowley, Michael F.; Uberbacher, Edward C.; Cheng, Xiaolin
Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity
BIOPHYSICAL JOURNAL, 104:904-912, FEB 19 2013
abstract, full text, DOI:10.1016/j.bpj.2012.12.052

Soto-Liebe, Katia; Lopez-Cortes, Xaviera A.; Jose Fuentes-Valdes, Juan; Stucken, Karina; Gonzalez-Nilo, Fernando; Vasquez, Monica
In Silico Analysis of Putative Paralytic Shellfish Poisoning Toxins Export Proteins in Cyanobacteria
PLOS ONE, 8 Art. No. e55664, FEB 15 2013
abstract, full text, DOI:10.1371/journal.pone.0055664

Cai Wensheng; Chipot, Christophe
Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems
ACTA CHIMICA SINICA, 71:159-168, FEB 15 2013
abstract, full text, DOI:10.6023/A12110930

Surdutovich, Eugene; Yakubovich, Alexander V.; Solov'yov, Andrey V.
Biodamage via shock waves initiated by irradiation with ions
SCIENTIFIC REPORTS, 3 Art. No. 1289, FEB 15 2013
abstract, full text, DOI:10.1038/srep01289

Zimnicka, Magdalena; Chung, Thomas W.; Moss, Christopher L.; Turecek, Frantisek
Perturbing Peptide Cation-Radical Electronic States by Thioxoamide Groups: Formation, Dissociations, and Energetics of Thioxopeptide Cation-Radicals
JOURNAL OF PHYSICAL CHEMISTRY A, 117:1265-1275, FEB 14 2013
abstract, full text, DOI:10.1021/jp305865q

Peters, Gunther H.; Wang, Chunhua; Cruys-Bagger, Nicolaj; Velardez, Gustavo F.; Madsen, Jesper J.; Westh, Peter
Binding of Serotonin to Lipid Membranes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2164-2171, FEB 13 2013
abstract, full text, DOI:10.1021/ja306681d

Mowrey, David; Cheng, Mary Hongying; Liu, Lu Tian; Willenbring, Dan; Lu, Xinghua; Wymore, Troy; Xu, Yan; Tang, Pei
Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2172-2180, FEB 13 2013
abstract, full text, DOI:10.1021/ja307275v

Gumbart, James C.; Teo, Ivan; Roux, Benoit; Schulten, Klaus
Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane-Protein Insertion
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2291-2297, FEB 13 2013
abstract, full text, TCBG publications, DOI:10.1021/ja310777k

Krems, Matt; Di Ventra, Massimiliano
Ionic Coulomb blockade in nanopores
JOURNAL OF PHYSICS-CONDENSED MATTER, 25 Art. No. 065101, FEB 13 2013
abstract, full text, DOI:10.1088/0953-8984/25/6/065101

Liang, Guizhao; Zhao, Jun; Yu, Xiang; Zheng, Jie
Comparative Molecular Dynamics Study of Human Islet Amyloid Polypeptide (IAPP) and Rat IAPP Oligomers
BIOCHEMISTRY, 52:1089-1100, FEB 12 2013
abstract, full text, DOI:10.1021/bi301525e

Corry, Ben
Na+/Ca2+ selectivity in the bacterial voltage-gated sodium channel NavAb
PEERJ, 1 Art. No. e16, FEB 12 2013
abstract, full text, DOI:10.7717/peerj.16

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Generalized Born forces: Surface integral formulation
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 054112, FEB 7 2013
abstract, full text, DOI:10.1063/1.4789537

Hilder, Tamsyn A.; Chung, Shin-Ho
Conduction and Block of Inward Rectifier K+ Channels: Predicted Structure of a Potent Blocker of Kir2.1
BIOCHEMISTRY, 52:967-974, FEB 5 2013
abstract, full text, DOI:10.1021/bi301498x

Yang, Li; Ahmed, Alauddin; Sandler, Stanley I.
Comparison of two simulation methods to compute solvation free energies and partition coefficients
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:284-293, FEB 5 2013
abstract, full text, DOI:10.1002/jcc.23127

Popov, Alexander V.; Vorobjev, Yury N.; Zharkov, Dmitry O.
MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:319-325, FEB 5 2013
abstract, full text, DOI:10.1002/jcc.23135

Murphy, Megan K.; Yue, Ling; Pan, Ruimin; Boliar, Saikat; Sethi, Anurag; Tian, Jianhui; Pfafferot, Katja; Karita, Etienne; Allen, Susan A.; Cormier, Emmanuel; Goepfert, Paul A.; Borrow, Persephone; Robinson, James E.; Gnanakaran, S.; Hunter, Eric; Kong, Xiang-Peng; Derdeyn, Cynthia A.
Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth
PLOS PATHOGENS, 9 Art. No. e1003173, FEB 2013
abstract, full text, DOI:10.1371/journal.ppat.1003173

Ferreira, Leonardo G.; dos Santos, Ricardo N.; Andricopulo, Adriano D.
Structure-Based Drug Design Studies on a Series of Aldolase Inhibitors
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 24:201-211, FEB 2013
abstract, full text

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.
A new structural framework for integrating replication protein A into DNA processing machinery
NUCLEIC ACIDS RESEARCH, 41:2313-2327, FEB 2013
abstract, full text, DOI:10.1093/nar/gks1332

Landry, Markita P.; Zou, Xueqing; Wang, Lei; Huang, Wai Mun; Schulten, Klaus; Chemla, Yann R.
DNA target sequence identification mechanism for dimer-active protein complexes
NUCLEIC ACIDS RESEARCH, 41:2416-2427, FEB 2013
abstract, full text, TCBG publications, DOI:10.1093/nar/gks1345

Ciubotaru, Mihai; Trexler, Adam J.; Spiridon, Laurentiu N.; Surleac, Marius D.; Rhoades, Elizabeth; Petrescu, Andrei J.; Schatz, David G.
RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes
NUCLEIC ACIDS RESEARCH, 41:2437-2454, FEB 2013
abstract, full text, DOI:10.1093/nar/gks1294

Guo, Qiang; Goto, Simon; Chen, Yuling; Feng, Boya; Xu, Yanji; Muto, Akira; Himeno, Hyouta; Deng, Haiteng; Lei, Jianlin; Gao, Ning
Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process
NUCLEIC ACIDS RESEARCH, 41:2609-2620, FEB 2013
abstract, full text, DOI:10.1093/nar/gks1256

Witte, Kristina; Olausson, Bjoern E. S.; Walrant, Astrid; Alves, Isabel D.; Vogel, Alexander
Structure and dynamics of the two amphipathic arginine-rich peptides RW9 and RL9 in a lipid environment investigated by solid-state NMR and MD simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:824-833, FEB 2013
abstract, full text, DOI:10.1016/j.bbamem.2012.11.014

Hilder, Tamsyn A.; Chung, Shin-Ho
Conductance properties of the inwardly rectifying channel, Kir3.2: Molecular and Brownian dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:471-478, FEB 2013
abstract, full text, DOI:10.1016/j.bbamem.2012.09.022

Karoulia, Zoi; Papadopoulos, Georgios; Nomikos, Michail; Thanassoulas, Angelos; Papadopoulou, Theodora Choli; Nounesis, George; Kontou, Maria; Stathopoulos, Constantinos; Leonidas, Demetres D.
Studies on the Essential Intramolecular Interaction Between the A1 and A2 Domains of von Willebrand Factor
PROTEIN AND PEPTIDE LETTERS, 20:231-240, FEB 2013
abstract, full text

Thomas, Michael; Jayatilaka, Dylan; Corry, Ben
How does overcoordination create ion selectivity?
BIOPHYSICAL CHEMISTRY, 172:37-42, FEB 2013
abstract, full text, DOI:10.1016/j.bpc.2012.11.005

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Docking and MD study of histamine H4R based on the crystal structure of H1R
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 39:1-12, FEB 2013
abstract, full text, DOI:10.1016/j.jmgm.2012.10.003

Caballero, Julio; Poblete, Horacio; Navarro, Cristell; Alzate-Morales, Jans H.
Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 39:71-78, FEB 2013
abstract, full text, DOI:10.1016/j.jmgm.2012.11.003

Jung, Segun; Schlick, Tamar
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site
NUCLEIC ACIDS RESEARCH, 41:1483-1495, FEB 2013
abstract, full text, DOI:10.1093/nar/gks1302

Koldso, Heidi; Christiansen, Anja B.; Sinning, Steffen; Schiott, Birgit
Comparative Modeling of the Human Monoamine Transporters: Similarities in Substrate Binding
ACS CHEMICAL NEUROSCIENCE, 4:295-309, FEB 2013
abstract, full text, DOI:10.1021/cn300148r

Lane, Thomas J.; Shukla, Diwakar; Beauchamp, Kyle A.; Pande, Vijay S.
To milliseconds and beyond: challenges in the simulation of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 23:58-65, FEB 2013
abstract, full text, DOI:10.1016/j.sbi.2012.11.002

Thomas, Michael; Jayatilaka, Dylan; Corry, Ben
An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002914, FEB 2013
abstract, full text, DOI:10.1371/journal.pcbi.1002914

Sundermann, Uschi; Bravo-Rodriguez, Kenny; Klopries, Stephan; Kushnir, Susanna; Gomez, Hansel; Sanchez-Garcia, Elsa; Schulz, Frank
Enzyme-Directed Mutasynthesis: A Combined Experimental and Theoretical Approach to Substrate Recognition of a Polyketide Synthase
ACS CHEMICAL BIOLOGY, 8:443-450, FEB 2013
abstract, full text, DOI:10.1021/cb300505w

Chen, Rong; Chung, Shin-Ho
Effect of Gating Modifier Toxins on Membrane Thickness: Implications for Toxin Effect on Gramicidin and Mechanosensitive Channels
TOXINS, 5:456-471, FEB 2013
abstract, full text, DOI:10.3390/toxins5020456

Velikonja, Aljaz; Perutkova, Sarka; Gongadze, Ekaterina; Kramar, Peter; Polak, Andraz; Macek-Lebar, Alenka; Iglic, Ales
Monovalent Ions and Water Dipoles in Contact with Dipolar Zwitterionic Lipid Headgroups-Theory and MD Simulations
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 14:2846-2861, FEB 2013
abstract, full text, DOI:10.3390/ijms14022846

Nagagarajan, Shanthi; Xue, Fengtian; MacKerell, Alexander D., Jr.
Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:452-460, FEB 2013
abstract, full text, DOI:10.1021/ci300506y

Wei, Chenyu; Pohorille, Andrew
Permeation of Aldopentoses and Nucleosides Through Fatty Acid and Phospholipid Membranes: Implications to the Origins of Life
ASTROBIOLOGY, 13:177-188, FEB 2013
abstract, full text, DOI:10.1089/ast.2012.0901

Comer, Jeffrey; Chipot, Christophe; Gonzalez-Nilo, Fernando D.
Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:876-882, FEB 2013
abstract, full text, DOI:10.1021/ct300867e

Lapelosa, Mauro; Abrams, Cameron F.
A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1265-1271, FEB 2013
abstract, full text, DOI:10.1021/ct300862j

Mirjalili, Vahid; Feig, Michael
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1294-1303, FEB 2013
abstract, full text, DOI:10.1021/ct300962x

Nemkevich, Alexandra; Spackman, Mark A.; Corry, Ben
Simulations of Guest Transport in Clathrates of Dianin's Compound and Hydroquinone
CHEMISTRY-A EUROPEAN JOURNAL, 19:2676-2684, FEB 2013
abstract, full text, DOI:10.1002/chem.201202035

Grimm, Christiane; Meyer, Thomas; Czapla, Sylvia; Nikolaus, Joerg; Scheidt, Holger A.; Vogel, Alexander; Herrmann, Andreas; Wessig, Pablo; Huster, Daniel; Mueller, Peter
Structure and Dynamics of Molecular Rods in Membranes: Application of a Spin-Labeled Rod
CHEMISTRY-A EUROPEAN JOURNAL, 19:2703-2710, FEB 2013
abstract, full text, DOI:10.1002/chem.201202500

Hofheinz, Katharina; Kakularam, Kumar Reddy; Adel, Susan; Anton, Monika; Polymarasetty, Aparoy; Reddanna, Pallu; Kuhn, Hartmut; Horn, Thomas
Conversion of pro-inflammatory murine Alox5 into an anti-inflammatory 15S-lipoxygenating enzyme by multiple mutations of sequence determinants
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 530:40-47, FEB 1 2013
abstract, full text, DOI:10.1016/j.abb.2012.11.015

Wang, Li; Li, Qian; Wu, Lianfeng; Liu, Shengwu; Zhang, Yong; Yang, Xuan; Zhu, Pingping; Zhang, Honglian; Zhang, Kai; Lou, Jizhong; Liu, Pingsheng; Tong, Liang; Sun, Fei; Fan, Zusen
Identification of SERPINB1 As a Physiological Inhibitor of Human Granzyme H
JOURNAL OF IMMUNOLOGY, 190:1319-1330, FEB 1 2013
abstract, full text, DOI:10.4049/jimmunol.1202542

Ballut, Lionel; Sapay, Nicolas; Chautard, Emilie; Imberty, Anne; Ricard-Blum, Sylvie
Mapping of heparin/heparan sulfate binding sites on alpha v beta 3 integrin by molecular docking
JOURNAL OF MOLECULAR RECOGNITION, 26:76-85, FEB 2013
abstract, full text, DOI:10.1002/jmr.2250

Wang, Sha; Zhao, Wei-Jie; Liu, Huihui; Gong, Haipeng; Yan, Yong-Bin
Increasing beta B1-crystallin sensitivity to proteolysis caused by the congenital cataract-microcornea syndrome mutation S129R
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1832:302-311, FEB 2013
abstract, full text, DOI:10.1016/j.bbadis.2012.11.005

Bhatti, Gaurav; Jayanthi, Lakshmi; VandeVord, Pamela; Gebremichael, Yeshitila
Computational investigation of the key factors affecting the second stage activation mechanisms of domain II m-calpain
JOURNAL OF MOLECULAR MODELING, 19:779-792, FEB 2013
abstract, full text, DOI:10.1007/s00894-012-1604-z

Toubar, Rabab A.; Zhmurov, Artem; Barsegov, Valeri; Marx, Kenneth A.
Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:174-194, FEB 1 2013
abstract, full text, DOI:10.1080/07391102.2012.698381

Chaudhari, Sachin Rama; Mogurampelly, Santosh; Suryaprakash, N.
Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 117:1123-1129, JAN 31 2013
abstract, full text, DOI:10.1021/jp310798d

Pester, Oxana; Barrett, Paul J.; Hornburg, Daniel; Hornburg, Philipp; Proebstle, Rasmus; Widmaier, Simon; Kutzner, Christoph; Duerrbaum, Milena; Kapurniotu, Aphrodite; Sanders, Charles R.; Scharnagl, Christina; Langosch, Dieter
The Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix Provides a Rationale for the Sequential Cleavage Mechanism of gamma-Secretase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:1317-1329, JAN 30 2013
abstract, full text, DOI:10.1021/ja3112093

Hsu, Yuan-Hao; Bucher, Denis; Cao, Jian; Li, Sheng; Yang, Sheng-Wei; Kokotos, George; Woods, Virgil L., Jr.; McCammon, J. Andrew; Dennis, Edward A.
Fluoroketone Inhibition of Ca2+-Independent Phospholipase A(2) through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:1330-1337, JAN 30 2013
abstract, full text, DOI:10.1021/ja306490g

Xia, Zhen; Tien Huynh; Ren, Pengyu; Zhou, Ruhong
Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process
PLOS ONE, 8 Art. No. e54620, JAN 29 2013
abstract, full text, DOI:10.1371/journal.pone.0054620

Pal, Somedatta; Bandyopadhyay, Sanjoy
Importance of Protein Conformational Motions and Electrostatic Anchoring Sites on the Dynamics and Hydrogen Bond Properties of Hydration Water
LANGMUIR, 29:1162-1173, JAN 29 2013
abstract, full text, DOI:10.1021/la303959m

Barucha-Kraszewska, Justyna; Kraszewski, Sebastian; Ramseyer, Christophe
Will C-Laurdan Dethrone Laurdan in Fluorescent Solvent Relaxation Techniques for Lipid Membrane Studies?
LANGMUIR, 29:1174-1182, JAN 29 2013
abstract, full text, DOI:10.1021/la304235r

Lin, Yen-Lin; Meng, Yilin; Jiang, Wei; Roux, Benoit
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:1664-1669, JAN 29 2013
abstract, full text, DOI:10.1073/pnas.1214330110

Shaikh, Saher A.; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
BIOCHEMISTRY, 52:569-587, JAN 29 2013
abstract, full text, DOI:10.1021/bi301086x

Kamiya, Motoshi; Kato, Hideaki E.; Ishitani, Ryuichiro; Nureki, Osamu; Hayashi, Shigehiko
Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations
CHEMICAL PHYSICS LETTERS, 556:266-271, JAN 29 2013
abstract, full text, DOI:10.1016/j.cplett.2012.11.066

Saito, Hiroaki; Iwayama, Masashi; Mizukami, Taku; Kang, Jiyoung; Tateno, Masaru; Nagao, Hidemi
Molecular dynamics study on binding free energy of Azurin-Cytochrome c551 complex
CHEMICAL PHYSICS LETTERS, 556:297-302, JAN 29 2013
abstract, full text, DOI:10.1016/j.cplett.2012.12.016

Kim, Sun Young; Colpitts, Che C.; Wiedemann, Gertrud; Jepson, Christina; Rahimi, Mehrieh; Rothwell, Jordan R.; McInnes, Adam D.; Hasebe, Mitsuyasu; Reski, Ralf; Sterenberg, Brian T.; Suh, Dae-Yeon
Physcomitrella PpORS, Basal to Plant Type III Polyketide Synthases in Phylogenetic Trees, Is a Very Long Chain 2 '-Oxoalkylresorcinol Synthase
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:2767-2777, JAN 25 2013
abstract, full text, DOI:10.1074/jbc.M112.430686

Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin
A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences
JOURNAL OF PHYSICAL CHEMISTRY B, 117:750-762, JAN 24 2013
abstract, full text, DOI:10.1021/jp3080578

Wang, Xiaoqing; Hirao, Hajime
ONIOM (DFT:MM) Study of the Catalytic Mechanism of myo-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 117:833-842, JAN 24 2013
abstract, full text, DOI:10.1021/jp312483n

Anastasio, Noelle C.; Gilbertson, Scott R.; Bubar, Marcy J.; Agarkov, Anton; Stutz, Sonja J.; Jeng, Yowjiun; Bremer, Nicole M.; Smith, Thressa D.; Fox, Robert G.; Swinford, Sarah E.; Seitz, Patricia K.; Charendoff, Marc N.; Craft, John W., Jr.; Laezza, Fernanda M.; Watson, Cheryl S.; Briggs, James M.; Cunningham, Kathryn A.
Peptide Inhibitors Disrupt the Serotonin 5-HT2C Receptor Interaction with Phosphatase and Tensin Homolog to Allosterically Modulate Cellular Signaling and Behavior
JOURNAL OF NEUROSCIENCE, 33:1615-1630, JAN 23 2013
abstract, full text, DOI:10.1523/JNEUROSCI.2656-12.2013

Lai, Ying; Diao, Jiajie; Liu, Yanxin; Ishitsuka, Yuji; Su, Zengliu; Schulten, Klaus; Ha, Taekjip; Shin, Yeon-Kyun
Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:1333-1338, JAN 22 2013
abstract, full text, TCBG publications, DOI:10.1073/pnas.1218818110

Liu, Yingting; Zhu, Fangqiang
Collective Diffusion Model for Ion Conduction through Microscopic Channels
BIOPHYSICAL JOURNAL, 104:368-376, JAN 22 2013
abstract, full text, DOI:10.1016/j.bpj.2012.11.3826

Vazquez, Francisco X.; Unger, Vinzenz M.; Voth, Gregory A.
Autoinhibition of Endophilin in Solution via Interdomain Interactions
BIOPHYSICAL JOURNAL, 104:396-403, JAN 22 2013
abstract, full text, DOI:10.1016/j.bpj.2012.12.009

Schkolnik, Gal; Utesch, Tillmann; Zhao, Junjie; Jiang, Shu; Thompson, Matthew K.; Mroginski, Maria-Andrea; Hildebrandt, Peter; Franzen, Stefan
Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics - application of the vibrational Stark effect to understand enzyme kinetics
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 430:1011-1015, JAN 18 2013
abstract, full text, DOI:10.1016/j.bbrc.2012.12.047

Faller, Christina E.; Reilly, Kyle A.; Hills, Ronald D., Jr.; Guvench, Olgun
Peptide Backbone Sampling Convergence with the Adaptive Biasing Force Algorithm
JOURNAL OF PHYSICAL CHEMISTRY B, 117:518-526, JAN 17 2013
abstract, full text, DOI:10.1021/jp309741j

Wang, Jingwen; Zhao, Yuqi; Wang, Yanjie; Huang, Jingfei
Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex
FEBS LETTERS, 587:136-141, JAN 16 2013
abstract, full text, DOI:10.1016/j.febslet.2012.11.001

Imhof, Petra; Zahran, Mai
The Effect of a G:T Mispair on the Dynamics of DNA
PLOS ONE, 8 Art. No. e53305, JAN 15 2013
abstract, full text, DOI:10.1371/journal.pone.0053305

Utesch, Tillmann; Millo, Diego; Ana Castro, Maria; Hildebrandt, Peter; Zebger, Ingo; Andrea Mroginski, Maria
Effect of the Protonation Degree of a Self-Assembled Monolayer on the Immobilization Dynamics of a [NiFe] Hydrogenase
LANGMUIR, 29:673-682, JAN 15 2013
abstract, full text, DOI:10.1021/la303635q

Zhu, Li; Zhong, Xiaowei; Chen, S. R. Wayne; Banavali, Nilesh; Liu, Zheng
Modeling a Ryanodine Receptor N-terminal Domain Connecting the Central Vestibule and the Corner Clamp Region
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:903-914, JAN 11 2013
abstract, full text, DOI:10.1074/jbc.M112.429670

Bagai, Sampada; Sun, Chongbo; Tang, Tian
Potential of Mean Force of Polyethylenimine-Mediated DNA Attraction
JOURNAL OF PHYSICAL CHEMISTRY B, 117:49-56, JAN 10 2013
abstract, full text, DOI:10.1021/jp308132y

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Development and Optimization of a New Force Field for Flexible Aluminosilicates, Enabling Fast Molecular Dynamics Simulations on Parallel Architectures
JOURNAL OF PHYSICAL CHEMISTRY C, 117:503-509, JAN 10 2013
abstract, full text, DOI:10.1021/jp311411b

Uttarwar, Rohan G.; Potoff, Jeffrey; Huang, Yinlun
Study on Interfacial Interaction between Polymer and Nanoparticle in a Nanocoating Matrix: A MARTINI Coarse-Graining Method
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 52:73-82, JAN 9 2013
abstract, full text, DOI:10.1021/ie301228f

Cheng, Jiongjia; Karri, Sashank; Grauffel, Cedric; Wang, Fang; Reuter, Nathalie; Roberts, Mary F.; Wintrode, Patrick L.; Gershenson, Anne
Does Changing the Predicted Dynamics of a Phospholipase C Alter Activity and Membrane Binding?
BIOPHYSICAL JOURNAL, 104:185-195, JAN 8 2013
abstract, full text, DOI:10.1016/j.bpj.2012.11.015

Severin, Philip M. D.; Zou, Xueqing; Schulten, Klaus; Gaub, Hermann E.
Effects of Cytosine Hydroxymethylation on DNA Strand Separation
BIOPHYSICAL JOURNAL, 104:208-215, JAN 8 2013
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2012.11.013

Ziervogel, Brigitte K.; Roux, Benoit
The Binding of Antibiotics in OmpF Porin
STRUCTURE, 21:76-87, JAN 8 2013
abstract, full text, DOI:10.1016/j.str.2012.10.014

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
How Does (E)-2-(Acetamidomethylene)succinate Bind to Its Hydrolase? From the Binding Process to the Final Result
PLOS ONE, 8 Art. No. e53811, JAN 7 2013
abstract, full text, DOI:10.1371/journal.pone.0053811

da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Analysis of the performance of DFT functionals in the study of light emission by oxyluciferin analogs
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 113:45-51, JAN 5 2013
abstract, full text, DOI:10.1002/qua.24014

Hilbers, Florian; Junge, Wolfgang; Sielaff, Hendrik
The Torque of Rotary F-ATPase Can Unfold Subunit Gamma If Rotor and Stator Are Cross-Linked
PLOS ONE, 8 Art. No. e53754, JAN 3 2013
abstract, full text, DOI:10.1371/journal.pone.0053754

Russell, J.; Wang, B.; Patra, N.; Kral, P.
Water Nanodroplets: Molecular Drag and Self-assembly
NANODROPLETS, 18:301-327, 2013
abstract, full text, DOI:10.1007/978-1-4614-9472-0_13

Herbordt, Martin C.
Architecture/Algorithm Codesign of Molecular Dynamics Processors
2013 ASILOMAR CONFERENCE ON SIGNALS, SYSTEMS AND COMPUTERS, 1442-1446, 2013
abstract, full text

Novalbos, Marcos; Gonzalez, Jaime; Otaduy, Miguel Angel; Lopez-Medrano, Alvaro; Sanchez, Alberto
On-Board Multi-GPU Molecular Dynamics
EURO-PAR 2013 PARALLEL PROCESSING, 8097:862-873, 2013
abstract, full text

Balaji, N.; Ramya, L.; Gautham, N.
THE INHERENT STRUCTURE LANDSCAPE OF MET-ENKEPHALIN DETERMINED BY THE MOLS TECHNIQUE
BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE RAMACHANDRAN MAP, 492-502, 2013
abstract, full text

Karachevtsev, M. V.; Gladchenko, G. O.; Karachevtsev, V. A.
Comparison of Poly(rI) and Poly(rA) Adsorption on Carbon Nanotubes
NANOMATERIALS IMAGING TECHNIQUES, SURFACE STUDIES, AND APPLICATIONS, 146:275-290, 2013
full text, DOI:10.1007/978-1-4614-7675-7_19

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.
Study of Nanocomposites of Amino Acids and Organic Polyethers by Means of Mass Spectrometry and Molecular Dynamics Simulation
NANOMATERIALS IMAGING TECHNIQUES, SURFACE STUDIES, AND APPLICATIONS, 146:327-338, 2013
full text, DOI:10.1007/978-1-4614-7675-7_22

Jandt, U.; You, C.; Zhang, Y. H. -P.; Zeng, A. -P.
Compartmentalization and Metabolic Channeling for Multienzymatic Biosynthesis: Practical Strategies and Modeling Approaches
FUNDAMENTALS AND APPLICATION OF NEW BIOPRODUCTION SYSTEMS, 137:41-65, 2013
abstract, full text, DOI:10.1007/10_2013_221

Kannam, Sridhar K.; Downton, Matthew T.; Gunn, Natalie; Kim, Sung Cheol; Rogers, Priscilla R.; Schieber, Christine; Baldauf, Julia S.; Wagner, John M.; Scott, Daniel; Bathgate, Ross; Skafidas, Stan; Harrer, Stefan
Nanosensors for next generation drug screening
MICRO/NANO MATERIALS, DEVICES, AND SYSTEMS, 8923 Art. No. 89230I, 2013
abstract, full text, DOI:10.1117/12.2033737

Driscoll, Michael; Georganas, Evangelos; Koanantakool, Penporn; Solomonik, Edgar; Yelick, Katherine
A Communication-Optimal N-Body Algorithm for Direct Interactions
IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013), 1075-1084, 2013
abstract, full text, DOI:10.1109/IPDPS.2013.108

Morozov, Vitali; Kumaran, Kalyan; Vishwanath, Venkatram; Meng, Jiayuan; Papka, Michael E.
Early Experience on the Blue Gene/Q Supercomputing System
IEEE 27TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS 2013), 1229-1240, 2013
abstract, full text, DOI:10.1109/IPDPS.2013.106

Medeiros, Bruno; Sobral, Joao L.
AOmpLib: An Aspect Library for Large-Scale Multi-Core Parallel Programming
2013 42ND ANNUAL INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP), 270-279, 2013
abstract, full text, DOI:10.1109/ICPP.2013.36

Subramanian, Deepa; Boughter, Christopher T.; Klauda, Jeffery B.; Hammouda, Boualem; Anisimov, Mikhail A.
Mesoscale inhomogeneities in aqueous solutions of small amphiphilic molecules
FARADAY DISCUSSIONS, 167:217-238, 2013
abstract, full text, DOI:10.1039/c3fd00070b

Idrissi, Abdenacer; Oparin, Roman D.; Krishtal, Sergey P.; Krupin, Sergey V.; Vorobiev, Evgeny A.; Frolov, Andrey I.; Dubois, Leo; Kiselev, Mikhail G.
The study of correlations between hydrogen bonding characteristics in liquid, sub- and supercritical methanol. Molecular dynamics simulations and Raman spectroscopy analysis
FARADAY DISCUSSIONS, 167:551-566, 2013
abstract, full text, DOI:10.1039/c3fd00103b

Hurley, Margaret M.; Sellers, Michael S.
Prediction of Protein-Peptide Interactions: Application of the XPairIt API to anthrax lethal factor and substrates
SMART BIOMEDICAL AND PHYSIOLOGICAL SENSOR TECHNOLOGY X, 8719 Art. No. 87190A, 2013
abstract, full text, DOI:10.1117/12.2014767

Guixa-Gonzalez, Ramon; Manuel Ramirez-Anguita, Juan; Kaczor, Agnieszka A.; Selent, Jana
Simulating G Protein-Coupled Receptors in Native-Like Membranes: From Monomers to Oligomers
RECEPTOR-RECEPTOR INTERACTIONS, 117:63-90, 2013
abstract, full text, DOI:10.1016/B978-0-12-408143-7.00004-9

Bertran, Oscar; Curco, David; Zanuy, David; Aleman, Carlos
Atomistic organization and characterization of tube-like assemblies comprising peptide-polymer conjugates: computer simulation studies
FARADAY DISCUSSIONS, 166:59-82, 2013
abstract, full text, DOI:10.1039/c3fd00079f

Lu, Xiuli; Zhang, Yong; Chen, Shuchao; Li, Yang; Jia, Dan; Wang, Weiqi; Gao, Bing; Liu, Hongsheng
Molecular Dynamics Simulation Study on the Mechanism of the Inhibition of ATP Hydrolysis with Inhibitors in Human Papillomavirus Type 18 E1 Helicase
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON COMPUTER, NETWORKS AND COMMUNICATION ENGINEERING (ICCNCE 2013), 30:44-47, 2013
abstract, full text

Chen, Zhiguo; Fu, Yi; Xu, Wenbo; Li, Ming
Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability
MATHEMATICAL PROBLEMS IN ENGINEERING, Art. No. 504183, 2013
abstract, full text, DOI:10.1155/2013/504183

Ugolini, Giovanni S.; Gautieri, Alfonso; Redaelli, Alberto; Soncini, Monica
Structural analysis and ion translocation mechanisms of the muscle-type acetylcholine receptor channel
JOURNAL OF APPLIED BIOMATERIALS & FUNCTIONAL MATERIALS, 11:53-60, 2013
abstract, full text, DOI:10.5301/JABFM.5000148

Giangreco, Francesco; Yamamoto, Eiji; Hirano, Yoshinori; Hodoscek, Milan; Knecht, Volker; di Giosia, Matteo; Calvaresi, Matteo; Zerbetto, Francesco; Yasuoka, Kenji; Narumi, Tetsu; Yasui, Masato; Hoefinger, Siegfried
Common Force Field Thermodynamics of Cholesterol
SCIENTIFIC WORLD JOURNAL, Art. No. 207287, 2013
abstract, full text, DOI:10.1155/2013/207287

Elder, Robert M.; Jayaraman, Arthi
Structure and thermodynamics of ssDNA oligomers near hydrophobic and hydrophilic surfaces
SOFT MATTER, 9:11521-11533, 2013
abstract, full text, DOI:10.1039/c3sm50958c

Zanuy, David; Aleman, Carlos
Resolving the subnanometric structure of ultrathin films of poly(3,4-ethylenedioxythiophene) on steel surfaces: a molecular modeling approach
SOFT MATTER, 9:11634-11644, 2013
abstract, full text, DOI:10.1039/c3sm52477a

Picaud, Fabien; Kraszewski, Sebastian; Ramseyer, Christophe; Balme, Sebastien; Dejardin, Philippe; Janot, Jean Marc; Henn, Francois
Enhanced potassium selectivity in a bioinspired solid nanopore
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:19601-19607, 2013
abstract, full text, DOI:10.1039/c3cp52123k

Lopez-Perez, Daniel E.; Revilla-Lopez, Guillermo; Hamley, I. W.; Aleman, Carlos
Molecular insights into aggregates made of amphiphilic Fmoc-tetrapeptides
SOFT MATTER, 9:11021-11032, 2013
abstract, full text, DOI:10.1039/c3sm51826d

Palese, Luigi Leonardo
Protein Dynamics: Complex by Itself
COMPLEXITY, 18:48-56, JAN 2013
abstract, full text, DOI:10.1002/cplx.21434

Ozturk, Mehmet Ali
Computational design of a pentapeptide inhibitor for fibroblast growth factor receptor 3b (FGFR3b)
TURKISH JOURNAL OF BIOLOGY, 37:675-682, 2013
abstract, full text, DOI:10.3906/biy-1212-15

Podolska, N. I.; Zhmakin, A. I.
Water flow in micro- and nanochannels. Molecular dynamics simulations.
15TH RUSSIAN YOUTH CONFERENCE ON PHYSICS AND ASTRONOMY (PHYSICA.SPB), 461 Art. No. UNSP 012034, 2013
abstract, full text, DOI:10.1088/1742-6596/461/1/012034

D'Agostino, Daniele; Clematis, Andrea; Quarati, Alfonso; Cesini, Daniele; Chiappori, Federica; Milanesi, Luciano; Merelli, Ivan
Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects
BIOMED RESEARCH INTERNATIONAL, Art. No. 138012, 2013
abstract, full text, DOI:10.1155/2013/138012

Jones, Peter M.; Curmi, Paul M. G.; Valenzuela, Stella M.; George, Anthony M.
Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1
BIOMED RESEARCH INTERNATIONAL, Art. No. 170586, 2013
abstract, full text, DOI:10.1155/2013/170586

LeBard, David N.; Martin, Daniel R.; Lin, Su; Woodbury, Neal W.; Matyushov, Dmitry V.
Protein dynamics to optimize and control bacterial photosynthesis
CHEMICAL SCIENCE, 4:4127-4136, 2013
abstract, full text, DOI:10.1039/c3sc51327k

Lacerda, Lara; Ali-Boucetta, Hanene; Kraszewski, Sebastian; Tarek, Mounir; Prato, Maurizio; Ramseyer, Christophe; Kostarelos, Kostas; Bianco, Alberto
How do functionalized carbon nanotubes land on, bind to and pierce through model and plasma membranes
NANOSCALE, 5:10242-10250, 2013
abstract, full text, DOI:10.1039/c3nr03184e

Wang, Boyang
Direct Generation of Electric Currents from Flowing Neutral Ionic Solutions
SCIENTIFIC WORLD JOURNAL, Art. No. 320427, 2013
abstract, full text, DOI:10.1155/2013/320427

Wu, Ming-Chya; Forbes, Jeffrey G.; Wang, Kuan
Correlated vibrations in ion-pair dynamics in mechanoactivation identify functional domains of force-dependent titin kinase
SOFT MATTER, 9:9897-9906, 2013
abstract, full text, DOI:10.1039/c3sm51539g

Luis, Luis; Luisa Serrano, Maria; Hidalgo, Mariana; Mendoza-Leon, Alexis
Comparative Analyses of the beta-Tubulin Gene and Molecular Modeling Reveal Molecular Insight into the Colchicine Resistance in Kinetoplastids Organisms
BIOMED RESEARCH INTERNATIONAL, Art. No. 843748, 2013
abstract, full text, DOI:10.1155/2013/843748

Bajaj, Chandrajit; Bauer, Benedikt; Bettadapura, Radhakrishna; Vollrath, Antje
NONUNIFORM FOURIER TRANSFORMS FOR RIGID-BODY AND MULTIDIMENSIONAL ROTATIONAL CORRELATIONS
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 35:B821-B845, 2013
abstract, full text, DOI:10.1137/120892386

Pippig, Michael; Potts, Daniel
PARALLEL THREE-DIMENSIONAL NONEQUISPACED FAST FOURIER TRANSFORMS AND THEIR APPLICATION TO PARTICLE SIMULATION
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 35:C411-C437, 2013
abstract, full text, DOI:10.1137/120888478

Paterno, Giuseppe; Warren, Anna J.; Spencer, Jacob; Evans, Gwyndaf; Sakai, Victoria Garcia; Blumberger, Jochen; Cacialli, Franco
Micro-focused X-ray diffraction characterization of high-quality [6,6]-phenyl-C-61-butyric acid methyl ester single crystals without solvent impurities
JOURNAL OF MATERIALS CHEMISTRY C, 1:5619-5623, 2013
abstract, full text, DOI:10.1039/c3tc31075b

Coghlan, S.; Kumaran, K.; Loy, R. M.; Messina, P.; Morozov, V.; Osborn, J. C.; Parker, S.; Riley, K. M.; Romero, N. A.; Williams, T. J.
Argonne applications for the IBM Blue Gene/Q, Mira
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 57 Art. No. 12, JAN-MAR 2013
abstract, full text, DOI:10.1147/JRD.2013.2238371

Lu, Diannan
Accelerating water transport through a charged SWCNT: a molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:14447-14457, 2013
abstract, full text, DOI:10.1039/c3cp51855h

Bochenkova, Anastasia V.; Andersen, Lars H.
Ultrafast dual photoresponse of isolated biological chromophores: link to the photoinduced mode-specific non-adiabatic dynamics in proteins
FARADAY DISCUSSIONS, 163:297-319, 2013
abstract, full text, DOI:10.1039/c3fd20150c

Yin, Xiaohui; Zhao, Lina; Kang, Seung-gu; Pan, Jun; Song, Yan; Zhang, Mingyi; Xing, Gengmei; Wang, Fei; Li, Jingyuan; Zhou, Ruhong; Zhao, Yuliang
Impacts of fullerene derivatives on regulating the structure and assembly of collagen molecules
NANOSCALE, 5:7341-7348, 2013
abstract, full text, DOI:10.1039/c3nr01469j

Huang, Yang; Nam, Kwangho; Westlund, Per-Olof
The water R-1(omega) NMRD profiles of a hydrated protein from molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:14089-14097, 2013
abstract, full text, DOI:10.1039/c3cp51147b

Liang, Xudong; Zu, Yan; Cao, Yan-Ping; Yang, Chun
A dual-scale model for the caveolin-mediated vesiculation
SOFT MATTER, 9:7981-7987, 2013
abstract, full text, DOI:10.1039/c3sm50956g

Muthukumar, Lakshmi; Khare, Rajesh
Molecular Dynamics Simulation of Free Energy of Desorption of Cellohexaose from a Cellulose Crystal Surface
APPLICATIONS OF MOLECULAR MODELING TO CHALLENGES IN CLEAN ENERGY, 1133:1-17, 2013
abstract, full text

Raz, Yoav; Rubinov, Boris; Matmor, Maayan; Rapaport, Hanna; Ashkenasy, Gonen; Miller, Yifat
Effects of mutations in de novo designed synthetic amphiphilic beta-sheet peptides on self-assembly of fibrils
CHEMICAL COMMUNICATIONS, 49:6561-6563, 2013
abstract, full text, DOI:10.1039/c3cc42879f

Xu, Lei; Li, Youyong; Sun, Huiyong; Li, Dan; Hou, Tingjun
Structural basis of the interactions between CXCR4 and CXCL12/SDF-1 revealed by theoretical approaches
MOLECULAR BIOSYSTEMS, 9:2107-2117, 2013
abstract, full text, DOI:10.1039/c3mb70120d

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Transport of nucleosides in the vcCNT facilitated by sodium gradients from molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 9:2142-2153, 2013
abstract, full text, DOI:10.1039/c3mb70126c

Freddolino, Peter L.; Gardner, Kevin H.; Schulten, Klaus
Signaling mechanisms of LOV domains: new insights from molecular dynamics studies
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 12:1158-1170, 2013
abstract, full text, TCBG publications, DOI:10.1039/c3pp25400c

Dreher, Matthieu; Piuzzi, Marc; Turki, Ahmed; Chavent, Matthieu; Baaden, Marc; Ferey, Nicolas; Limet, Sebastien; Raffin, Bruno; Robert, Sophie
Interactive Molecular Dynamics: Scaling up to Large Systems
2013 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 18:20-29, 2013
abstract, full text, DOI:10.1016/j.procs.2013.05.165

Nunez Castillo, Carlos; Lugones, Diego; Franco, Daniel; Luque, Emilio; Collier, Martin
Predictive and distributed routing balancing, an application-aware approach
2013 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 18:179-188, 2013
abstract, full text, DOI:10.1016/j.procs.2013.05.181

Hadri, Bilel; Fahey, Mark
Mining Software Usage with the Automatic Library Tracking Database (ALTD)
2013 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 18:1834-1843, 2013
abstract, full text, DOI:10.1016/j.procs.2013.05.352

Solov'yov, Ilia A.; Solov'yov, Andrey V.
Simulation of nanofractal dynamics with MBN Explorer
INTERNATIONAL CONFERENCE ON DYNAMICS OF SYSTEMS ON THE NANOSCALE (DYSON 2012), 438 Art. No. UNSP 012006, 2013
abstract, full text, DOI:10.1088/1742-6596/438/1/012006

Kamath, Ganesh; Deshmukh, Sanket A.; Baker, Gary A.; Mancini, Derrick C.; Sankaranarayanan, Subramanian K. R. S.
Thermodynamic considerations for solubility and conformational transitions of poly-N-isopropyl-acrylamide
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:12667-12673, 2013
abstract, full text, DOI:10.1039/c3cp44076a

Loh, Jonathan; Ketterhagen, William; Elliott, James
Multiscale Modelling of Pharmaceutical Powders: Macroscopic Behaviour Prediction
POWDERS AND GRAINS 2013, 1542:161-164, 2013
abstract, full text, DOI:10.1063/1.4811892

Kumar, Amit; Chakravarty, Harapriya; Bal, Naresh C.; Balaraju, Tuniki; Jena, Nivedita; Misra, Gauri; Bal, Chandralata; Pieroni, Enrico; Periasamy, Muthu; Sharon, Ashoke
Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization
MOLECULAR BIOSYSTEMS, 9:1949-1957, 2013
abstract, full text, DOI:10.1039/c3mb25588c

Yu, Xiang; Wang, Qiuming; Pan, Qingfen; Zhou, Feimeng; Zheng, Jie
Molecular interactions of Alzheimer amyloid-beta oligomers with neutral and negatively charged lipid bilayers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:8878-8889, 2013
abstract, full text, DOI:10.1039/c3cp44448a

Shukla, Diwakar; Trout, Bernhardt L.
Understanding the Role of Arginine and Citrate as Eluents in Affinity Chromatography
DEVELOPMENTS IN BIOTECHNOLOGY AND BIOPROCESSING, 1125:67-86, 2013
abstract, full text

Homem, Debora Pacheco; Flores, Rogerio, Jr.; Tosqui, Priscilla; Rozada, Thiago de Castro; Basso, Ernani Abicht; Gasparotto, Arquimedes, Jr.; Vicente Seixas, Flavio Augusto
Homology modeling of dihydrofolate reductase from T. gondii bonded to antagonists: molecular docking and molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 9:1308-1315, 2013
abstract, full text, DOI:10.1039/c3mb25530a

Thompson, Damien; Sikora, Mateusz; Szymczak, Piotr; Cieplak, Marek
A multi-scale molecular dynamics study of the assembly of micron-size supraparticles from 30 nm alkyl-coated nanoparticles
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:8132-8143, 2013
abstract, full text, DOI:10.1039/c3cp50523e

Balme, Sebastien; Picaud, Fabien; Kraszewski, Sebastian; Dejardin, Philippe; Janot, Jean Marc; Lepoitevin, Mathilde; Capomanes, Jhon; Ramseyer, Christophe; Henn, Francois
Controlling potassium selectivity and proton blocking in a hybrid biological/solid-state polymer nanoporous membrane
NANOSCALE, 5:3961-3968, 2013
abstract, full text, DOI:10.1039/c3nr00564j

Saito, Hiroaki; Nishimura, Megumi; Takagi, Hiroyuki; Miyakawa, Takeshi; Kawaguchi, Kazutomo; Nagao, Hidemi
Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A
4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU, 1518:633-636, 2013
abstract, full text, DOI:10.1063/1.4794649

Akdag, Ihsan Omur; Ozkirimli, Elif
The Uptake Mechanism of the Cell-Penetrating pVEC Peptide
JOURNAL OF CHEMISTRY, Art. No. 851915, 2013
abstract, full text, DOI:10.1155/2013/851915

Wassman, Christopher D.; Baronio, Roberta; Demir, Oezlem; Wallentine, Brad D.; Chen, Chiung-Kuang; Hall, Linda V.; Salehi, Faezeh; Lin, Da-Wei; Chung, Benjamin P.; Hatfield, G. Wesley; Chamberlin, A. Richard; Luecke, Hartmut; Lathrop, Richard H.; Kaiser, Peter; Amaro, Rommie E.
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
NATURE COMMUNICATIONS, 4 Art. No. 1407, JAN 2013
abstract, full text, DOI:10.1038/ncomms2361

Bhatnagar, Navendu; Kamath, Ganesh; Potoff, Jeffrey J.
Prediction of 1-octanol-water and air-water partition coefficients for nitro-aromatic compounds from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:6467-6474, 2013
abstract, full text, DOI:10.1039/c3cp44284e

Ortoleva, P.; Singharoy, A.; Pankavich, S.
Hierarchical multiscale modeling of macromolecules and their assemblies
SOFT MATTER, 9:4319-4335, 2013
abstract, full text, DOI:10.1039/c3sm50176k

Burkhardt, Jonathan B.; Skelton, Adam A.; Fried, J. R.
The water-channel forming ability of heptapeptide-based anion channels: insights from molecular dynamics simulations
SOFT MATTER, 9:4444-4454, 2013
abstract, full text, DOI:10.1039/c3sm00061c

Kang, Seung-gu; Tien Huynh; Zhou, Ruhong
Metallofullerenol Gd@C-82(OH)(22) distracts the proline-rich-motif from putative binding on the SH3 domain
NANOSCALE, 5:2703-2712, 2013
abstract, full text, DOI:10.1039/c3nr33756a

Pandey, Shubha; Baker, Gary A.; Sze, Leonhard; Pandey, Siddharth; Kamath, Ganesh; Zhao, Hua; Baker, Sheila N.
Ionic liquids containing fluorinated beta-diketonate anions: synthesis, characterization and potential applications
NEW JOURNAL OF CHEMISTRY, 37:909-919, 2013
abstract, full text, DOI:10.1039/c3nj40855h

Moussa, S. G.; Stern, A. C.; Raff, J. D.; Dilbeck, C. W.; Tobias, D. J.; Finlayson-Pitts, B. J.
Experimental and theoretical studies of the interaction of gas phase nitric acid and water with a self-assembled monolayer
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:448-458, 2013
abstract, full text, DOI:10.1039/c2cp42405c

Sezer, Deniz
Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:526-540, 2013
abstract, full text, DOI:10.1039/c2cp42430d

Ormeno, David; Romero, Fernando; Lopez-Fenner, Julio; Avila, Andres; Martinez-Torres, Ataulfo; Parodi, Jorge
Ethanol Reduces Amyloid Aggregation In Vitro and Prevents Toxicity in Cell Lines
ARCHIVES OF MEDICAL RESEARCH, 44:1-7, JAN 2013
abstract, full text, DOI:10.1016/j.arcmed.2012.12.004

Chen, Liao Y.
Glycerol inhibits water permeation through Plasmodium Falciparum aquaglyceroporin
JOURNAL OF STRUCTURAL BIOLOGY, 181:71-76, JAN 2013
abstract, full text, DOI:10.1016/j.jsb.2012.10.007

Lemmin, Thomas; Soto, Cinque S.; Clinthorne, Graham; DeGrado, William F.; Dal Peraro, Matteo
Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002878, JAN 2013
abstract, full text, DOI:10.1371/journal.pcbi.1002878

Pujato, Mario; MacCarthy, Thomas; Fiser, Andras; Bergman, Aviv
The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002865, JAN 2013
abstract, full text, DOI:10.1371/journal.pcbi.1002865

Yu, Hang; Schulten, Klaus
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1002892, JAN 2013
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1002892

Zhang, Liming; Wang, Zunliang; Lu, Zhuoxuan; Shen, He; Huang, Jie; Zhao, Qinghuan; Liu, Min; He, Nongyue; Zhang, Zhijun
PEGylated reduced graphene oxide as a superior ssRNA delivery system
JOURNAL OF MATERIALS CHEMISTRY B, 1:749-755, 2013
abstract, full text, DOI:10.1039/c2tb00096b

Prigozhin, M. B.; Gruebele, M.
Microsecond folding experiments and simulations: a match is made
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:3372-3388, 2013
abstract, full text, DOI:10.1039/c3cp43992e

Rahaman, O.; Melchionna, S.; Laage, D.; Sterpone, F.
The effect of protein composition on hydration dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:3570-3576, 2013
abstract, full text, DOI:10.1039/c3cp44582h

Carlson, James; Baxter, Sarah A.; Dreau, Didier; Nesmelova, Irina V.
The heterodimerization of platelet-derived chemokines
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:158-168, JAN 2013
abstract, full text, DOI:10.1016/j.bbapap.2012.09.010

Zhang, Y. B.; Chen, L. Y.
In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid
BIOPHYSICAL CHEMISTRY, 171:24-30, JAN 2013
abstract, full text, DOI:10.1016/j.bpc.2012.09.004

Moran, Oscar; Grottesi, Alessandro; Chadbum, Andrew J.; Tammaro, Paolo
Parametrisation of the free energy of ATP binding to wild-type and mutant Kir6.2 potassium channels
BIOPHYSICAL CHEMISTRY, 171:76-83, JAN 2013
abstract, full text, DOI:10.1016/j.bpc.2012.10.006

Ferraro, Daniel J.; Bhave, Sandeep R.; Kotipatruni, Rama P.; Hunn, Jeremy C.; Wildman, Scott A.; Hong, Charles; Dadey, David Y. A.; Muhoro, Lincoln K.; Jaboin, Jerry J.; Thotala, Dinesh; Hallahan, Dennis E.
High-throughput identification of putative receptors for cancer-binding peptides using biopanning and microarray analysis
INTEGRATIVE BIOLOGY, 5:342-350, 2013
abstract, full text, DOI:10.1039/c2ib20187a

Wang, Xue; Xu, Fengting; Liu, Jiasen; Gao, Bingquan; Liu, Yanxin; Zhai, Yujia; Ma, Jun; Zhang, Kai; Baker, Timothy S.; Schulten, Klaus; Zheng, Dong; Pang, Hai; Sun, Fei
Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography
PLOS PATHOGENS, 9 Art. No. e1003132, JAN 2013
abstract, full text, TCBG publications, DOI:10.1371/journal.ppat.1003132

Pavan, Giovanni M.; Barducci, Alessandro; Albertazzi, Lorenzo; Parrinello, Michele
Combining metadynamics simulation and experiments to characterize dendrimers in solution
SOFT MATTER, 9:2593-2597, 2013
abstract, full text, DOI:10.1039/c3sm27706b

Pietra, Francesco
On the Pathways for CO Egress from Carboxy Human Cytoglobin. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 10:86-95, JAN 2013
abstract, full text, DOI:10.1002/cbdv.201200374

Sadiq, S. K.; Guixa-Gonzalez, R.; Dainese, E.; Pastor, M.; De Fabritiis, G.; Selent, J.
Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs
CURRENT MEDICINAL CHEMISTRY, 20:22-38, JAN 2013
abstract, full text

Luo, Yun; Jiang, Wei; Yu, Haibo; MacKerell, Alexander D., Jr.; Roux, Benoit
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field
FARADAY DISCUSSIONS, 160:135-149, 2013
abstract, full text, DOI:10.1039/c2fd20068f

Sukenik, Shahar; Sapir, Liel; Gilman-Politi, Regina; Harries, Daniel
Diversity in the mechanisms of cosolute action on biomolecular processes
FARADAY DISCUSSIONS, 160:225-237, 2013
abstract, full text, DOI:10.1039/c2fd20101a

Wiktor, Maciej; Morin, Sebastien; Sass, Hans-Juergen; Kebbel, Fabian; Grzesiek, Stephan
Biophysical and structural investigation of bacterially expressed and engineered CCR5, a G protein-coupled receptor
JOURNAL OF BIOMOLECULAR NMR, 55:79-95, JAN 2013
abstract, full text, DOI:10.1007/s10858-012-9688-4

Arrar, Mehrnoosh; de Oliveira, Cesar Augusto F.; Fajer, Mikolai; Sinko, William; McCammon, J. Andrew
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:18-23, JAN 2013
abstract, full text, DOI:10.1021/ct300896h

Lee, Tai-Sung; Radak, Brian K.; Pabis, Anna; York, Darrin M.
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:153-164, JAN 2013
abstract, full text, DOI:10.1021/ct300703z

Eastman, Peter; Friedrichs, Mark S.; Chodera, John D.; Radmer, Randall J.; Bruns, Christopher M.; Ku, Joy P.; Beauchamp, Kyle A.; Lane, Thomas J.; Wang, Lee-Ping; Shukla, Diwakar; Tye, Tony; Houston, Mike; Stich, Timo; Klein, Christoph; Shirts, Michael R.; Pande, Vijay S.
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:461-469, JAN 2013
abstract, full text, DOI:10.1021/ct300857j

Lemmin, Thomas; Bovigny, Christophe; Lancon, Diane; Dal Peraro, Matteo
Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:670-678, JAN 2013
abstract, full text, DOI:10.1021/ct300590v

Gumbart, James C.; Roux, Benoit; Chipot, Christophe
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:794-802, JAN 2013
abstract, full text, DOI:10.1021/ct3008099

Grebner, Christoph; Kaestner, Johannes; Thiel, Walter; Engels, Bernd
A New Tabu-Search-Based Algorithm for Solvation of Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:814-821, JAN 2013
abstract, full text, DOI:10.1021/ct300898d

Jang, Hyunbum; Connelly, Laura; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Mechanisms for the Insertion of Toxic, Fibril-like beta-Amyloid Oligomers into the Membrane
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:822-833, JAN 2013
abstract, full text, DOI:10.1021/ct300916f

Jain, Vipin; Hilton, Benjamin; Lin, Bin; Patnaik, Satyakam; Liang, Fengting; Darian, Eva; Zou, Yue; MacKerell, Alexander D., Jr.; Cho, Bongsup P.
Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor
NUCLEIC ACIDS RESEARCH, 41:869-880, JAN 2013
abstract, full text, DOI:10.1093/nar/gks1077

Fawcett, Timothy M.; Irausquin, Stephanie J.; Simin, Mikhail; Valafar, Homayoun
An artificial neural network approach to improving the correlation between protein energetics and the backbone structure
PROTEOMICS, 13:230-238, JAN 2013
abstract, full text, DOI:10.1002/pmic.201200330

Zanuy, David; Teixeira-Dias, Bruno; del Valle, Luis J.; Poater, Jordi; Sola, Miquel; Aleman, Carlos
Examining the formation of specific interactions between poly(3,4-ethylenedioxythiophene) and nucleotide bases
RSC ADVANCES, 3:2639-2649, 2013
abstract, full text, DOI:10.1039/c2ra22640e

Goncalves, Marcos Brown; Dreyer, Jens; Lupieri, Paola; Barrera-Patino, Claudia; Ippoliti, Emiliano; Webb, Martin R.; Corrie, John E. T.; Carloni, Paolo
Structural prediction of a rhodamine-based biosensor and comparison with biophysical data
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:2177-2183, 2013
abstract, full text, DOI:10.1039/c2cp42396k

Grouzmann, Eric; Gualtierotti, Jean-Baptiste; Gerber-Lemaire, Sandrine; Abid, Karim; Brakch, Noureddine; Pedretti, Alessandro; Testa, Bernard; Vistoli, Giulio
Lack of Enantioselectivity in the SULT1A3-catalyzed Sulfoconjugation of Normetanephrine Enantiomers: An In Vitro and Computational Study
CHIRALITY, 25:28-34, JAN 2013
abstract, full text, DOI:10.1002/chir.22108

Textor, Larissa C.; Colussi, Francieli; Silveira, Rodrigo L.; Serpa, Viviane; de Mello, Bruno L.; Muniz, Joao Renato C.; Squina, Fabio M.; Pereira, Nei, Jr.; Skaf, Munir S.; Polikarpov, Igor
Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I from Trichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity
FEBS JOURNAL, 280:56-69, JAN 2013
abstract, full text, DOI:10.1111/febs.12049

Arias, Hugo R.; Fedorov, Nikolai B.; Benson, Lisa C.; Lippiello, Patrick M.; Gatto, Greg J.; Feuerbach, Dominik; Ortells, Marcelo O.
Functional and Structural Interaction of (-)-Reboxetine with the Human alpha 4 beta 2 Nicotinic Acetylcholine Receptor
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 344:113-123, JAN 2013
abstract, full text, DOI:10.1124/jpet.112.197905

Tillman, Tommy; Cheng, Mary H.; Chen, Qiang; Tang, Pei; Xu, Yan
Reversal of ion-charge selectivity renders the pentameric ligand-gated ion channel GLIC insensitive to anaesthetics
BIOCHEMICAL JOURNAL, 449:61-68, JAN 1 2013
abstract, full text, DOI:10.1042/BJ20121072

Swift, Robert V.; Amaro, Rommie E.
Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?
CHEMICAL BIOLOGY & DRUG DESIGN, 81:61-71, JAN 2013
abstract, full text, DOI:10.1111/cbdd.12074

Elgabarty, Hossam; Schmieder, Peter; Sebastiani, Daniel
Unraveling the existence of dynamic water channels in light-harvesting proteins: alpha-C-phycocyanobilin in vitro
CHEMICAL SCIENCE, 4:755-763, 2013
abstract, full text, DOI:10.1039/c2sc21145a

Cui, Ying-Lu; Zhang, Ji-Long; Zheng, Qing-Chuan; Niu, Rui-Juan; Xu, Yu; Zhang, Hong-Xing; Sun, Chia-Chung
Structural and Dynamic Basis of Human Cytochrome P4507B1: A Survey of Substrate Selectivity and Major Active Site Access Channels
CHEMISTRY-A EUROPEAN JOURNAL, 19:548-556, JAN 2013
abstract, full text, DOI:10.1002/chem.201202627

Halder, Puspita; Taraphder, Srabani
Modeling the structure and proton transfer pathways of the mutant His-107-Tyr of human carbonic anhydrase II
JOURNAL OF MOLECULAR MODELING, 19:289-298, JAN 2013
abstract, full text, DOI:10.1007/s00894-012-1549-2

Liu, Yingting; Agrawal, Neeraj J.; Radhakrishnan, Ravi
A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3 beta, and CDK2/Cyclin A protein kinases
JOURNAL OF MOLECULAR MODELING, 19:371-382, JAN 2013
abstract, full text, DOI:10.1007/s00894-012-1555-4

Davis, Brittny C.; Thorpe, Ian F.
Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:40-52, JAN 2013
abstract, full text, DOI:10.1002/prot.24154

Romanowska, Julia; Reuter, Nathalie; Trylska, Joanna
Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:63-80, JAN 2013
abstract, full text, DOI:10.1002/prot.24163

Li, Yongle; Guo, Hua
Atomistic simulations of an antimicrobial molecule interacting with a model bacterial membrane
THEORETICAL CHEMISTRY ACCOUNTS, 132 Art. No. 1303, JAN 2013
abstract, full text, DOI:10.1007/s00214-012-1303-y

Wan, Hua; Hu, Jian-ping; Tian, Xu-hong; Chang, Shan
Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:1241-1251, 2013
abstract, full text, DOI:10.1039/c2cp41388d

Jana, Asis K.; Jose, Jaya C.; Sengupta, Neelanjana
Critical roles of key domains in complete adsorption of A beta peptide on single-walled carbon nanotubes: insights with point mutations and MD simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:837-844, 2013
abstract, full text, DOI:10.1039/c2cp42933k

Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Halperin, Avraham; Kroeger, Martin; Aleman, Carlos
Computer simulation of dendronized polymers: organization and characterization at the atomistic level
RSC ADVANCES, 3:126-140, 2013
abstract, full text, DOI:10.1039/c2ra22034b

Thiele, Daniela; Kraszewski, Sebastian; Balme, Sebastien; Picaud, Fabien; Janot, Jean-Marc; Dejardin, Philippe
Structure and ionic selectivity of a hybrid polyene/artificial polymer solid state membrane
SOFT MATTER, 9:684-691, 2013
abstract, full text, DOI:10.1039/c2sm26703a

Qiu, Wanzhi; Thanh Cong Nguyen; Skafidas, Efstratios
Detection of Weak Nano-biosensor Signals Corrupted by Shot Noise
2013 13TH IEEE CONFERENCE ON NANOTECHNOLOGY (IEEE-NANO), 305-310, 2013
abstract, full text

Krommydas, Konstantinos; Scogland, Thomas R. W.; Feng, Wu-chun
On the Programmability and Performance of Heterogeneous Platforms
2013 19TH IEEE INTERNATIONAL CONFERENCE ON PARALLEL AND DISTRIBUTED SYSTEMS (ICPADS 2013), 224-231, 2013
abstract, full text, DOI:10.1109/ICPADS.2013.41

Zhuang, Yu; Rajagopalan, R.; Hase, William L.; Lourderaj, Upakarasamy
A Load-Balancing Force Decomposition Scheme for Parallel Simulation of Chemical Dynamics with Multiple Inter-Atomic Force Models
2013 IEEE 16TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE AND ENGINEERING (CSE 2013), 15-19, 2013
abstract, full text, DOI:10.1109/CSE.2013.13

Niu, Jin; Bai, Shuju; Khosravi, Ebrahim; Park, Seung-Jong
A Hadoop Approach to Advanced Sampling Algorithms in Molecular Dynamics Simulation on Cloud Computing
2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM), , 2013
abstract, full text

Kunaseth, Manaschai; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya
A Scalable Parallel Algorithm for Dynamic Range-Limited n-Tuple Computation in Many-Body Molecular Dynamics Simulation
2013 INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC), DOI:10.1145/2503210.2503235, 2013
abstract, full text, DOI:10.1145/2503210.2503235

Ni, Xiang; Meneses, Esteban; Jain, Nikhil; Kale, Laxmikant V.
ACR: Automatic Checkpoint/Restart for Soft and Hard Error Protection
2013 INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC), DOI:10.1145/2503210.2503266, 2013
abstract, full text, DOI:10.1145/2503210.2503266

Pishkenari, H. Nejat; Mahboobi, S. H.; Mahjour, M. A.; Meghdari, A.
SIMULATION OF BIOMANIPULATION USING MOLECULAR DYNAMICS
INTERNATIONAL MECHANICAL ENGINEERING CONGRESS AND EXPOSITION - 2012, VOL 9, PTS A AND B, 137-143, 2013
abstract, full text

Caballero, Julio
Receptor-Guided Structure-Activity Modeling of Inhibitors of Juvenile Hormone Epoxide Hydrolases
JUVENILE HORMONES AND JUVENOIDS: MODELING BIOLOGICAL EFFECTS AND ENVIRONMENTAL FATE, 267-289, 2013
abstract, full text

Knizhnik, Andrei Aleksandrovich; Minkin, Aleksandr Sergeevich; Potapkin, B.V.
Implementation properties of many-body potentials on heteroheneous computing systems
Mathematical Models and Computer Simulations, 25:123-136, 2013
full text

Rabinovich, A.L.; Lyubartsev, A.P.
COMPUTER SIMULATION OF LIPID MEMBRANES: METHODOLOGY AND ACHIEVEMENTS
Polymer Science Series A, 55:971-989, 2013
abstract, full text, DOI:10.7868/S050754751307012X

Zhang, Ning; Chen, Cong; Feng, Yujing; Pang, Qingnan; Li, Weizhong
Molecular Dynamics Simulation of the Hydrogen Bonding Structure of Water Molecules inside Carbon Nanotube
PROCEEDINGS OF THE 11TH INTERNATIONAL CONFERENCE ON NANOCHANNELS, MICROCHANNELS, AND MINICHANNELS, 2013, Art. No. V001T12A002, 2013
abstract, full text

Khrenova, M.G.; Polyakov, I.V.; Grigorenko, B.L.; Nemukhin, A...V.
Molecular Model of the Light Harvesting Complex LH1 of the Bacterial Photosynthetic Center of Thermochromatium tepidum
Vestnik Moskovskogo universiteta. Seriya 2: Khimiya, 54:78-80, 2013
abstract, full text

Cho, Kang R.; Salter, E. Alan; De Yoreo, James J.; Wierzbicki, Andrzej; Elhadj, Selim; Huang, Yu; Qiu, S. Roger
Growth inhibition of calcium oxalate monohydrate crystal by linear aspartic acid enantiomers investigated by in situ atomic force microscopy
CRYSTENGCOMM, 15:54-64, 2013
abstract, full text, DOI:10.1039/c2ce25936b

Witkowski, M.; Oleksiak, A.; Piontek, T.; Weglarz, J.
Practical power consumption estimation for real life HPC applications
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 29:208-217, JAN 2013
abstract, full text, DOI:10.1016/j.future.2012.06.003

Causa, F.; Della Moglie, R.; Iaccino, E.; Mimmi, S.; Marasco, D.; Scognamiglio, P. L.; Battista, E.; Palmieri, C.; Cosenza, C.; Sanguigno, L.; Quinto, I.; Scala, G.; Netti, P. A.
Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 389:220-229, JAN 1 2013
abstract, full text, DOI:10.1016/j.jcis.2012.08.046

Votapka, Lane W.; Czapla, Luke; Zhenirovskyy, Maxim; Amaro, Rommie E.
DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 13:256-268, JAN 2013
abstract, full text, DOI:10.4208/cicp.170711.111111s

Isin, Basak; Estiu, Guillermina; Wiest, Olaf; Oltvai, Zoltan N.
Identifying Ligand Binding Conformations of the beta 2-Adrenergic Receptor by Using Its Agonists as Computational Probes
PLOS ONE, 7 Art. No. e50186, DEC 31 2012
abstract, full text, DOI:10.1371/journal.pone.0050186

Yamaguchi, Yoshiki; Nishima, Wataru; Re, Suyong; Sugita, Yuji
Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 26:2877-2884, DEC 30 2012
abstract, full text, DOI:10.1002/rcm.6412

Grauffel, Cedric; Abboud, Angele; Liszczak, Glen; Marmorstein, Ronen; Arnesen, Thomas; Reuter, Nathalie
Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
PLOS ONE, 7 Art. No. e52642, DEC 28 2012
abstract, full text, DOI:10.1371/journal.pone.0052642

Edens, Lance E.; Brozik, James A.; Keller, David J.
Coarse-Grained Model DNA: Structure, Sequences, Stems, Circles, Hairpins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14735-14743, DEC 27 2012
abstract, full text, DOI:10.1021/jp3009095

Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A.; Mostofian, Barmak; Kucerka, Norbert; Drazba, Paul; Katsaras, John
Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14829-14838, DEC 27 2012
abstract, full text, DOI:10.1021/jp310345j

Cembran, Alessandro; Masterson, Larry R.; McClendon, Christopher L.; Taylor, Susan S.; Gao, Jiali; Veglia, Gianluigi
Conformational Equilibrium of N-Myristoylated cAMP-Dependent Protein Kinase A by Molecular Dynamics Simulations
BIOCHEMISTRY, 51:10186-10196, DEC 25 2012
abstract, full text, DOI:10.1021/bi301279f

Sodt, Alexander J.; Pastor, Richard W.
The tension of a curved surface from simulation
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 234101, DEC 21 2012
abstract, full text, DOI:10.1063/1.4769880

Sahu, Bhavani S.; Obbineni, Jagan M.; Sahu, Giriraj; Allu, Prasanna K. R.; Subramanian, Lakshmi; Sonawane, Parshuram J.; Singh, Pradeep K.; Sasi, Binu K.; Senapati, Sanjib; Maji, Samir K.; Bera, Amal K.; Gomathi, Balashankar S.; Mullasari, Ajit S.; Mahapatra, Nitish R.
Functional Genetic Variants of the Catecholamine-Release-Inhibitory Peptide Catestatin in an Indian Population ALLELE-SPECIFIC EFFECTS ON METABOLIC TRAITS
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:43840-43852, DEC 21 2012
abstract, full text, DOI:10.1074/jbc.M112.407916

Kotsyubynskyy, Dmytro; Zerbetto, Mirco; Soltesova, Maria; Engstrom, Olof; Pendrill, Robert; Kowalewski, Jozef; Widmalm, Goran; Polimeno, Antonin
Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14541-14555, DEC 20 2012
abstract, full text, DOI:10.1021/jp306627q

Gaborek, Timothy J.; Chipot, Christophe; Madura, Jeffry D.
Conformational Free-Energy Landscapes for a Peptide in Saline Environments
BIOPHYSICAL JOURNAL, 103:2513-2520, DEC 19 2012
abstract, full text, DOI:10.1016/j.bpj.2012.11.001

Kitam, Volodymyr O.; Maksymchuk, Oksana V.; Chashchyn, Mykola O.
The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them
BMC STRUCTURAL BIOLOGY, 12 Art. No. 33, DEC 17 2012
abstract, full text, DOI:10.1186/1472-6807-12-33

Turecek, Frantisek; Moss, Christopher L.; Chung, Thomas W.
Correlating ETD fragment ion intensities with peptide ion conformational and electronic structure
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 330:207-219, DEC 15 2012
abstract, full text, DOI:10.1016/j.ijms.2012.08.001

Saito, Hiroaki; Iwayama, Masashi; Takagi, Hiroyuki; Nishimura, Megumi; Miyakawa, Takeshi; Kawaguchi, Kazutomo; Takasu, Masako; Mizukami, Taku; Nagao, Hidemi
Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:3834-3839, DEC 15 2012
abstract, full text, DOI:10.1002/qua.24248

Strunk, T.; Wolf, M.; Brieg, M.; Klenin, K.; Biewer, A.; Tristram, F.; Ernst, M.; Kleine, P. J.; Heilmann, N.; Kondov, I.; Wenzel, W.
SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2602-2613, DEC 15 2012
abstract, full text, DOI:10.1002/jcc.23089

Barakat, Khaled H.; Jordheim, Lars P.; Perez-Pineiro, Rolando; Wishart, David; Dumontet, Charles; Tuszynski, Jack A.
Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction
PLOS ONE, 7 Art. No. e51329, DEC 14 2012
abstract, full text, DOI:10.1371/journal.pone.0051329

Miller, Kerry A.; Williams, Louise H.; Rose, Elizabeth; Kuiper, Michael; Dahl, Hans-Henrik M.; Manji, Shehnaaz S. M.
Inner Ear Morphology Is Perturbed in Two Novel Mouse Models of Recessive Deafness
PLOS ONE, 7 Art. No. e51284, DEC 12 2012
abstract, full text, DOI:10.1371/journal.pone.0051284

Rui, Huan; Rivera, Mario; Im, Wonpil
Protein Dynamics and Ion Traffic in Bacterioferritin
BIOCHEMISTRY, 51:9900-9910, DEC 11 2012
abstract, full text, DOI:10.1021/bi3013388

Vargiu, Attilio V.; Nikaido, Hiroshi
Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:20637-20642, DEC 11 2012
abstract, full text, DOI:10.1073/pnas.1218348109

Kang, Seung-gu; Huynh, Tien; Zhou, Ruhong
Non-destructive Inhibition of Metallofullerenol Gd@C-82(OH)(22) on WW domain: Implication on Signal Transduction Pathway
SCIENTIFIC REPORTS, 2 Art. No. 957, DEC 11 2012
abstract, full text, DOI:10.1038/srep00957

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio
Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 215105, DEC 7 2012
abstract, full text, DOI:10.1063/1.4768901

Rippers, Yvonne; Horch, Marius; Hildebrandt, Peter; Zebger, Ingo; Mroginski, Maria Andrea
Revealing the Absolute Configuration of the CO and CN- Ligands at the Active Site of a [NiFe] Hydrogenase
CHEMPHYSCHEM, 13:3852-3856, DEC 7 2012
abstract, full text, DOI:10.1002/cphc.201200562

Modi, Niraj; Benz, Roland; Hancock, Robert E. W.; Kleinekathoefer, Ulrich
Modeling the Ion Selectivity of the Phosphate Specific Channel OprP
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:3639-3645, DEC 6 2012
abstract, full text, DOI:10.1021/jz301637d

Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P.
Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction
NATURE, 492:128-+, DEC 6 2012
abstract, full text, DOI:10.1038/nature11590

Haspel, Nurit; Laurent, Adele D.; Zanuy, David; Nussinov, Ruth; Aleman, Carlos; Puiggali, Jordi; Revilla-Lopez, Guillem
Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities As Self-Aggregating Materials
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13941-13952, DEC 6 2012
abstract, full text, DOI:10.1021/jp3043363

Mula, Sam; McConnell, Michael D.; Ching, Amy; Zhao, Nan; Gordon, Heather L.; Hastings, Gary; Redding, Kevin E.; van der Est, Art
Introduction of a Hydrogen Bond between Phylloquinone PhQ(A) and a Threonine Side-Chain OH Group in Photosystem I
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14008-14016, DEC 6 2012
abstract, full text, DOI:10.1021/jp309410w

Fujimoto, Yukiji K.; Green, David F.
Carbohydrate Recognition by the Antiviral Lectin Cyanovirin-N
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:19639-19651, DEC 5 2012
abstract, full text, DOI:10.1021/ja305755b

Lockhart, Christopher; Klimov, Dmitri K.
Molecular Interactions of Alzheimer's Biomarker FDDNP with A beta Peptide
BIOPHYSICAL JOURNAL, 103:2341-2351, DEC 5 2012
abstract, full text, DOI:10.1016/j.bpj.2012.10.003

Tyka, Michael D.; Jung, Kenneth; Baker, David
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2483-+, DEC 5 2012
abstract, full text, DOI:10.1002/jcc.23069

Kirkpatrick, Andrea; Heo, Jiyoung; Abrol, Ravinder; Goddard, William A., I.I.I.
Predicted structure of agonist-bound glucagon-like peptide 1 receptor, a class B G protein-coupled receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:19988-19993, DEC 4 2012
abstract, full text, DOI:10.1073/pnas.1218051109

Chen, Rong; Robinson, Anna; Chung, Shin-Ho
Binding of Hanatoxin to the Voltage Sensor of Kv2.1
TOXINS, 4:1552-1564, DEC 2012
abstract, full text, DOI:10.3390/toxins4121552

Wu, Qing-Yun; Li, Feng; Guo, Hua-Yan; Cao, Jiang; Chen, Chong; Chen, Wei; Zhao, Kai; Zeng, Ling-Yu; Han, Zheng-Xiang; Li, Zhen-Yu; Wang, Xiao-Yun; Xu, Kai-Lin
Amino acid residue E543 in JAK2 C618R is a potential therapeutic target for myeloproliferative disorders caused by JAK2 C618R mutation
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 528:57-66, DEC 1 2012
abstract, full text, DOI:10.1016/j.abb.2012.08.010

Maienschein-Cline, Mark; Dinner, Aaron R.; Hlavacek, William S.; Mu, Fangping
Improved predictions of transcription factor binding sites using physicochemical features of DNA
NUCLEIC ACIDS RESEARCH, 40 Art. No. e175, DEC 2012
abstract, full text, DOI:10.1093/nar/gks771

Cho, Kang Rae; Salter, E. Alan; De Yoreo, James J.; Wierzbicki, Andrzej; Elhadj, Selim; Huang, Yu; Qiu, S. Roger
Impact of Chiral Molecules on the Formation of Biominerals: A Calcium Oxalate Monohydrate Example
CRYSTAL GROWTH & DESIGN, 12:5939-5947, DEC 2012
abstract, full text, DOI:10.1021/cg3009317

Lacroix, Jerome J.; Pless, Stephan A.; Maragliano, Luca; Campos, Fabiana V.; Galpin, Jason D.; Ahern, Christopher A.; Roux, Benoit; Bezanilla, Francisco
Intermediate state trapping of a voltage sensor
JOURNAL OF GENERAL PHYSIOLOGY, 140:635-652, DEC 2012
abstract, full text, DOI:10.1085/jgp.201210827

Abolbashari, M. H.; Ameli, S.
Mechanical unfolding of titin I27 domain: Nanoscale simulation of mechanical properties based on virial theorem via steered molecular dynamics technique
SCIENTIA IRANICA, 19:1526-1533, DEC 2012
abstract, full text, DOI:10.1016/j.scient.2012.10.022

Mwaura, Juddy; Tao, Zhen; James, Herbert; Albers, Thomas; Schwartz, Alexander; Grewer, Christof
Protonation State of a Conserved Acidic Amino Acid Involved in Na+ Binding to the Glutamate Transporter EAAC1
ACS CHEMICAL NEUROSCIENCE, 3:1073-1083, DEC 2012
abstract, full text, DOI:10.1021/cn300163p

Pietra, Francesco
On 3LEZ, a Deep-Sea Halophilic Protein with in vitro Class-A beta-Lactamase Activity: Molecular-Dynamics, Docking, and Reactivity Simulations
CHEMISTRY & BIODIVERSITY, 9:2659-2684, DEC 2012
abstract, full text, DOI:10.1002/cbdv.201200331

Ferreira-Cerca, Sebastien; Sagar, Vatsala; Schaefer, Thorsten; Diop, Momar; Wesseling, Anne-Maria; Lu, Haiyun; Chai, Eileen; Hurt, Ed; LaRonde-LeBlanc, Nicole
ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 19:1316-+, DEC 2012
abstract, full text, DOI:10.1038/nsmb.2403

Kappel, Kalli; Wereszczynski, Jeff; Clubb, Robert T.; McCammon, J. Andrew
The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations
PROTEIN SCIENCE, 21:1858-1871, DEC 2012
abstract, full text, DOI:10.1002/pro.2168

Gentile, Francesco; Moretti, Manola; Limongi, Tania; Falqui, Andrea; Bertoni, Giovanni; Scarpellini, Alice; Santoriello, Stefania; Maragliano, Luca; Zaccaria, Remo Proietti; di Fabrizio, Enzo
Direct Imaging of DNA Fibers: The Visage of Double Helix
NANO LETTERS, 12:6453-6458, DEC 2012
abstract, full text, DOI:10.1021/nl3039162

Sotomayor-Zarate, Ramon; Quirozi, Gabriel; Araya, Katherine A.; Abarea, Jorge; Ibanez, Maria R.; Montecinos, Alejandro; Guajardo, Carlos; Nunez, Gabriel; Fierro, Angelica; Moya, Pablo R.; Iturriaga-Vasquez, Patricio; Gomez-Molina, Cristobal; Gysling, Katia; Reyes-Parada, Miguel
4-Methylthioamphetamine Increases Dopamine in the Rat Striatum and has Rewarding Effects In Vivo
BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY, 111:371-379, DEC 2012
abstract, full text, DOI:10.1111/j.1742-7843.2012.00926.x

Li, Mai Suan; Binh Khanh Mai
Steered Molecular Dynamics-A Promising Tool for Drug Design
CURRENT BIOINFORMATICS, 7:342-351, DEC 2012
abstract, full text

Shenoy, Siddharth S.; Nanda, Hirsh; Loesche, Mathias
Membrane association of the PTEN tumor suppressor: Electrostatic interaction with phosphatidylserine-containing bilayers and regulatory role of the C-terminal tail
JOURNAL OF STRUCTURAL BIOLOGY, 180:394-408, DEC 2012
abstract, full text, DOI:10.1016/j.jsb.2012.10.003

Venkateshwari, Sureshkumar; Veluraja, Kasinadar
Molecular Modelling and Molecular Dynamics studies of GD1A, GD1B and their complexes with BoNT/B - Perspectives in interaction and specificity
JOURNAL OF STRUCTURAL BIOLOGY, 180:497-508, DEC 2012
abstract, full text, DOI:10.1016/j.jsb.2012.08.003

Salvi, M.; Trashi, E.; Cozza, G.; Franchin, C.; Arrigoni, G.; Pinna, L. A.
Investigation on PLK2 and PLK3 substrate recognition
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1824:1366-1373, DEC 2012
abstract, full text, DOI:10.1016/j.bbapap.2012.07.003

Yogesh, R.; Behera, R. N.
Molecular Dynamics Simulations of Micellization of Alkyl Ethoxylate
ASIAN JOURNAL OF CHEMISTRY, 24:5785-5788, DEC 2012
abstract, full text

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Selectivity and activation of dopamine D3R from molecular dynamics
JOURNAL OF MOLECULAR MODELING, 18:5051-5063, DEC 2012
abstract, full text, DOI:10.1007/s00894-012-1509-x

Srivastava, Amit; Ben Halevi, Roee; Veksler, Alexander; Granek, Rony
Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2692-2700, DEC 2012
abstract, full text, DOI:10.1002/prot.24153

Simonson, Thomas; Satpati, Priyadarshi
Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2742-2757, DEC 2012
abstract, full text, DOI:10.1002/prot.24158

Gur, Mert; Erman, Burak
Quasi-harmonic fluctuations of two bound peptides
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2769-2779, DEC 2012
abstract, full text, DOI:10.1002/prot.24160

Atilgan, Canan; Inanc, Ibrahim; Atilgan, Ali Rana
On modifying properties of polymeric melts by nanoscopic particles
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 50:1653-1662, DEC 1 2012
abstract, full text, DOI:10.1002/polb.23179

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Zhou, Yong; Volk, David E.; Gorenstein, David G.; Dial, Elizabeth; Lichtenberger, Lenard M.; Gorfe, Alemayehu A.
Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:3040-3047, DEC 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.07.029

Zhao, Jun; Luo, Yin; Jang, Hyunbum; Yu, Xiang; Wei, Guanghong; Nussinov, Ruth; Zheng, Jie
Probing ion channel activity of human islet amyloid polypeptide (amylin)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:3121-3130, DEC 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.08.012

Wang, Shen; Tu, Yusong; Wan, Rongzheng; Fang, Haiping
Evaporation of Tiny Water Aggregation on Solid Surfaces with Different Wetting Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13863-13867, NOV 29 2012
abstract, full text, DOI:10.1021/jp302142s

Hansen, F. Y.; Peters, G. H.; Taub, H.; Miskowiec, A.
Diffusion of water and selected atoms in DMPC lipid bilayer membranes
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 204910, NOV 28 2012
abstract, full text, DOI:10.1063/1.4767568

Timko, Jeff; Kuyucak, Serdar
Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 205106, NOV 28 2012
abstract, full text, DOI:10.1063/1.4768247

Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Tame, Jeremy R. H.; Kidera, Akinori
Influence of Structural Symmetry on Protein Dynamics
PLOS ONE, 7 Art. No. e50011, NOV 26 2012
abstract, full text, DOI:10.1371/journal.pone.0050011

Rosenhouse-Dantsker, Avia; Noskov, Sergei; Han, Huazhi; Adney, Scott K.; Tang, Qiong-Yao; Rodriguez-Menchaca, Aldo A.; Kowalsky, Gregory B.; Petrou, Vasileios I.; Osborn, Catherine V.; Logothetis, Diomedes E.; Levitan, Irena
Distant Cytosolic Residues Mediate a Two-way Molecular Switch That Controls the Modulation of Inwardly Rectifying Potassium (Kir) Channels by Cholesterol and Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P-2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:40266-40278, NOV 23 2012
abstract, full text, DOI:10.1074/jbc.M111.336339

San Martin, Loreto; Cerda, Fabian; Jimenez, Veronica; Fuentealba, Jorge; Munoz, Braulio; Aguayo, Luis G.; Guzman, Leonardo
Inhibition of the Ethanol-induced Potentiation of alpha 1 Glycine Receptor by a Small Peptide That Interferes with G beta gamma Binding
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:40713-40721, NOV 23 2012
abstract, full text, DOI:10.1074/jbc.M112.393603

Cheng, Mary Hongying; Coalson, Rob D.
Energetics and Ion permeation Characteristics in a Glutamate-Gated Chloride (GluCl) Receptor Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13637-13643, NOV 22 2012
abstract, full text, DOI:10.1021/jp3074915

Furini, Simone; Domene, Carmen
Nonselective Conduction in a Mutated NaK Channel with Three Cation-Binding Sites
BIOPHYSICAL JOURNAL, 103:2106-2114, NOV 21 2012
abstract, full text, DOI:10.1016/j.bpj.2012.10.004

Miao, Yinglong; Yi, Zheng; Cantrell, Carey; Glass, Dennis C.; Baudry, Jerome; Jain, Nitin; Smith, Jeremy C.
Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 103:2167-2176, NOV 21 2012
abstract, full text, DOI:10.1016/j.bpj.2012.10.013

Collu, Francesca; Vargiu, Attilio V.; Dreier, Juerg; Cascella, Michele; Ruggerone, Paolo
Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:19146-19158, NOV 21 2012
abstract, full text, DOI:10.1021/ja307803m

Lopez de Victoria, Aliana; Tamamis, Phanourios; Kieslich, Chris A.; Morikis, Dimitrios
Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops
PLOS ONE, 7 Art. No. e49925, NOV 19 2012
abstract, full text, DOI:10.1371/journal.pone.0049925

Faure, Elise; Starek, Greg; McGuire, Hugo; Berneche, Simon; Blunck, Rikard
A Limited 4 angstrom Radial Displacement of the S4-S5 Linker Is Sufficient for Internal Gate Closing in Kv Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 287, NOV 16 2012
abstract, full text, DOI:10.1074/jbc.M112.415497

Mayer, Florian; Leone, Vanessa; Langer, Julian D.; Faraldo-Gomez, Jose D.; Mueller, Volker
A c Subunit with Four Transmembrane Helices and One Ion (Na+)-binding Site in an Archaeal ATP Synthase IMPLICATIONS FOR c RING FUNCTION AND STRUCTURE
JOURNAL OF BIOLOGICAL CHEMISTRY, 287, NOV 16 2012
abstract, full text, DOI:10.1074/jbc.M112.411223

Pennington, Michael W.; Rashid, M. Harunur; Tajhya, Rajeev B.; Beeton, Christine; Kuyucak, Serdar; Norton, Raymond S.
A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3
FEBS LETTERS, 586:3996-4001, NOV 16 2012
abstract, full text, DOI:10.1016/j.febslet.2012.09.038

Luan, Binquan; Wang, Deqiang; Zhou, Ruhong; Harrer, Stefan; Peng, Hongbo; Stolovitzky, Gustavo
Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol
NANOTECHNOLOGY, 23 Art. No. 455102, NOV 16 2012
abstract, full text, DOI:10.1088/0957-4484/23/45/455102

Ngo, Van A.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
Molecular Mechanism of Flip-Flop in Triple-Layer Oleic-Acid Membrane: Correlation between Oleic Acid and Water
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13416-13423, NOV 15 2012
abstract, full text, DOI:10.1021/jp307227r

Zhao, Kuiwen; Wu, Huiying
Size Effects of Pore Density and Solute Size on Water Osmosis through Nanoporous Membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13459-13466, NOV 15 2012
abstract, full text, DOI:10.1021/jp3076595

Solov'yov, Ilia A.; Yakubovich, Alexander V.; Nikolaev, Pavel V.; Volkovets, Ilya; Solov'yov, Andrey V.
MesoBioNano exploreruA universal program for multiscale computer simulations of complex molecular structure and dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2412-2439, NOV 15 2012
abstract, full text, DOI:10.1002/jcc.23086

Flatt, Justin W.; Fox, Tara L.; Makarova, Natalia; Blackwell, Jerry L.; Dmitriev, Igor P.; Kashentseva, Elena A.; Curiel, David T.; Stewart, Phoebe L.
CryoEM Visualization of an Adenovirus Capsid-Incorporated HIV Antigen
PLOS ONE, 7 Art. No. e49607, NOV 14 2012
abstract, full text, DOI:10.1371/journal.pone.0049607

Burgess, Don E.; Bartos, Daniel C.; Reloj, Allison R.; Campbell, Kenneth S.; Johnson, Jonathan N.; Tester, David J.; Ackerman, Michael J.; Fressart, Veronique; Denjoy, Isabelle; Guicheney, Pascale; Moss, Arthur J.; Ohno, Seiko; Horie, Minoru; Delisle, Brian P.
High-Risk Long QT Syndrome Mutations in the Kv7.1 (KCNQ1) Pore Disrupt the Molecular Basis for Rapid K+ Permeation
BIOCHEMISTRY, 51:9076-9085, NOV 13 2012
abstract, full text, DOI:10.1021/bi3009449

Pasquino, R.; Zhang, B.; Sigel, R.; Yu, H.; Ottiger, M.; Bertran, O.; Aleman, C.; Schlueter, A. D.; Vlassopoulos, D.
Linear Viscoelastic Response of Dendronized Polymers
MACROMOLECULES, 45:8813-8823, NOV 13 2012
abstract, full text, DOI:10.1021/ma301029t

Navaratnarajah, Chanakha K.; Negi, Surendra; Braun, Werner; Cattaneo, Roberto
Membrane Fusion Triggering THREE MODULES WITH DIFFERENT STRUCTURE AND FUNCTION IN THE UPPER HALF OF THE MEASLES VIRUS ATTACHMENT PROTEIN STALK
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:38543-38551, NOV 9 2012
abstract, full text, DOI:10.1074/jbc.M112.410563

Shim, Joong-Youn; Bertalovitz, Alexander C.; Kendall, Debra A.
Probing the Interaction of SR141716A with the CB1 Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:38741-38754, NOV 9 2012
abstract, full text, DOI:10.1074/jbc.M112.390955

Lai, Chun-Liang; Jao, Christine C.; Lyman, Edward; Gallop, Jennifer L.; Peter, Brian J.; McMahon, Harvey T.; Langen, Ralf; Voth, Gregory A.
Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain
JOURNAL OF MOLECULAR BIOLOGY, 423:800-817, NOV 9 2012
abstract, full text, DOI:10.1016/j.jmb.2012.08.010

Rogaski, Brent; Klauda, Jeffery B.
Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations
JOURNAL OF MOLECULAR BIOLOGY, 423:847-861, NOV 9 2012
abstract, full text, DOI:10.1016/j.jmb.2012.08.015

Zerbetto, Mirco; Kotsyubynskyy, Dmytro; Kowalewski, Jozef; Widmalm, Goran; Polimeno, Antonino
Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. I. Internal Dynamics of Cyclodextrins: gamma-Cyclodextrin as a Case Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13159-13171, NOV 8 2012
abstract, full text, DOI:10.1021/jp306624d

Zhang, Yong; Lou, Jizhong
The Ca2+ Influence on Calmodulin Unfolding Pathway: A Steered Molecular Dynamics Simulation Study
PLOS ONE, 7 Art. No. e49013, NOV 7 2012
abstract, full text, DOI:10.1371/journal.pone.0049013

Andersson, Magnus; Bondar, Ana-Nicoleta; Freites, J. Alfredo; Tobias, Douglas J.; Kaback, H. Ronald; White, Stephen H.
Proton-Coupled Dynamics in Lactose Permease
STRUCTURE, 20:1893-1904, NOV 7 2012
abstract, full text, DOI:10.1016/j.str.2012.08.021

Kubiak-Ossowska, Karina; Mulheran, Paul A.
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
LANGMUIR, 28:15577-15585, NOV 6 2012
abstract, full text, DOI:10.1021/la303323r

Kang, Peng; Qin, Wu; Zheng, Zong-Ming; Dong, Chang-Qing; Yang, Yong-Ping
Theoretical study on the mechanisms of cellulose dissolution and precipitation in the phosphoric acid-acetone process
CARBOHYDRATE POLYMERS, 90:1771-1778, NOV 6 2012
abstract, full text, DOI:10.1016/j.carbpol.2012.07.068

Ceccarini, Luisa; Masetti, Matteo; Cavalli, Andrea; Recanatini, Maurizio
Ion Conduction through the hERG Potassium Channel
PLOS ONE, 7 Art. No. e49017, NOV 2 2012
abstract, full text, DOI:10.1371/journal.pone.0049017

Ghemtio, Leo; Perez-Nueno, Violeta I.; Leroux, Vincent; Asses, Yasmine; Souchet, Michel; Mavridis, Lazaros; Maigret, Bernard; Ritchie, David W.
Recent Trends and Applications in 3D Virtual Screening
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING, 15:749-769, NOV 2012
abstract, full text

Kekenes-Huskey, Peter Michael; Lindert, Steffen; McCammon, James Andrew
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002777, NOV 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002777

Zhang, Dandan; Liu, Guangqiao; Xue, Jiaying; Lou, Jizhong; Nierhaus, Knud H.; Gong, Weimin; Qin, Yan
Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome
NUCLEIC ACIDS RESEARCH, 40:10851-10865, NOV 2012
abstract, full text, DOI:10.1093/nar/gks833

Plsikova, Jana; Janovec, Ladislav; Koval, Jan; Ungvarsky, Jan; Mikes, Jaromir; Jendzelovsky, Rastislav; Fedorocko, Peter; Imrich, Jan; Kristian, Pavol; Kasparkova, Jana; Brabec, Viktor; Kozurkova, Maria
3,6-Bis(3-alkylguanidino)acridines as DNA-intercalating antitumor agents
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 57:283-295, NOV 2012
abstract, full text, DOI:10.1016/j.ejmech.2012.09.020

Simard, Jean; Ammi, Mehdi; Auvray, Malika
Collaborative Strategies for the Search of 3-D Targets in Molecular Environments
IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART C-APPLICATIONS AND REVIEWS, 42:1555-1565, NOV 2012
abstract, full text, DOI:10.1109/TSMCC.2012.2206805

Zheng, Yishan; Gun'ko, Vladimir M.; Howell, Carol A.; Sandeman, Susan R.; Phillips, Gary J.; Kozynchenko, Oleksandr P.; Tennison, Stephen R.; Ivanov, Alexander E.; Mikhalovsky, Sergey V.
Composites with Macroporous Poly(vinyl alcohol) Cryogels with Attached Activated Carbon Microparticles with Controlled Accessibility of a Surface
ACS APPLIED MATERIALS & INTERFACES, 4:5936-5944, NOV 2012
abstract, full text, DOI:10.1021/am301577c

Mohebbi, Ali
Prediction of specific heat and thermal conductivity of nanofluids by a combined equilibrium and non-equilibrium molecular dynamics simulation
JOURNAL OF MOLECULAR LIQUIDS, 175:51-58, NOV 2012
abstract, full text, DOI:10.1016/j.molliq.2012.08.010

Zhao, Hongtao; Huang, Danzhi; Caflisch, Amedeo
Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics
CHEMMEDCHEM, 7:1983-1990, NOV 2012
abstract, full text, DOI:10.1002/cmdc.201200331

Stauch, Benjamin; Orts, Julien; Carlomagno, Teresa
The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method
JOURNAL OF BIOMOLECULAR NMR, 54:245-256, NOV 2012
abstract, full text, DOI:10.1007/s10858-012-9662-1

Wan, Shunzhou; Coveney, Peter V.
Regulation of JAK2 Activation by Janus Homology 2: Evidence from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2992-3000, NOV 2012
abstract, full text, DOI:10.1021/ci300308g

Louet, Maxime; Charlier, Landry; Martinez, Jean; Floquet, Nicolas
Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by G(alpha) Subunit Binding to GTP
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:3022-3027, NOV 2012
abstract, full text, DOI:10.1021/ci3003717

Han, Wei; Schulten, Klaus
Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4413-4424, NOV 2012
abstract, full text, TCBG publications, DOI:10.1021/ct300696c

Piggot, Thomas J.; Pineiro, Angel; Khalid, Syma
Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4593-4609, NOV 2012
abstract, full text, DOI:10.1021/ct3003157

Ruymgaart, A. Peter; Elber, Ron
Revisiting Molecular Dynamics on a CPU/GPU System: Water Kernel and SHAKE Parallelization
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4624-4636, NOV 2012
abstract, full text, DOI:10.1021/ct300324k

Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoit
Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4672-4680, NOV 2012
abstract, full text, DOI:10.1021/ct300468g

Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto
Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4837-4844, NOV 2012
abstract, full text, DOI:10.1021/ct300709u

Lockhart, Christopher; Kim, Seongwon; Klimov, Dmitri K.
Explicit Solvent Molecular Dynamics Simulations of A beta Peptide Interacting with Ibuprofen Ligands
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12922-12932, NOV 1 2012
abstract, full text, DOI:10.1021/jp306208n

Calligari, Paolo; Abergel, Daniel
Toward the Characterization of Fractional Stochastic Processes Underlying Methyl Dynamics in Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12955-12965, NOV 1 2012
abstract, full text, DOI:10.1021/jp307050v

Lin, Po-Hsun; Tsai, Ching-Wei; Wu, Josephine W.; Ruaan, Ruoh-Chyu; Chen, Wen-Yih
Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide
BIOTECHNOLOGY JOURNAL, 7, NOV 2012
abstract, full text, DOI:10.1002/biot.201200003

Unzueta, Ugutz; Ferrer-Miralles, Neus; Cedano, Juan; Xu Zikung; Pesarrodona, Mireia; Saccardo, Paolo; Garcia-Fruitos, Elena; Domingo-Espin, Joan; Kumar, Pradeep; Gupta, Kailash C.; Mangues, Ramon; Villaverde, Antonio; Vazquez, Esther
Non-amyloidogenic peptide tags for the regulatable self-assembling of protein-only nanoparticles
BIOMATERIALS, 33:8714-8722, NOV 2012
abstract, full text, DOI:10.1016/j.biomaterials.2012.08.033

Suplatov, D. A.; Besenmatter, W.; Svedas, V. K.; Svendsen, A.
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities
PROTEIN ENGINEERING DESIGN & SELECTION, 25:689-697, NOV 2012
abstract, full text, DOI:10.1093/protein/gzs068

Defonsi Lestard, Maria E.; Diaz, Sonia B.; Tuttolomondo, Maria E.; Sanchez Cortez, Santiago; Puiatti, Marcelo; Pierini, Adriana B.; Ben Altabef, Aida
Interaction of S-methyl methanethiosulfonate with DPPC bilayer
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 97:479-489, NOV 2012
abstract, full text, DOI:10.1016/j.saa.2012.06.045

Liu, Hong-Mei; Roberts, Jason A.; Moore, Deborah; Anderson, Barbara; Pallansch, Mark A.; Pevear, Daniel C.; Collett, Marc S.; Oberste, M. Steven
Characterization of Poliovirus Variants Selected for Resistance to the Antiviral Compound V-073
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56:5568-5574, NOV 2012
abstract, full text, DOI:10.1128/AAC.00539-12

Tuszynski, Jack A.; Craddock, Travis J. A.; Mane, Jonathan Y.; Barakat, Khaled; Tseng, Chih-Yuan; Gajewski, Melissa; Winter, Philip; Alisaraie, Laleh; Patterson, Jordan; Carpenter, Eric; Wang, Weiwei; Deyholos, Michael K.; Li, Linji; Sun, Xiao; Zhang, Yong; Wong, Gane Ka-Shu
Modeling the Yew Tree Tubulin and a Comparison of its Interaction with Paclitaxel to Human Tubulin
PHARMACEUTICAL RESEARCH, 29:3007-3021, NOV 2012
abstract, full text, DOI:10.1007/s11095-012-0829-y

Nandi, Tapas K.; Bairagya, Hridoy R.; Mishra, Deepak K.; Mukhopadhyay, Bishnu P.; Banerjee, Avik
Structural and Putative Functional Role of Conserved Water Molecular Cluster in the X-ray Structures of Plant Thiol Proteases: A Molecular Dynamics Simulation Study
JOURNAL OF CHEMICAL CRYSTALLOGRAPHY, 42:1105-1118, NOV 2012
abstract, full text, DOI:10.1007/s10870-012-0364-z

del Val, Coral; White, Stephen H.; Bondar, Ana-Nicoleta
Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics
JOURNAL OF MEMBRANE BIOLOGY, 245:717-730, NOV 2012
abstract, full text, DOI:10.1007/s00232-012-9452-4

Lee, C. J.; Wu, S.; Bartolotti, L. J.; Pedersen, L. G.
Molecular dynamic simulations of the binary complex of human tissue factor (TF1-242) and factor VIIa (TF1-242/FVIIa) on a 4:1 POPC/POPS lipid bilayer
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 10:2402-2405, NOV 2012
full text, DOI:10.1111/j.1538-7836.2012.04920.x

Broadley, Simon Gareth; Gumbart, James Conrad; Weber, Brandon William; Marakalala, Mohlopheni Jackson; Steenkamp, Daniel Jacobus; Sewell, Bryan Trevor
A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 68:1450-1459, NOV 2012
abstract, full text, DOI:10.1107/S090744491203449X

Caulfield, Thomas; Devkota, Batsal
Motion of transfer RNA from the A/T state into the A-site using docking and simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2489-2500, NOV 2012
abstract, full text, DOI:10.1002/prot.24131

Losasso, Valeria; Schiffer, Sonja; Barth, Stefan; Carloni, Paolo
Design of human granzyme B variants resistant to serpin B9
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2514-2522, NOV 2012
abstract, full text, DOI:10.1002/prot.24133

Qiu, Hu; Shen, Rong; Guo, Wanlin
Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2529-2535, NOV 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.06.003

Tsai, Hui-Hsu Gavin; Lai, Wei-Xiang; Lin, Hong-Da; Lee, Jian-Bin; Juang, Wei-Fu; Tseng, Wen-Hsin
Molecular dynamics simulation of cation-phospholipid clustering in phospholipid bilayers: Possible role in stalk formation during membrane fusion
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2742-2755, NOV 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.05.029

Kraszewski, Sebastian; Picaud, Fabien; Elhechmi, Imen; Gharbi, Tijani; Ramseyer, Christophe
How long a functionalized carbon nanotube can passively penetrate a lipid membrane
CARBON, 50:5301-5308, NOV 2012
abstract, full text, DOI:10.1016/j.carbon.2012.07.018

Paris, Guillaume; Kraszewski, Sebastian; Ramseyer, Christophe; Enescu, Mironel
About the structural role of disulfide bridges in serum albumins: Evidence from protein simulated unfolding
BIOPOLYMERS, 97:889-898, NOV 2012
abstract, full text, DOI:10.1002/bip.22096

Bellacchio, Emanuele
In silico analysis of the two tandem somatomedin B domains of ENPP1 reveals hints on the homodimerization of the protein
JOURNAL OF CELLULAR PHYSIOLOGY, 227:3566-3574, NOV 2012
abstract, full text, DOI:10.1002/jcp.24058

Solov'yov, Ilia A.; Domratcheva, Tatiana; Shahi, Abdul Rehaman Moughal; Schulten, Klaus
Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:18046-18052, OCT 31 2012
abstract, full text, TCBG publications, DOI:10.1021/ja3074819

Khafizov, Kamil; Perez, Camilo; Koshy, Caroline; Quick, Matthias; Fendler, Klaus; Ziegler, Christine; Forrest, Lucy R.
Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E3035-E3044, OCT 30 2012
abstract, full text, DOI:10.1073/pnas.1209039109

Marek, Peter J.; Patsalo, Vadim; Green, David F.; Raleigh, Daniel P.
Ionic Strength Effects on Amyloid Formation by Amylin Are a Complicated Interplay among Debye Screening, Ion Selectivity, and Hofmeister Effects
BIOCHEMISTRY, 51:8478-8490, OCT 30 2012
abstract, full text, DOI:10.1021/bi300574r

Nikolova, Evgenia N.; Bascom, Gavin D.; Andricioaei, Ioan; Al-Hashimi, Hashim M.
Probing Sequence-Specific DNA Flexibility in A-Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance C-13 Relaxation and Molecular Dynamics Simulations
BIOCHEMISTRY, 51:8654-8664, OCT 30 2012
abstract, full text, DOI:10.1021/bi3009517

Tam, Hok Hei; Asthagiri, Dilip; Paulaitis, Michael E.
Coordination state probabilities and the solvation free energy of Zn2+ in aqueous methanol solutions
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 164504, OCT 28 2012
abstract, full text, DOI:10.1063/1.4759452

Das, Debasis; Samanta, Dibyendu; Hasan, Salman; Das, Anindita; Bhattacharya, Arpita; Dasgupta, Santanu; Chakrabarti, Abhijit; Ghorai, Pradip; Das Gupta, Chanchal
Identical RNA-Protein Interactions in Vivo and in Vitro and a Scheme of Folding the Newly Synthesized Proteins by Ribosomes
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:37508-37521, OCT 26 2012
abstract, full text, DOI:10.1074/jbc.M112.396127

Remi Rodriguez-Rodriguez, Everardo; Ledezma-Candanoza, Luis M.; Gabriel Contreras-Ferrat, Luis; Olamendi-Portugal, Timoteo; Possani, Lourival D.; Becerril, Baltazar; Riano-Umbarila, Lidia
A Single Mutation in Framework 2 of the Heavy Variable Domain Improves the Properties of a Diabody and a Related Single-Chain Antibody
JOURNAL OF MOLECULAR BIOLOGY, 423:337-350, OCT 26 2012
abstract, full text, DOI:10.1016/j.jmb.2012.07.007

Favia, Angelo D.; Habrant, Damien; Scarpelli, Rita; Migliore, Marco; Albani, Clara; Bertozzi, Sine Mandrup; Dionisi, Mauro; Tarozzo, Glauco; Piomelli, Daniele; Cavalli, Andrea; De Vivo, Marco
Identification and Characterization of Carprofen as a Multitarget Fatty Acid Amide Hydrolase/Cyclooxygenase Inhibitor
JOURNAL OF MEDICINAL CHEMISTRY, 55:8807-8826, OCT 25 2012
abstract, full text, DOI:10.1021/jm3011146

Banas, Pavel; Sklenovsky, Petr; Wedekind, Joseph E.; Sponer, Jiri; Otyepka, Michal
Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12721-12734, OCT 25 2012
abstract, full text, DOI:10.1021/jp309230v

Interlandi, Gianluca; Ling, Minhua; Tu, An Yue; Chung, Dominic W.; Thomas, Wendy E.
Structural Basis of Type 2A von Willebrand Disease Investigated by Molecular Dynamics Simulations and Experiments
PLOS ONE, 7 Art. No. e45207, OCT 23 2012
abstract, full text, DOI:10.1371/journal.pone.0045207

Hill, Eric H.; Stratton, Kelly; Whitten, David G.; Evans, Deborah G.
Molecular Dynamics Simulation Study of the Interaction of Cationic Biocides with Lipid Bilayers: Aggregation Effects and Bilayer Damage
LANGMUIR, 28:14849-14854, OCT 23 2012
abstract, full text, DOI:10.1021/la303158c

Abderemane-Ali, Fayal; Es-Salah-Lamoureux, Zeineb; Delemotte, Lucie; Kasimova, Marina A.; Labro, Alain J.; Snyders, Dirk J.; Fedida, David; Tarek, Mounir; Baro, Isabelle; Loussouarn, Gildas
Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP2 on Shaker K+ Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:36158-36167, OCT 19 2012
abstract, full text, DOI:10.1074/jbc.M112.382085

Payne, Christina M.; Baban, Jamil; Horn, Svein J.; Backe, Paul H.; Arvai, Andrew S.; Dalhus, Bjorn; Bjoras, Magnar; Eijsink, Vincent G. H.; Sorlie, Morten; Beckham, Gregg T.; Vaaje-Kolstad, Gustav
Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:36322-36330, OCT 19 2012
abstract, full text, DOI:10.1074/jbc.M112.402149

Laurent, Adele D.; Mironov, Vladimir A.; Chapagain, Prem P.; Nemukhin, Alexander V.; Krylov, Anna I.
Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12426-12440, OCT 18 2012
abstract, full text, DOI:10.1021/jp3060944

Fisette, Olivier; Gagne, Stephane; Laguee, Patrick
Molecular Dynamics of Class A beta-lactamases-Effects of Substrate Binding
BIOPHYSICAL JOURNAL, 103:1790-1801, OCT 17 2012
abstract, full text, DOI:10.1016/j.bpj.2012.09.009

Gkionis, Konstantinos; Rungger, Ivan; Sanvito, Stefano; Schwingenschloegl, Udo
Protocol for classical molecular dynamics simulations of nano-junctions in solution
JOURNAL OF APPLIED PHYSICS, 112 Art. No. 083714, OCT 15 2012
abstract, full text, DOI:10.1063/1.4759291

Hadi-Alijanvand, Hamid; Proctor, Elizabeth A.; Goliaei, Bahram; Dokholyan, Nikolay V.; Moosavi-Movahedi, Ali A.
Thermal Unfolding Pathway of PHD2 Catalytic Domain in Three Different PHD2 Species: Computational Approaches
PLOS ONE, 7 Art. No. e47061, OCT 15 2012
abstract, full text, DOI:10.1371/journal.pone.0047061

Ylilauri, Mikko; Pentikainen, Olli T.
Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism
PLOS ONE, 7 Art. No. e47604, OCT 15 2012
abstract, full text, DOI:10.1371/journal.pone.0047604

Florencia Martini, M.; Pickholz, Monica
Molecular dynamics study of uncharged bupivacaine enantiomers in phospholipid bilayers
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:3341-3345, OCT 15 2012
abstract, full text, DOI:10.1002/qua.24208

Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M.; Gain, James
Efficient compression of molecular dynamics trajectory files
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2131-2141, OCT 15 2012
abstract, full text, DOI:10.1002/jcc.23050

El-Hendawy, Morad M.; Garate, Jose-Antonio; English, Niall J.; O'Reilly, Stephen; Mooney, Damian A.
Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 145103, OCT 14 2012
abstract, full text, DOI:10.1063/1.4757021

Jover, J.; Haslam, A. J.; Galindo, A.; Jackson, G.; Mueller, E. A.
Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 144505, OCT 14 2012
abstract, full text, DOI:10.1063/1.4754275

Yu, Cong; Lou, Jizhong; Wu, Jingjing; Pan, Lifeng; Feng, Wei; Zhang, Mingjie
Membrane-induced Lever Arm Expansion Allows Myosin VI to Walk with Large and Variable Step Sizes
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:35021-35035, OCT 12 2012
abstract, full text, DOI:10.1074/jbc.M111.328781

Dillon, Stephanie L.; Williamson, Danielle M.; Elferich, Johannes; Radler, David; Joshi, Rajendra; Thomas, Gary; Shinde, Ujwal
Propeptides Are Sufficient to Regulate Organelle-Specific pH-Dependent Activation of Furin and Proprotein Convertase 1/3
JOURNAL OF MOLECULAR BIOLOGY, 423:47-62, OCT 12 2012
abstract, full text, DOI:10.1016/j.jmb.2012.06.023

Giambasu, George M.; Lee, Tai-Sung; Scott, William G.; York, Darrin M.
Mapping L1 Ligase Ribozyme Conformational Switch
JOURNAL OF MOLECULAR BIOLOGY, 423:106-122, OCT 12 2012
abstract, full text, DOI:10.1016/j.jmb.2012.06.035

Zhao, Junjie; de Serrano, Vesna; Dumarieh, Rania; Thompson, Matt; Ghiladi, Reza A.; Franzen, Stefan
The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12065-12077, OCT 11 2012
abstract, full text, DOI:10.1021/jp300014b

Canchi, Deepak R.; Jayasimha, Pruthvi; Rau, Donald C.; Makhatadze, George I.; Garcia, Angel E.
Molecular Mechanism for the Preferential Exclusion of TMAO from Protein Surfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12095-12104, OCT 11 2012
abstract, full text, DOI:10.1021/jp304298c

Liu, Yingzhe; Wu, Ming; Feng, Xizeng; Shao, Xueguang; Cai, Wensheng
Adsorption Behavior of Hydrophobin Proteins on Polydimethylsiloxane Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12227-12234, OCT 11 2012
abstract, full text, DOI:10.1021/jp304796p

Chen, Rong; Chung, Shin-Ho
Structural Basis of the Selective Block of Kv1.2 by Maurotoxin from Computer Simulations
PLOS ONE, 7 Art. No. e47253, OCT 10 2012
abstract, full text, DOI:10.1371/journal.pone.0047253

Deng, Lu; Broom, Aron; Kitova, Elena N.; Richards, Michele R.; Zheng, Ruixiang Blake; Shoemaker, Glen K.; Meiering, Elizabeth M.; Klassen, John S.
Kinetic Stability of the Streptavidin-Biotin Interaction Enhanced in the Gas Phase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:16586-16596, OCT 10 2012
abstract, full text, DOI:10.1021/ja305213z

Larue, Ross; Gupta, Kushol; Wuensch, Christiane; Shkriabai, Nikolozi; Kessl, Jacques J.; Danhart, Eric; Feng, Lei; Taltynov, Oliver; Christ, Frauke; Van Duyne, Gregory D.; Debyser, Zeger; Foster, Mark P.; Kvaratskhelia, Mamuka
Interaction of the HIV-1 Intasome with Transportin 3 Protein (TNPO3 or TRN-SR2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:34044-34058, OCT 5 2012
abstract, full text, DOI:10.1074/jbc.M112.384669

Priyadarzini, Thanu R. K.; Selvin, Jeyasigamani F. A.; Gromiha, M. Michael; Fukui, Kazuhiko; Veluraja, Kasinadar
Theoretical Investigation on the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza A Virus by Molecular Dynamics Simulations
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:34547-34557, OCT 5 2012
abstract, full text, DOI:10.1074/jbc.M112.357061

Shen, Rong; Guo, Wanlin
Mechanism for Variable Selectivity and Conductance in Mutated NaK Channels
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2887-2891, OCT 4 2012
abstract, full text, DOI:10.1021/jz301225d

Koyama, Michio; Nishimasu, Hiroshi; Ishitani, Ryuichiro; Nureki, Osamu
Molecular Dynamics Simulation of Autotaxin: Roles of the Nuclease-like Domain and the Glycan Modification
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11798-11808, OCT 4 2012
abstract, full text, DOI:10.1021/jp303198u

Halder, Sukanya; Bhattacharyya, Dhananjay
Structural Variations of Single and Tandem Mismatches in RNA Duplexes: A Joint MD Simulation and Crystal Structure Database Analysis
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11845-11856, OCT 4 2012
abstract, full text, DOI:10.1021/jp305628v

Averett, Rodney D.; Menn, Bryant; Lee, Eric H.; Helms, Christine C.; Barker, Thomas; Guthold, Martin
A Modular Fibrinogen Model that Captures the Stress-Strain Behavior of Fibrin Fibers
BIOPHYSICAL JOURNAL, 103:1537-1544, OCT 3 2012
abstract, full text, DOI:10.1016/j.bpj.2012.08.038

Khelashvili, George; Galli, Aurelio; Weinstein, Harel
Phosphatidylinositol 4,5-Biphosphate (PIP2) Lipids Regulate the Phosphorylation of Syntaxin N-Terminus by Modulating Both Its Position and Local Structure
BIOCHEMISTRY, 51:7685-7698, OCT 2 2012
abstract, full text, DOI:10.1021/bi300833z

Chen, Rong; Chung, Shin-Ho
Binding Modes and Functional Surface of Anti-mammalian Scorpion alpha-Toxins to Sodium Channels
BIOCHEMISTRY, 51:7775-7782, OCT 2 2012
abstract, full text, DOI:10.1021/bi300776g

Shaitan, K. V.; Sokolova, O. S.; Shaitan, A. K.; Kasimova, M. A.; Novoseletsky, V. N.; Kirpichnikov, M. P.
INFLUENCE OF INTERIONIC INTERACTIONS ON FUNCTIONAL STATE OF KV CHANNELS AND ON BLOCKER BINDING
Vestnik Moskovskogo Universiteta Seriya 16 Biologiya, Issue 4, 17-23, OCT-NOV 2012
abstract, full text

Sencanski, Milan V.; Sukalovic, Vladimir B.; Dosen-Micovic, Ljiljana I.; Soskic, Vukic; Andric, Deana B.; Roglic, Goran M.; Kostic-Rajacic, Sladjana V.
MODELING INTERACTIONS OF alpha(1A) ADRENERGIC RECEPTOR AND DIFFERENT ARYLPIPERAZINE LIGANDS
DIGEST JOURNAL OF NANOMATERIALS AND BIOSTRUCTURES, 7:1767-1777, OCT-DEC 2012
abstract, full text

Hilder, Tamsyn A.; Pace, Ron J.; Chung, Shin-Ho
Computational Design of a Carbon Nanotube Fluorofullerene Biosensor
SENSORS, 12:13720-13735, OCT 2012
abstract, full text, DOI:10.3390/s121013720

Montero-Alejo, V.; Acosta-Alba, J.; Perdomo-Morales, R.; Perera, E.; Hernandez-Rodriguez, E. W.; Estrada, M. P.; Porto-Verdecia, M.
Defensin like peptide from Panulirus argus relates structurally with beta defensin from vertebrates
FISH & SHELLFISH IMMUNOLOGY, 33:872-879, OCT 2012
abstract, full text, DOI:10.1016/j.fsi.2012.07.013

Shang, Zhiguo; Sigworth, Fred J.
Hydration-layer models for cryo-EM image simulation
JOURNAL OF STRUCTURAL BIOLOGY, 180:10-16, OCT 2012
abstract, full text, DOI:10.1016/j.jsb.2012.04.021

Zeng, Yingying; Larson, Steven B.; Heitsch, Christine E.; McPherson, Alexander; Harvey, Stephen C.
A model for the structure of satellite tobacco mosaic virus
JOURNAL OF STRUCTURAL BIOLOGY, 180:110-116, OCT 2012
abstract, full text, DOI:10.1016/j.jsb.2012.06.008

Harvey, Matthew J.; De Fabritiis, Gianni
High-throughput molecular dynamics: the powerful new tool for drug discovery
DRUG DISCOVERY TODAY, 17:1059-1062, OCT 2012
abstract, full text, DOI:10.1016/j.drudis.2012.03.017

Kim, Hyun-Woo; McIntosh, J. Michael
alpha 6 nAChR subunit residues that confer alpha-conotoxin BuIA selectivity
FASEB JOURNAL, 26:4102-4110, OCT 2012
abstract, full text, DOI:10.1096/fj.12-204487

Torzilli, Peter A.; Bourne, Jonathan W.; Cigler, Tessa; Vincent, C. Theresa
A new paradigm for mechanobiological mechanisms in tumor metastasis
SEMINARS IN CANCER BIOLOGY, 22:385-395, OCT 2012
abstract, full text, DOI:10.1016/j.semcancer.2012.05.002

Chen, Yi; Cruz-Chu, Eduardo R.; Woodard, Jaie C.; Gartia, Manas R.; Schulten, Klaus; Liu, Logan
Electrically Induced Conformational Change of Peptides on Metallic Nanosurfaces
ACS NANO, 6:8847-8856, OCT 2012
abstract, full text, TCBG publications, DOI:10.1021/nn3027408

Kang, Seung-gu; Li, Hai; Tien Huynh; Zhang, Fuchun; Xia, Zhen; Zhang, Yi; Zhou, Ruhong
Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides
ACS NANO, 6:9276-9282, OCT 2012
abstract, full text, DOI:10.1021/nn303740j

Singharoy, A.; Joshi, H.; Ortoleva, P. J.
Multiscale Macromolecular Simulation: Role of Evolving Ensembles
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2638-2649, OCT 2012
abstract, full text, DOI:10.1021/ci3002952

Schmidt, Thomas H.; Kandt, Christian
LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2657-2669, OCT 2012
abstract, full text, DOI:10.1021/ci3000453

Ozorowski, Gabriel; Ryan, Christopher M.; Whitelegge, Julian P.; Luecke, Hartmut
Withaferin A binds covalently to the N-terminal domain of annexin A2
BIOLOGICAL CHEMISTRY, 393:1151-1163, OCT 2012
abstract, full text, DOI:10.1515/hsz-2012-0184

Kramar, Peter; Delemotte, Lucie; Lebar, Alenka Macek; Kotulska, Malgorzata; Tarek, Mounir; Miklavcic, Damijan
Molecular-Level Characterization of Lipid Membrane Electroporation using Linearly Rising Current
JOURNAL OF MEMBRANE BIOLOGY, 245:651-659, OCT 2012
abstract, full text, DOI:10.1007/s00232-012-9487-6

Zhu, Fangqiang; Hummer, Gerhard
Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3759-3768, OCT 2012
abstract, full text, DOI:10.1021/ct2009279

Kekenes-Huskey, Peter M.; Metzger, Vincent T.; Grant, Barry J.; McCammon, J. Andrew
Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca2+ATPase
PROTEIN SCIENCE, 21:1429-1443, OCT 2012
abstract, full text, DOI:10.1002/pro.2129

Landstrom, Jens; Persson, Karina; Rademacher, Christoph; Lundborg, Magnus; Wakarchuk, Warren; Peters, Thomas; Widmalm, Goran
Small molecules containing hetero-bicyclic ring systems compete with UDP-Glc for binding to WaaG glycosyltransferase
GLYCOCONJUGATE JOURNAL, 29:491-502, OCT 2012
abstract, full text, DOI:10.1007/s10719-012-9411-4

Fackeldey, Konstantin; Klimm, Martina; Weber, Marcus
A coarse graining method for the dimension reduction of the state space of biomolecules
JOURNAL OF MATHEMATICAL CHEMISTRY, 50:2623-2635, OCT 2012
abstract, full text, DOI:10.1007/s10910-012-0051-5

Tan, Qinliang; Qin, Wu; Chen, Qiuluan; Dong, Changqing; Li, Wenyan; Yang, Yongping
Synergetic effect of ZrO2 on the oxidation-reduction reaction of Fe2O3 during chemical looping combustion
APPLIED SURFACE SCIENCE, 258:10022-10027, OCT 1 2012
abstract, full text, DOI:10.1016/j.apsusc.2012.06.067

Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil
Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study
BIOPOLYMERS, 97:766-777, OCT 2012
abstract, full text, DOI:10.1002/bip.22057

Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee
Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 124101, SEP 28 2012
abstract, full text, DOI:10.1063/1.4752735

Holland, Bryan W.; Gray, Chris G.; Tomberli, Bruno
Calculating diffusion and permeability coefficients with the oscillating forward-reverse method
PHYSICAL REVIEW E, 86 Art. No. 036707, SEP 27 2012
abstract, full text, DOI:10.1103/PhysRevE.86.036707

Chagovets, Vitaliy V.; Kosevich, Marina V.; Stepanian, Stepan G.; Boryak, Oleg A.; Shelkovsky, Vadim S.; Orlov, Vadim V.; Leontiev, Victor S.; Pokrovskiy, Valerij A.; Adamowicz, Ludwik; Karachevtsev, Victor A.
Noncovalent Interaction of Methylene Blue with Carbon Nanotubes: Theoretical and Mass Spectrometry Characterization
JOURNAL OF PHYSICAL CHEMISTRY C, 116:20579-20590, SEP 27 2012
abstract, full text, DOI:10.1021/jp306333c

Baxa, Michael C.; Haddadian, Esmael J.; Jha, Abhishek K.; Freed, Karl F.; Sosnick, Tobin R.
Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:15929-15936, SEP 26 2012
abstract, full text, DOI:10.1021/ja3064028

Zheng, Xiange; Wu, Chuanjie; Ponder, Jay W.; Marshall, Garland R.
Molecular Dynamics of beta-Hairpin Models of Epigenetic Recognition Motifs
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:15970-15978, SEP 26 2012
abstract, full text, DOI:10.1021/ja306803v

Zhou, Andy; Abu-Baker, Shadi; Sahu, Indra D.; Liu, Lishan; McCarrick, Robert M.; Dabney-Smith, Carole; Lorigan, Gary A.
Determining alpha-Helical and beta-Sheet Secondary Structures via Pulsed Electron Spin Resonance Spectroscopy
BIOCHEMISTRY, 51:7417-7419, SEP 25 2012
abstract, full text, DOI:10.1021/bi3010736

Rubach, Jon K.; Cui, Guanglei; Schneck, Jessica L.; Taylor, Amy N.; Zhao, Baoguang; Smallwood, Angela; Nevins, Neysa; Wisnoski, David; Thrall, Sara H.; Meek, Thomas D.
The Amino-Acid Substituents of Dipeptide Substrates of Cathepsin C Can Determine the Rate-Limiting Steps of Catalysis
BIOCHEMISTRY, 51:7551-7568, SEP 25 2012
abstract, full text, DOI:10.1021/bi300719b

Tsai, C. Wei; Chen, W. Yih; Ruaan, R. Chyu
Retention Prediction of Peptide Diastereomers in Reversed-Phase Liquid Chromatography Assisted by Molecular Dynamics Simulation
LANGMUIR, 28:13601-13608, SEP 25 2012
abstract, full text, DOI:10.1021/la302312m

Apte-Sengupta, Swapna; Negi, Surendra; Leonard, Vincent H. J.; Oezguen, Numan; Navaratnarajah, Chanakha K.; Braun, Werner; Cattaneo, Roberto
Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:33026-33035, SEP 21 2012
abstract, full text, DOI:10.1074/jbc.M112.373308

Moscoso, Cristian; Vergara-Jaque, Ariela; Marquez-Miranda, Valeria; Sepulveda, Romina V.; Valencia, Ignacio; Diaz-Franulic, Ignacio; Gonzalez-Nilo, Fernando; Naranjo, David
K+ Conduction and Mg2+ Blockade in a Shaker Kv-Channel Single Point Mutant with an Unusually High Conductance
BIOPHYSICAL JOURNAL, 103:1198-1207, SEP 19 2012
abstract, full text, DOI:10.1016/j.bpj.2012.08.015

Fan, Jun; Saunders, Marissa G.; Voth, Gregory A.
Coarse-Graining Provides Insights on the Essential Nature of Heterogeneity in Actin Filaments
BIOPHYSICAL JOURNAL, 103:1334-1342, SEP 19 2012
abstract, full text, DOI:10.1016/j.bpj.2012.08.029

Zheng, Wenjun; Tekpinar, Mustafa
Structure-Based Simulations of the Trans location Mechanism of the Hepatitis C Virus NS3 Helicase along Single-Stranded Nucleic Acid
BIOPHYSICAL JOURNAL, 103:1343-1353, SEP 19 2012
abstract, full text, DOI:10.1016/j.bpj.2012.08.026

Vagenende, Vincent; Trout, Bernhardt L.
Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure
BIOPHYSICAL JOURNAL, 103:1354-1362, SEP 19 2012
abstract, full text, DOI:10.1016/j.bpj.2012.08.011

Zomot, Elia; Bahar, Ivet
A Conformational Switch in a Partially Unwound Helix Selectively Determines the Pathway for Substrate Release from the Carnitine/gamma-Butyrobetaine Antiporter CaiT
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:31823-31832, SEP 14 2012
abstract, full text, DOI:10.1074/jbc.M112.397364

Carpenter, Timothy S.; Lau, Edmond Y.; Lightstone, Felice C.
A Role for Loop F in Modulating GABA Binding Affinity in the GABA(A) Receptor
JOURNAL OF MOLECULAR BIOLOGY, 422:310-323, SEP 14 2012
abstract, full text, DOI:10.1016/j.jmb.2012.05.025

Minh, David D. L.
Implicit ligand theory: Rigorous binding free energies and thermodynamic expectations from molecular docking
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 104106, SEP 14 2012
abstract, full text, DOI:10.1063/1.4751284

Ngo, Van A.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
Supercrystals of DNA-Functionalized Gold Nanoparticles: A Million-Atom Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 116:19579-19585, SEP 13 2012
abstract, full text, DOI:10.1021/jp306133v

Nagata, Takeshi; Fedorov, Dmitri G.; Sawada, Toshihiko; Kitaura, Kazuo
Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin-Carbohydrate Complex
JOURNAL OF PHYSICAL CHEMISTRY A, 116:9088-9099, SEP 13 2012
abstract, full text, DOI:10.1021/jp304991a

Liu, Lishan; Sahu, Indra D.; Mayo, Daniel J.; McCarrick, Robert M.; Troxel, Kaylee; Zhou, Andy; Shockley, Erin; Lorigan, Gary A.
Enhancement of Electron Spin Echo Envelope Modulation Spectroscopic Methods to Investigate the Secondary Structure of Membrane Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11041-11045, SEP 13 2012
abstract, full text, DOI:10.1021/jp304669b

MacMillan, Amanda C.; McIntire, Theresa M.; Freites, J. Alfredo; Tobias, Douglas J.; Nizkorodov, Sergey A.
Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11255-11265, SEP 13 2012
abstract, full text, DOI:10.1021/jp305029n

Abi, T. G.; Taraphder, Srabani
Proton transfer reactions in carbon nanotubes endohedrally functionalized with selected polar amino acid sidechains
CHEMICAL PHYSICS, 405:107-116, SEP 11 2012
abstract, full text, DOI:10.1016/j.chemphys.2012.06.014

Liu Ying-Zhe; Cai Wen-Sheng; Shao Xue-Guang
Molecular Dynamics Simulation of Hydrophobin Proteins on the Surface of Single-walled Carbon Nanotubes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 33:2013-2018, SEP 10 2012
abstract, full text, DOI:10.3969/j.issn.0251-0790.2012.09.024

Luan, Binquan; Zhou, Ruhong
Nanopore-Based Sensors for Detecting Toxicity of a Carbon Nanotube to Proteins
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2337-2341, SEP 6 2012
abstract, full text, DOI:10.1021/jz3007832

Fujita, Takatoshi; Brookes, Jennifer C.; Saikin, Semion K.; Aspuru-Guzik, Alan
Memory-Assisted Exciton Diffusion in the Chlorosome Light-Harvesting Antenna of Green Sulfur Bacteria
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2357-2361, SEP 6 2012
abstract, full text, DOI:10.1021/jz3008326

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio
Homology Modeling of Dopamine D-2 and D-3 Receptors: Molecular Dynamics Refinement and Docking Evaluation
PLOS ONE, 7 Art. No. e44316, SEP 6 2012
abstract, full text, DOI:10.1371/journal.pone.0044316

Eilers, Markus; Goncalves, Joseph A.; Abuja, Shivani; Kirkup, Colleen; Hirshfeld, Amiram; Simmerling, Carlos; Reeves, Philip J.; Sheves, Mordechai; Smith, Steven O.
Structural Transitions of Transmembrane Helix 6 in the Formation of Metarhodopsin I
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10477-10489, SEP 6 2012
abstract, full text, DOI:10.1021/jp3019183

Schlamadinger, Diana E.; Wang, Yi; McCammon, J. Andrew; Kim, Judy E.
Spectroscopic and Computational Study of Melittin, Cecropin A, and the Hybrid Peptide CM15
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10600-10608, SEP 6 2012
abstract, full text, DOI:10.1021/jp304021t

Ghane, Tahereh; Brancolini, Giorgia; Varsano, Daniele; Di Felice, Rosa
Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10693-10702, SEP 6 2012
abstract, full text, DOI:10.1021/jp304818s

Vashisth, Harish; Skiniotis, Georgios; Brooks, Charles L., I.I.I.
Using Enhanced Sampling and Structural Restraints to Refine Atomic Structures into Low-Resolution Electron Microscopy Maps
STRUCTURE, 20:1453-1462, SEP 5 2012
abstract, full text, DOI:10.1016/j.str.2012.08.007

Topol, Igor; Collins, Jack; Mironov, Vladimir; Savitsky, Alexander; Nemukhin, Alexander
Modeling absorption of the kindling fluorescent protein with the neutral form of the chromophore
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:2947-2951, SEP 5 2012
abstract, full text, DOI:10.1002/qua.24134

Zhao, Chunfeng; Stolzenberg, Sebastian; Gracia, Luis; Weinstein, Harel; Noskov, Sergei; Shi, Lei
Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT
BIOPHYSICAL JOURNAL, 103:878-888, SEP 5 2012
abstract, full text, DOI:10.1016/j.bpj.2012.07.044

Alcaino, Jennifer; Fuentealba, Matias; Cabrera, Ricardo; Baeza, Marcelo; Cifuentes, Victor
Modeling the Interfacial Interactions between CrtS and CrtR from Xanthophyllomyces dendrorhous, a P450 System Involved in Astaxanthin Production
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 60:8640-8647, SEP 5 2012
abstract, full text, DOI:10.1021/jf302287f

Singh, Nitin K.; Pakkkianathan, Britto C.; Kumar, Manish; Daddam, Jayssima R.; Jayavel, Sridhar; Kannan, Mani; Pillai, Girinath G.; Krishnan, Muthukalingan
Computational Studies on Molecular Interactions of 6-Thioguanosine Analogs with Anthrax Toxin Receptor 1
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 4:183-189, SEP 2012
abstract, full text, DOI:10.1007/s12539-012-0126-9

Nichols, Sara E.; Swift, Robert V.; Amaro, Rommie E.
Rational Prediction with Molecular Dynamics for Hit Identification
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 12:2002-2012, SEP 2012
abstract, full text

Merchant, Bonnie A.; Madura, Jeffry D.
Insights from molecular dynamics: The binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:1-12, SEP 2012
abstract, full text, DOI:10.1016/j.jmgm.2012.05.007

Ai, Rizi; Chang, Chia-en A.
Ligand-specific homology modeling of human cannabinoid (CB1) receptor
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:155-164, SEP 2012
abstract, full text, DOI:10.1016/j.jmgm.2012.05.002

Roberts, Jason A.; Kuiper, Michael J.; Thorley, Bruce R.; Smooker, Peter M.; Hung, Andrew
Investigation of a predicted N-terminal amphipathic et-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:165-173, SEP 2012
abstract, full text, DOI:10.1016/j.jmgm.2012.06.009

Hamulakova, Slavka; Janovec, Ladislav; Hrabinova, Martina; Kristian, Pavol; Kuca, Kamil; Banasova, Maria; Imrich, Jan
Synthesis, design and biological evaluation of novel highly potent tacrine congeners for the treatment of Alzheimer's disease
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 55:23-31, SEP 2012
abstract, full text, DOI:10.1016/j.ejmech.2012.06.051

Tarasov, D. S.; Ibragimova, M. Y.; Izotova, E. D.; Akberova, N. I.; Zhdanov, R. I.
Molecular dynamics and free energy of binding of oleic acid to DNA in aqueous solutions
DOKLADY BIOCHEMISTRY AND BIOPHYSICS, 446:223-228, SEP 2012
full text, DOI:10.1134/S1607672912050043

Wang, Han; Zhang, Pingwen; Schuette, Christof
On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3243-3256, SEP 2012
abstract, full text, DOI:10.1021/ct300343y

Best, Robert B.; Zhu, Xiao; Shim, Jihyun; Lopes, Pedro E. M.; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D., Jr.
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone phi, psi and Side-Chain chi(1) and chi(2) Dihedral Angles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3257-3273, SEP 2012
abstract, full text, DOI:10.1021/ct300400x

Weber, Valery; Asthagiri, D.
Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3409-3415, SEP 2012
abstract, full text, DOI:10.1021/ct300505b

Delemotte, Lucie; Tarek, Mounir
Molecular Dynamics Simulations of Lipid Membrane Electroporation
JOURNAL OF MEMBRANE BIOLOGY, 245:531-543, SEP 2012
abstract, full text, DOI:10.1007/s00232-012-9434-6

Chandler, Danielle E.; Penin, Francois; Schulten, Klaus; Chipot, Christophe
The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002702, SEP 2012
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1002702

Kurkcuoglu, Zeynep; Bakan, Ahmet; Kocaman, Duygu; Bahar, Ivet; Doruker, Pemra
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002705, SEP 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002705

Sun, Chongbo; Tang, Tian; Uludag, Hasan
Probing the Effects of Lipid Substitution on Polycation Mediated DNA Aggregation: A Molecular Dynamics Simulations Study
BIOMACROMOLECULES, 13:2982-2988, SEP 2012
abstract, full text, DOI:10.1021/bm301045b

Langeslay, Derek J.; Young, Robert P.; Beni, Szabolcs; Beecher, Consuelo N.; Mueller, Leonard J.; Larive, Cynthia K.
Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra
GLYCOBIOLOGY, 22:1173-1182, SEP 2012
abstract, full text, DOI:10.1093/glycob/cws085

Graciano, Luciana; Correa, Juliana Moco; Gandra, Rinaldo Ferreira; Vicente Seixas, Flavio Augusto; Kadowaki, Marina Kimiko; Sampaio, Silvio Cesar; da Conceicao Silva, Jose Luis; Osaku, Clarice Aoki; Garcia Simao, Rita de Cassia
The cloning, expression, purification, characterization and modeled structure of Caulobacter crescentus beta-Xylosidase I
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, 28:2879-2888, SEP 2012
abstract, full text, DOI:10.1007/s11274-012-1099-x

Banerjee, Amit Kumar; Arora, Neelima; Murty, Upadhyayula Surya Narayana
Aspartate carbamoyltransferase of Plasmodium falciparum as a potential drug target for designing anti-malarial chemotherapeutic agents
MEDICINAL CHEMISTRY RESEARCH, 21:2480-2493, SEP 2012
abstract, full text, DOI:10.1007/s00044-011-9757-3

Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
Validation of previous computer models and MD simulations of discoidal HDL by a recent crystal structure of apoA-I
JOURNAL OF LIPID RESEARCH, 53:1851-1863, SEP 2012
abstract, full text, DOI:10.1194/jlr.M026229

Gushchin, Ivan Y.; Gordeliy, Valentin I.; Grudinin, Sergei
A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating
JOURNAL OF MOLECULAR MODELING, 18:4053-4060, SEP 2012
abstract, full text, DOI:10.1007/s00894-012-1404-5

Lin, Ying-Wu; Nie, Chang-Ming; Liao, Li-Fu
Rational design of a nitrite reductase based on myoglobin: a molecular modeling and dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 18:4409-4415, SEP 2012
abstract, full text, DOI:10.1007/s00894-012-1451-y

Sutto, Ludovico; Marsili, Simone; Luigi Gervasio, Francesco
New advances in metadynamics
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:771-779, SEP-OCT 2012
abstract, full text, DOI:10.1002/wcms.1103

Gao, Weimin; Kong, Lingxue; Hodgson, Peter
Atomic interaction of functionalized carbon nanotube-based nanofluids with a heating surface and its effect on heat transfer
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER, 55:5007-5015, SEP 2012
abstract, full text, DOI:10.1016/j.ijheatmasstransfer.2012.04.044

Barber, Annika F.; Carnevale, Vincenzo; Raju, S. G.; Amaral, Cristiano; Treptow, Werner; Klein, Michael L.
Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2120-2125, SEP 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.05.002

Reddy, A. Srinivas; Warshaviak, Dora Toledo; Chachisvilis, Mirianas
Effect of membrane tension on the physical properties of DOPC lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2271-2281, SEP 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.05.006

Spijker, Peter; Anciaux, Guillaume; Molinari, Jean-Francois
The effect of loading on surface roughness at the atomistic level
COMPUTATIONAL MECHANICS, 50:273-283, SEP 2012
abstract, full text, DOI:10.1007/s00466-011-0574-9

Vassiliev, Sergey; Zaraiskaya, Tatiana; Bruce, Doug
Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:1671-1678, SEP 2012
abstract, full text, DOI:10.1016/j.bbabio.2012.05.016

Chan, Kwok-Yan; Trabuco, Leonardo G.; Schreiner, Eduard; Schulten, Klaus
Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method
BIOPOLYMERS, 97:678-686, SEP 2012
abstract, full text, TCBG publications, DOI:10.1002/bip.22042

Huang, Yu-ming M.; Kang, Myungshim; Chang, Chia-en A.
Mechanistic Insights into Phosphopeptide-BRCT Domain Association: Preorganization, Flexibility, and Phosphate Recognition
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10247-10258, AUG 30 2012
abstract, full text, DOI:10.1021/jp305028d

Yu, Xiang; Zheng, Jie
Cholesterol Promotes the Interaction of Alzheimer beta-Amyloid Monomer with Lipid Bilayer
JOURNAL OF MOLECULAR BIOLOGY, 421:561-571, AUG 24 2012
abstract, full text, DOI:10.1016/j.jmb.2011.11.006

Tofoleanu, Florentina; Buchete, Nicolae-Viorel
Molecular Interactions of Alzheimer's A beta Protofilaments with Lipid Membranes
JOURNAL OF MOLECULAR BIOLOGY, 421:572-586, AUG 24 2012
abstract, full text, DOI:10.1016/j.jmb.2011.12.063

Liu, Peng; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
How Do alpha-Cyclodextrins Self-Organize on a Polymer Chain?
JOURNAL OF PHYSICAL CHEMISTRY C, 116:17913-17918, AUG 23 2012
abstract, full text, DOI:10.1021/jp304035q

Xiao, Botao; Tong, Chunfang; Jia, Xiaoling; Guo, Rui; Lu, Shouqin; Zhang, Yan; McEver, Rodger P.; Zhu, Cheng; Long, Mian
Tyrosine Replacement of PSGL-1 Reduces Association Kinetics with P- and L-Selectin on the Cell Membrane
BIOPHYSICAL JOURNAL, 103:777-785, AUG 22 2012
abstract, full text, DOI:10.1016/j.bpj.2012.07.028

Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 075101, AUG 21 2012
abstract, full text, DOI:10.1063/1.4739308

Fleurat-Lessard, Paul; Michel, Carine; Bulo, Rosa E.
Energy extrapolation schemes for adaptive multi-scale molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 074111, AUG 21 2012
abstract, full text, DOI:10.1063/1.4739743

Hall, Benjamin A.; Wright, David W.; Jha, Shantenu; Coveney, Peter V.
Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity
BIOCHEMISTRY, 51:6487-6489, AUG 21 2012
abstract, full text, DOI:10.1021/bi300432u

von Castelmur, Eleonore; Struempfer, Johan; Franke, Barbara; Bogomolovas, Julijus; Barbieri, Sonia; Qadota, Hiroshi; Konarev, Petr V.; Svergun, Dmitri I.; Labeit, Siegfried; Benian, Guy M.; Schulten, Klaus; Mayans, Olga
Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:13608-13613, AUG 21 2012
abstract, full text, TCBG publications, DOI:10.1073/pnas.1200697109

Qin, Zhao; Buehler, Markus
Molecular mechanics of dihydroxyphenylalanine at a silica interface
APPLIED PHYSICS LETTERS, 101 Art. No. 083702, AUG 20 2012
abstract, full text, DOI:10.1063/1.4747214

Kumar, Pradeep; Lehmann, Jean; Libchaber, Albert
Kinetics of Bulge Bases in Small RNAs and the Effect of Pressure on It
PLOS ONE, 7 Art. No. e42052, AUG 20 2012
abstract, full text, DOI:10.1371/journal.pone.0042052

Bai, Ming; Pang, Xiaoyun; Lou, Jizhong; Zhou, Qiangjun; Zhang, Kai; Ma, Jun; Li, Jian; Sun, Fei; Hsu, Victor W.
Mechanistic Insights into Regulated Cargo Binding by ACAP1 Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:28675-28685, AUG 17 2012
abstract, full text, DOI:10.1074/jbc.M112.378810

Biedermannova, Lada; Prokop, Zbynek; Gora, Artur; Chovancova, Eva; Kovacs, Mihaly; Damborsky, Jiri; Wade, Rebecca C.
A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:29062-29074, AUG 17 2012
abstract, full text, DOI:10.1074/jbc.M112.377853

Pacios, Luis F.; Gomez-Casado, Cristina; Tordesillas, Leticia; Palacin, Arantxa; Sanchez-Monge, Rosa; Diaz-Perales, Araceli
Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1831-1844, AUG 15 2012
abstract, full text, DOI:10.1002/jcc.23012

Zhang, Xiaohong; He, Xiao; Baker, Joseph; Tama, Florence; Chang, Geoffrey; Wright, Stephen H.
Twelve Transmembrane Helices Form the Functional Core of Mammalian MATE1 (Multidrug and Toxin Extruder 1) Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:27971-27982, AUG 10 2012
abstract, full text, DOI:10.1074/jbc.M112.386979

Amato, Angelica A.; Rajagopalan, Senapathy; Lin, Jean Z.; Carvalho, Bruno M.; Figueira, Ana C. M.; Lu, Jenny; Ayers, Stephen D.; Mottin, Melina; Silveira, Rodrigo L.; Souza, Paulo C. T.; Mourao, Rosa H. V.; Saad, Mario J. A.; Togashi, Marie; Simeoni, Luiz A.; Abdalla, Dulcineia S. P.; Skaf, Munir S.; Polikparpov, Igor; Lima, Maria C. A.; Galdino, Suely L.; Brennan, Richard G.; Baxter, John D.; Pitta, Ivan R.; Webb, Paul; Phillips, Kevin J.; Neves, Francisco A. R.
GQ-16, a Novel Peroxisome Proliferator-activated Receptor gamma (PPAR gamma) Ligand, Promotes Insulin Sensitization without Weight Gain
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:28169-28179, AUG 10 2012
abstract, full text, DOI:10.1074/jbc.M111.332106

da Silva, Luis Pinto; Vieira, Joao; Esteves da Silva, Joaquim C. G.
Comparative theoretical study of the binding of luciferyl-adenylate and dehydroluciferyl-adenylate to firefly luciferase
CHEMICAL PHYSICS LETTERS, 543:137-141, AUG 10 2012
abstract, full text, DOI:10.1016/j.cplett.2012.06.038

Turpin, Eleanor R.; Hirst, Jonathan D.
Transformation of the dihedral corrective map for D-amino residues using the CHARMM force field
CHEMICAL PHYSICS LETTERS, 543:142-147, AUG 10 2012
abstract, full text, DOI:10.1016/j.cplett.2012.06.041

Akhshi, Parisa; Acton, Gregory; Wu, Gang
Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G(3)T(4)G(4))](2) G-Quadruplex DNA Structure
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9363-9370, AUG 9 2012
abstract, full text, DOI:10.1021/jp304760k

Stober, Spencer T.; Abrams, Cameron F.
Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of beta 2-Microglobulin: On-the-Fly String Method Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9371-9375, AUG 9 2012
abstract, full text, DOI:10.1021/jp304805v

Klauda, Jeffery B.; Monje, Viviana; Kim, Taehoon; Im, Wonpil
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9424-9431, AUG 9 2012
abstract, full text, DOI:10.1021/jp304056p

Verde, Ana Vila; Bolhuis, Peter G.; Campen, R. Kramer
Statics and Dynamics of Free and Hydrogen-Bonded OH Groups at the Air/Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9467-9481, AUG 9 2012
abstract, full text, DOI:10.1021/jp304151e

Gautieri, Alfonso; Pate, Monica I.; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J.
Hydration and distance dependence of intermolecular shearing between collagen molecules in a model microfibril
JOURNAL OF BIOMECHANICS, 45:2079-2083, AUG 9 2012
abstract, full text, DOI:10.1016/j.jbiomech.2012.05.047

Wright, David W.; Sadiq, S. Kashif; De Fabritiis, Gianni; Coveney, Peter V.
Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:12885-12888, AUG 8 2012
abstract, full text, DOI:10.1021/ja301565k

Robertson, J. L.; Palmer, L. G.; Roux, B.
Multi-Ion Distributions in the Cytoplasmic Domain of Inward Rectifier Potassium Channels
BIOPHYSICAL JOURNAL, 103:434-443, AUG 8 2012
abstract, full text, DOI:10.1016/j.bpj.2012.06.023

Marin, Marioara B.; Ghenea, Simona; Spiridon, Laurentiu N.; Chiritoiu, Gabriela N.; Petrescu, Andrei-Jose; Petrescu, Stefana-Maria
Tyrosinase Degradation Is Prevented when EDEM1 Lacks the Intrinsically Disordered Region
PLOS ONE, 7 Art. No. e42998, AUG 8 2012
abstract, full text, DOI:10.1371/journal.pone.0042998

Raghuraman, H.; Cordero-Morales, Julio F.; Jogini, Vishwanath; Pan, Albert C.; Kollewe, Astrid; Roux, Benoit; Perozo, Eduardo
Mechanism of Cd2+ Coordination during Slow Inactivation in Potassium Channels
STRUCTURE, 20:1332-1342, AUG 8 2012
abstract, full text, DOI:10.1016/j.str.2012.03.027

Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos; Gaudet, Rachelle
Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel
BIOCHEMISTRY, 51:6195-6206, AUG 7 2012
abstract, full text, DOI:10.1021/bi300279b

Johnson, Quentin R.; Nellas, Ricky B.; Shen, Tongye
Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa
BIOCHEMISTRY, 51:6238-6245, AUG 7 2012
abstract, full text, DOI:10.1021/bi300557y

Jana, Madhurima; Bandyopadhyay, Sanjoy
Restricted dynamics of water around a protein-carbohydrate complex: Computer simulation studies
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 055102, AUG 7 2012
abstract, full text, DOI:10.1063/1.4739421

Gong, Rui; Wang, Yanping; Ying, Tianlei; Dimitrov, Dimiter S.
Bispecific Engineered Antibody Domains (Nanoantibodies) That Interact Noncompetitively with an HIV-1 Neutralizing Epitope and FcRn
PLOS ONE, 7 Art. No. e42288, AUG 7 2012
abstract, full text, DOI:10.1371/journal.pone.0042288

Natarajan, Kathiresan; Senapati, Sanjib
Understanding the Basis of Drug Resistance of the Mutants of alpha beta-Tubulin Dimer via Molecular Dynamics Simulations
PLOS ONE, 7 Art. No. e42351, AUG 7 2012
abstract, full text, DOI:10.1371/journal.pone.0042351

van Eijk, Martin; Rynkiewicz, Michael J.; White, Mitchell R.; Hartshorn, Kevan L.; Zou, Xueqing; Schulten, Klaus; Luo, Dong; Crouch, Erika C.; Cafarella, Tanya R.; Head, James F.; Haagsman, Henk P.; Seaton, Barbara A.
A Unique Sugar-binding Site Mediates the Distinct Anti-influenza Activity of Pig Surfactant Protein D
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:26666-26677, AUG 3 2012
abstract, full text, TCBG publications, DOI:10.1074/jbc.M112.368571

Yang, Zaixing; Xiu, Peng; Shi, Biyun; Hua, Lan; Zhou, Ruhong
Coherent Microscopic Picture for Urea-Induced Denaturation of Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8856-8862, AUG 2 2012
abstract, full text, DOI:10.1021/jp304114h

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2119-2131, AUG 2012
abstract, full text, DOI:10.1021/ci300250q

Liu, Jian; Fan, Jianfen; Cen, Min; Song, Xuezeng; Liu, Dongyan; Zhou, Weiqun; Liu, Zhao; Yan, Jianfeng
Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2132-2138, AUG 2012
abstract, full text, DOI:10.1021/ci300185c

Melo, Marcelo C. R.; Bernardi, Rafael C.; Fernandes, Tacio V. A.; Pascutti, Pedro G.
GSAFold: A new application of GSA to protein structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2305-2310, AUG 2012
abstract, full text, DOI:10.1002/prot.24120

Bhattacharya, Swati; Derrington, Ian M.; Pavlenok, Mikhail; Niederweis, Michael; Gundlach, Jens H.; Aksimentiev, Aleksei
Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence
ACS NANO, 6:6960-6968, AUG 2012
abstract, full text, DOI:10.1021/nn3019943

Pietra, Francesco
On CO Egress from, and Re-Uptake by, the Enzyme MauG, as a Mimic of the Acquisition of Oxidizing Agents by the pre-MADH_MauG System. A Molecular Mechanics Approach
CHEMISTRY & BIODIVERSITY, 9:1425-1435, AUG 2012
abstract, full text, DOI:10.1002/cbdv.201200176

Garcia-Fandino, Rebeca; Bernado, Pau; Ayuso-Tejedor, Sara; Sancho, Javier; Orozco, Modesto
Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002647, AUG 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002647

Pisliakov, Andrei V.; Hino, Tomoya; Shiro, Yoshitsugu; Sugita, Yuji
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002674, AUG 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002674

Jasinski, A.; Mikulska, K.; Krajnik, B.; Mackowski, S.; Nowak, W.
Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model
ACTA PHYSICA POLONICA A, 122:284-288, AUG 2012
abstract, full text

Romanowska, Julia; Nowinski, Krzysztof S.; Trylska, Joanna
Determining Geometrically Stable Domains in Molecular Conformation Sets
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2588-2599, AUG 2012
abstract, full text, DOI:10.1021/ct300206j

Liu, Peng; Dehez, Francois; Cai, Wensheng; Chipot, Christophe
A Toolkit for the Analysis of Free-Energy Perturbation Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2606-2616, AUG 2012
abstract, full text, DOI:10.1021/ct300242f

Wong-ekkabut, Jirasak; Karttunen, Mikko
Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2905-2911, AUG 2012
abstract, full text, DOI:10.1021/ct3001359

Trung Hai Nguyen; Arnesano, Fabio; Scintilla, Simone; Rossetti, Giulia; Ippoliti, Emiliano; Carloni, Paolo; Natile, Giovanni
Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2912-2920, AUG 2012
abstract, full text, DOI:10.1021/ct300167m

VanWart, Adam T.; Eargle, John; Luthey-Schulten, Zaida; Amaro, Rommie E.
Exploring Residue Component Contributions to Dynamical Network Models of Allostery
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2949-2961, AUG 2012
abstract, full text, DOI:10.1021/ct300377a

Mladenovic, Milan; Mihailovic, Mirjana; Bogojevic, Desanka; Vukovic, Nenad; Sukdolak, Slobodan; Matic, Sanja; Niciforovic, Neda; Mihailovic, Vladimir; Maskovic, Pavle; Vrvic, Miroslav M.; Solujic, Slavica
Biochemical and pharmacological evaluation of 4-hydroxychromen-2-ones bearing polar C-3 substituents as anticoagulants
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 54:144-158, AUG 2012
abstract, full text, DOI:10.1016/j.ejmech.2012.04.036

Fioramonte, Mariana; dos Santos, Aline Mara; McIlwain, Sean; Noble, William S.; Franchini, Kleber G.; Gozzo, Fabio C.
Analysis of secondary structure in proteins by chemical cross-linking coupled to MS
PROTEOMICS, 12:2746-2752, AUG 2012
abstract, full text, DOI:10.1002/pmic.201200040

Pradhan, Shashindra M.; Katti, Kalpana S.; Katti, Dinesh R.
Structural Hierarchy Controls Deformation Behavior of Collagen
BIOMACROMOLECULES, 13:2562-2569, AUG 2012
abstract, full text, DOI:10.1021/bm300801a

Mage, Michael G.; Dolan, Michael A.; Wang, Rui; Boyd, Lisa F.; Revilleza, Maria Jamela; Robinson, Howard; Natarajan, Kannan; Myers, Nancy B.; Hansen, Ted H.; Margulies, David H.
The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics
JOURNAL OF IMMUNOLOGY, 189:1391-1399, AUG 1 2012
abstract, full text, DOI:10.4049/jimmunol.1200831

Chen Bao-Dong; Yang Chuan-Lu; Wang Mei-Shan; Ma Xiao-Guang
Dynamic mechanism for encapsulating two HIV replication inhibitor peptides with carbon nanotubes
CHINESE PHYSICS B, 21 Art. No. 083103, AUG 2012
abstract, full text, DOI:10.1088/1674-1056/21/8/083103

Galloux, Marie; Tarus, Bogdan; Blazevic, Ilfad; Fix, Jenna; Duquerroy, Stephane; Eleouet, Jean-Francois
Characterization of a Viral Phosphoprotein Binding Site on the Surface of the Respiratory Syncytial Nucleoprotein
JOURNAL OF VIROLOGY, 86:8375-8387, AUG 2012
abstract, full text, DOI:10.1128/JVI.00058-12

Lee, One-Sun; Liu, Yamei; Schatz, George C.
Molecular dynamics simulation of beta-sheet formation in self-assembled peptide amphiphile fibers
JOURNAL OF NANOPARTICLE RESEARCH, 14 Art. No. 936, AUG 2012
abstract, full text, DOI:10.1007/s11051-012-0936-z

Hu, Guodong; Chen, Liao Y.; Wang, Jihua
Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z
JOURNAL OF MOLECULAR MODELING, 18:3731-3741, AUG 2012
abstract, full text, DOI:10.1007/s00894-012-1379-2

Lilkova, Elena; Nacheva, Genoveva; Petkov, Peicho; Petkov, Petko; Markov, Stoyan; Ilieva, Nevena; Litov, Leandar
Metadynamics study of mutant human interferon-gamma forms
COMPUTERS & MATHEMATICS WITH APPLICATIONS, 64:272-277, AUG 2012
abstract, full text, DOI:10.1016/j.camwa.2012.01.061

Friedman, Aaron J.; Durrant, Jacob D.; Pierce, Levi C. T.; McCorvie, Thomas J.; Timson, David J.; McCammon, J. Andrew
The Molecular Dynamics of Trypanosoma brucei UDP-Galactose 4 '-Epimerase: A Drug Target for African Sleeping Sickness
CHEMICAL BIOLOGY & DRUG DESIGN, 80:173-181, AUG 2012
abstract, full text, DOI:10.1111/j.1747-0285.2012.01392.x

Osguthorpe, David J.; Sherman, Woody; Hagler, Arnold T.
Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering
CHEMICAL BIOLOGY & DRUG DESIGN, 80:182-193, AUG 2012
abstract, full text, DOI:10.1111/j.1747-0285.2012.01396.x

Daga, Pankaj R.; Zaveri, Nurulain T.
Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights intoagonist binding and activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1948-1961, AUG 2012
abstract, full text, DOI:10.1002/prot.24077

Beveridge, Allan J.; Wallis, Russell; Samani, Nilesh J.
A molecular dynamics study of C1r and C1s dimers: Implications for the structure of the C1 complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1987-1997, AUG 2012
abstract, full text, DOI:10.1002/prot.24087

Rennebaum, Sandra; Caflisch, Amedeo
Inhibition of interdomain motion in g-actin by the natural product latrunculin: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1998-2008, AUG 2012
abstract, full text, DOI:10.1002/prot.24088

Gnanasambandan, Kavitha; Magis, Andrew T.; Sayeski, Peter P.
A shift in the salt bridge interaction of residues D620 and E621 mediates the constitutive activation of Jak2-H538Q/K539L
MOLECULAR AND CELLULAR BIOCHEMISTRY, 367:125-140, AUG 2012
abstract, full text, DOI:10.1007/s11010-012-1326-7

Fang, Xiang; Fang, Ying; Liu, Li; Liu, Guangjian; Wu, Jianhua
Mapping Paratope on Antithrombotic Antibody 6B4 to Epitope on Platelet Glycoprotein Ibalpha via Molecular Dynamic Simulations
PLOS ONE, 7 Art. No. e42263, JUL 30 2012
abstract, full text, DOI:10.1371/journal.pone.0042263

Wang, Luying; Dumont, Randall S.; Dickson, James M.
Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 044102, JUL 28 2012
abstract, full text, DOI:10.1063/1.4734484

O'Reilly, Andrias O.; Eberhardt, Esther; Weidner, Christian; Alzheimer, Christian; Wallace, B. A.; Lampert, Angelika
Bisphenol A Binds to the Local Anesthetic Receptor Site to Block the Human Cardiac Sodium Channel
PLOS ONE, 7 Art. No. e41667, JUL 27 2012
abstract, full text, DOI:10.1371/journal.pone.0041667

Chien, Chin-Hsiang; Gao, Quan-Ze; Cooper, Arthur J. L.; Lyu, Jyun-Hong; Sheu, Sheh-Yi
Structural Insights into the Catalytic Active Site and Activity of Human Nit2/omega-Amidase KINETIC ASSAY AND MOLECULAR DYNAMICS SIMULATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:25715-25726, JUL 27 2012
abstract, full text, DOI:10.1074/jbc.M111.259119

Sinitskiy, Anton V.; Saunders, Marissa G.; Voth, Gregory A.
Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8363-8374, JUL 26 2012
abstract, full text, DOI:10.1021/jp2108895

Shirvanyants, David; Ding, Feng; Tsao, Douglas; Ramachandran, Srinivas; Dokholyan, Nikolay V.
Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8375-8382, JUL 26 2012
abstract, full text, DOI:10.1021/jp2114576

Singharoy, Abhishek; Joshi, Harshad; Miao, Yinglong; Ortoleva, Peter J.
Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8423-8434, JUL 26 2012
abstract, full text, DOI:10.1021/jp2119247

Su, Guoxiong; Czader, Arkadiusz; Homouz, Dirar; Bernardes, Gabriela; Mateen, Sana; Cheung, Margaret S.
Multiscale Simulation on a Light-Harvesting Molecular Triad
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8460-8473, JUL 26 2012
abstract, full text, DOI:10.1021/jp212273n

Nishima, Wataru; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji; Re, Suyong
Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8504-8512, JUL 26 2012
abstract, full text, DOI:10.1021/jp212550z

Sereda, Yuriy V.; Singharoy, Abhishek B.; Jarrold, Martin F.; Ortoleva, Peter J.
Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8534-8544, JUL 26 2012
abstract, full text, DOI:10.1021/jp2126174

Ovchinnikov, Victor; Karplus, Martin
Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8584-8603, JUL 26 2012
abstract, full text, DOI:10.1021/jp212634z

Lyons, Joseph A.; Aragao, David; Slattery, Orla; Pisliakov, Andrei V.; Soulimane, Tewfik; Caffrey, Martin
Structural insights into electron transfer in caa(3)-type cytochrome oxidase
NATURE, 487:514-518, JUL 26 2012
abstract, full text, DOI:10.1038/nature11182

Sardroodi, Jaber Jahanbin; Azamat, Jafar; Rastkar, Alireza; Yousefnia, Negar Rad
The preferential permeation of ions across carbon and boron nitride nanotubes
CHEMICAL PHYSICS, 403:105-112, JUL 25 2012
abstract, full text, DOI:10.1016/j.chemphys.2012.05.017

Swett, Rebecca; Cisneros, G. Andres; Feig, Andrew L.
Conformational Analysis of Clostridium difficile Toxin B and Its Implications for Substrate Recognition
PLOS ONE, 7 Art. No. e41518, JUL 23 2012
abstract, full text, DOI:10.1371/journal.pone.0041518

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning
Hydrogen Bonding Analysis of Hydroxyl Groups in Glucose Aqueous Solutions by a Molecular Dynamics Simulation Study
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 33:2238-2246, JUL 20 2012
abstract, full text, DOI:10.5012/bkcs.2012.33.7.2238

Bellesia, Giovanni; Chundawat, Shishir P. S.; Langan, Paul; Redondo, Antonio; Dale, Bruce E.; Gnanakaran, S.
Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8031-8037, JUL 19 2012
abstract, full text, DOI:10.1021/jp300354q

Li, Bian; Li, Wei; Du, Peng; Yu, Kun Qian; Fu, Wei
Molecular Insights into the D1R Agonist and D2R/D3R Antagonist Effects of the Natural Product (-)-Stepholidine: Molecular Modeling and Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8121-8130, JUL 19 2012
abstract, full text, DOI:10.1021/jp3049235

Gumbart, James; Schreiner, Eduard; Wilson, Daniel N.; Beckmann, Roland; Schulten, Klaus
Mechanisms of SecM-Mediated Stalling in the Ribosome
BIOPHYSICAL JOURNAL, 103:331-341, JUL 18 2012
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2012.06.005

Kraszewski, Sebastian; Bianco, Alberto; Tarek, Mounir; Ramseyer, Christophe
Insertion of Short Amino-Functionalized Single-Walled Carbon Nanotubes into Phospholipid Bilayer Occurs by Passive Diffusion
PLOS ONE, 7 Art. No. e40703, JUL 16 2012
abstract, full text, DOI:10.1371/journal.pone.0040703

Verkhivker, Gennady M.
Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics
PLOS ONE, 7 Art. No. e40897, JUL 16 2012
abstract, full text, DOI:10.1371/journal.pone.0040897

Alies, Bruno; LaPenna, Giovanni; Sayen, Stephanie; Guillon, Emmanuel; Hureau, Christelle; Faller, Peter
Insights into the Mechanisms of Amyloid Formation of Zn-II-Ab11-28: pH-Dependent Zinc Coordination and Overall Charge as Key Parameters for Kinetics and the Structure of Zn-II-Ab11-28 Aggregates
INORGANIC CHEMISTRY, 51:7897-7902, JUL 16 2012
abstract, full text, DOI:10.1021/ic300972j

Berezniak, Tomasz; Jaeschke, Andres; Smith, Jeremy C.; Imhof, Petra
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1603-1614, JUL 15 2012
abstract, full text, DOI:10.1002/jcc.22993

Yesylevskyy, Semen O.
Pteros: Fast and easy to use open-source C++ library for molecular analysis
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1632-1636, JUL 15 2012
abstract, full text, DOI:10.1002/jcc.22989

Shadrina, Maria S.; English, Ann M.; Peslherbe, Gilles H.
Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O-2 Pathways and Escape Routes in T-state Deoxyhemoglobin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:11177-11184, JUL 11 2012
abstract, full text, DOI:10.1021/ja300903c

Bhatnagar, Navendu; Kamath, Ganesh; Chelst, Issac; Potoff, Jeffrey J.
Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137 Art. No. 014502, JUL 7 2012
abstract, full text, DOI:10.1063/1.4730040

Lahti, Jennifer L.; Tang, Grace W.; Capriotti, Emidio; Liu, Tianyun; Altman, Russ B.
Bioinformatics and variability in drug response: a protein structural perspective
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 9:1409-1437, JUL 7 2012
abstract, full text, DOI:10.1098/rsif.2011.0843

Liu, Ming; Wang, Shuang; Sun, Tingguang; Su, Jiguo; Zhang, Yuanxing; Yue, Junjie; Sun, Zhiwei
Insight into the Structure, Dynamics and the Unfolding Property of Amylosucrases: Implications of Rational Engineering on Thermostability
PLOS ONE, 7 Art. No. e40441, JUL 6 2012
abstract, full text, DOI:10.1371/journal.pone.0040441

Nemec, Antonia A.; Donigan, Katherine A.; Murphy, Drew L.; Jaeger, Joachim; Sweasy, Joann B.
Colon Cancer-associated DNA Polymerase beta Variant Induces Genomic Instability and Cellular Transformation
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:23840-23849, JUL 6 2012
abstract, full text, DOI:10.1074/jbc.M112.362111

Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil
Study of microheterogeneous environment of protein Human Serum Albumin by an extrinsic fluorescent reporter: A spectroscopic study in combination with Molecular Docking and Molecular Dynamics Simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 112:48-58, JUL 2 2012
abstract, full text, DOI:10.1016/j.jphotobiol.2012.04.007

Sawada, Yasuyuki; Murase, Masaki; Sokabe, Masahiro
The gating mechanism of the bacterial mechanosensitive channel MscL revealed by molecular dynamics simulations From tension sensing to channel opening
CHANNELS, 6:317-331, JUL-AUG 2012
abstract, full text, DOI:10.4161/chan.21895

Anderson, Janet S.; LeMaster, David M.
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation
BIOPHYSICAL CHEMISTRY, 168:28-39, JUL 2012
abstract, full text, DOI:10.1016/j.bpc.2012.05.005

Louet, Maxime; Martinez, Jean; Floquet, Nicolas
GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002595, JUL 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002595

de Brevern, Alexandre G.; Bornot, Aurelie; Craveur, Pierrick; Etchebest, Catherine; Gelly, Jean-Christophe
PredyFlexy: flexibility and local structure prediction from sequence
NUCLEIC ACIDS RESEARCH, 40:W317-W322, JUL 2012
abstract, full text, DOI:10.1093/nar/gks482

Kundu, Sangeeta; Mukherjee, Sanchita; Bhattacharyya, Dhananjay
Effect of temperature on DNA double helix: An insight from molecular dynamics simulation
JOURNAL OF BIOSCIENCES, 37:445-455, JUL 2012
abstract, full text, DOI:10.1007/s12038-012-9215-5

Dalton, James; Kalid, Ori; Schushan, Maya; Ben-Tal, Nir; Villa-Freixa, Jordi
New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1842-1853, JUL 2012
abstract, full text, DOI:10.1021/ci2005884

Senne, Martin; Trendelkamp-Schroer, Benjamin; Mey, Antonia S. J. S.; Schuette, Christof; Noe, Frank
EMMA: A Software Package for Markov Model Building and Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2223-2238, JUL 2012
abstract, full text, DOI:10.1021/ct300274u

Branduardi, Davide; Bussi, Giovanni; Parrinello, Michele
Metadynamics with Adaptive Gaussians
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2247-2254, JUL 2012
abstract, full text, DOI:10.1021/ct3002464

Flaig, Denis; Beer, Matthias; Ochsenfeld, Christian
Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2260-2271, JUL 2012
abstract, full text, DOI:10.1021/ct300036s

Harrison, Christopher B.; Schulten, Klaus
Quantum and Classical Dynamics Simulations of ATP Hydrolysis in Solution
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2328-2335, JUL 2012
abstract, full text, TCBG publications, DOI:10.1021/ct200886j

Bakan, Ahmet; Nevins, Neysa; Lakdawala, Ami S.; Bahar, Ivet
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2435-2447, JUL 2012
abstract, full text, DOI:10.1021/ct300117j

Tanner, David E.; Phillips, James C.; Schulten, Klaus
GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2521-2530, JUL 2012
abstract, full text, TCBG publications, DOI:10.1021/ct3003089

De Biase, Pablo M.; Solano, Carlos J. F.; Markosyan, Suren; Czapla, Luke; Noskov, Sergei Yu
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2540-2551, JUL 2012
abstract, full text, DOI:10.1021/ct3004244

Ezzeldin, Hussein M.; Klauda, Jeffery B.; Solares, Santiago D.
Modeling of the major gas vesicle protein, GvpA: From protein sequence to vesicle wall structure
JOURNAL OF STRUCTURAL BIOLOGY, 179:18-28, JUL 2012
abstract, full text, DOI:10.1016/j.jsb.2012.04.015

Chen, Bao-Dong; Yang, Chuan-Lu; Yang, Jun-Sheng; Wang, Mei-Shan; Ma, Xiao-Guang
The translocation of DNA oligonucleotide with the water stream in carbon nanotubes
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 991:93-97, JUL 1 2012
abstract, full text, DOI:10.1016/j.comptc.2012.04.003

Lu, Zheng; Hou, Jingli; Wang, You; Liu, Jianhua
Involvement of Ser94 in RNase HIII from Chlamydophila pneumoniae in the recognition of a single ribonucleotide misincorporated into double-stranded DNA
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1824:859-865, JUL 2012
abstract, full text, DOI:10.1016/j.bbapap.2012.04.003

Vistoli, Giulio; Straniero, Valentina; Pedretti, Alessandro; Fumagalli, Laura; Bolchi, Cristiano; Pallavicini, Marco; Valoti, Ermanno; Testa, Bernard
Predicting the physicochemical profile of diastereoisomeric histidine-containing dipeptides by property space analysis
CHIRALITY, 24:566-576, JUL 2012
abstract, full text, DOI:10.1002/chir.22056

Gomez, Hansel; Lluch, Jose M.; Masgrau, Laura
Essential role of glutamate 317 in galactosyl transfer by alpha 3GalT: a computational study
CARBOHYDRATE RESEARCH, 356:204-208, JUL 2012
abstract, full text, DOI:10.1016/j.carres.2012.03.027

Tsigelny, Igor F.; Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.
An All-Atom Model of the Structure of Human Copper Transporter 1
CELL BIOCHEMISTRY AND BIOPHYSICS, 63:223-234, JUL 2012
abstract, full text, DOI:10.1007/s12013-012-9358-x

Schow, Eric V.; Freites, J. Alfredo; Nizkorodov, Alex; White, Stephen H.; Tobias, Douglas J.
Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1726-1736, JUL 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.02.029

Walrant, Astrid; Vogel, Alexander; Correia, Isabelle; Lequin, Olivier; Olausson, Bjoern E. S.; Desbat, Bernard; Sagan, Sandrine; Alves, Isabel D.
Membrane interactions of two arginine-rich peptides with different cell internalization capacities
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1755-1763, JUL 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.02.024

Sun, Hui-Yong; Ji, Feng-Qin
A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 423:319-324, JUN 29 2012
abstract, full text, DOI:10.1016/j.bbrc.2012.05.120

Wang, Shihao; Orabi, Esam A.; Baday, Sefer; Berneche, Simon; Lamoureux, Guillaume
Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10419-10427, JUN 27 2012
abstract, full text, DOI:10.1021/ja300129x

He, Chengzhi; Genchev, Georgi Z.; Lu, Hui; Li, Hongbin
Mechanically Untying a Protein Slipknot: Multiple Pathways Revealed by Force Spectroscopy and Steered Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10428-10435, JUN 27 2012
abstract, full text, DOI:10.1021/ja3003205

Li, Minghui; Zheng, Wenjun
All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps
BIOCHEMISTRY, 51:5022-5032, JUN 26 2012
abstract, full text, DOI:10.1021/bi300362a

Wise, John G.
Catalytic Transitions in the Human MDR1 P-Glycoprotein Drug Binding Sites
BIOCHEMISTRY, 51:5125-5141, JUN 26 2012
abstract, full text, DOI:10.1021/bi300299z

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing
Molecular Dynamics Simulations Suggest Ligand's Binding to Nicotinamidase/Pyrazinamidase
PLOS ONE, 7 Art. No. e39546, JUN 26 2012
abstract, full text, DOI:10.1371/journal.pone.0039546

Atkinson, Sarah C.; Dogovski, Con; Downton, Matthew T.; Pearce, F. Grant; Reboul, Cyril F.; Buckle, Ashley M.; Gerrard, Juliet A.; Dobson, Renwick C. J.; Wagner, John; Perugini, Matthew A.
Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine
PLOS ONE, 7 Art. No. e38318, JUN 25 2012
abstract, full text, DOI:10.1371/journal.pone.0038318

Craddock, Travis J. A.; George, Marc St.; Freedman, Holly; Barakat, Khaled H.; Damaraju, Sambasivarao; Hameroff, Stuart; Tuszynski, Jack A.
Computational Predictions of Volatile Anesthetic Interactions with the Microtubule Cytoskeleton: Implications for Side Effects of General Anesthesia
PLOS ONE, 7 Art. No. e37251, JUN 25 2012
abstract, full text, DOI:10.1371/journal.pone.0037251

Klose, Daniel; Klare, Johann P.; Grohmann, Dina; Kay, Christopher W. M.; Werner, Finn; Steinhoff, Heinz-Juergen
Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements
PLOS ONE, 7 Art. No. e39492, JUN 25 2012
abstract, full text, DOI:10.1371/journal.pone.0039492

Negi, Sunita; Aykut, Ayse Ozlem; Atilgan, Ali Rana; Atilgan, Canan
Calmodulin Readily Switches Conformation upon Protonating High pK(a) Acidic Residues
JOURNAL OF PHYSICAL CHEMISTRY B, 116:7145-7153, JUN 21 2012
abstract, full text, DOI:10.1021/jp3032995

Li, Yunlang; Gridley, Chelsea L.; Jaeger, Joachim; Sweasy, Joann B.; Schlick, Tamar
Unfavorable Electrostatic and Steric Interactions in DNA Polymerase beta E295K Mutant Interfere with the Enzyme's Pathway
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:9999-10010, JUN 20 2012
abstract, full text, DOI:10.1021/ja300361r

Siddiqua, Ayisha; Luo, Yin; Meyer, Virginia; Swanson, Michael A.; Yu, Xiang; Wei, Guanghong; Zheng, Jie; Eaton, Gareth R.; Ma, Buyong; Nussinov, Ruth; Eaton, Sandra S.; Margittai, Martin
Conformational Basis for Asymmetric Seeding Barrier in Filaments of Three- and Four-Repeat Tau
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10271-10278, JUN 20 2012
abstract, full text, DOI:10.1021/ja303498q

Pogoryelov, Denys; Klyszejko, Adriana L.; Krasnoselska, Ganna O.; Heller, Eva-Maria; Leone, Vanessa; Langerd, Julian D.; Vonck, Janet; Mueller, Daniel J.; Faraldo-Gomez, Jose D.; Meier, Thomas
Engineering rotor ring stoichiometries in the ATP synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1599-E1608, JUN 19 2012
abstract, full text, DOI:10.1073/pnas.1120027109

Cueva, Juan G.; Hsin, Jen; Huang, Kerwyn Casey; Goodman, Miriam B.
Posttranslational Acetylation of alpha-Tubulin Constrains Protofilament Number in Native Microtubules
CURRENT BIOLOGY, 22:1066-1074, JUN 19 2012
abstract, full text, DOI:10.1016/j.cub.2012.05.012

Pettelkau, Jens; Schroeder, Thomas; Ihling, Christian H.; Olausson, Bjoern E. S.; Koelbel, Knut; Lange, Christian; Sinz, Andrea
Structural Insights into Retinal Guanylylcyclase-GCAP-2 Interaction Determined by Cross-Linking and Mass Spectrometry
BIOCHEMISTRY, 51:4932-4949, JUN 19 2012
abstract, full text, DOI:10.1021/bi300064v

Popp, David; Narita, Akihiro; Lee, Lin Jie; Ghoshdastider, Umesh; Xue, Bo; Srinivasan, Ramanujam; Balasubramanian, Mohan K.; Tanaka, Toshitsugu; Robinson, Robert C.
Novel Actin-like Filament Structure from Clostridium tetani
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:21121-21129, JUN 15 2012
abstract, full text, DOI:10.1074/jbc.M112.341016

Jaron-Mendelson, Michal; Yossef, Rami; Appel, Michael Y.; Zilka, Alon; Hadad, Uzi; Afergan, Fabian; Rosental, Benyamin; Engel, Stanislav; Nedvetzki, Shlomo; Braiman, Alex; Porgador, Angel
Dimerization of NKp46 Receptor Is Essential for NKp46-Mediated Lysis: Characterization of the Dimerization Site by Epitope Mapping
JOURNAL OF IMMUNOLOGY, 188:6165-6174, JUN 15 2012
abstract, full text, DOI:10.4049/jimmunol.1102496

Chen, Wentian; Sun, Shisheng; Li, Zheng
Two Glycosylation Sites in H5N1 Influenza Virus Hemagglutinin That Affect Binding Preference by Computer-Based Analysis
PLOS ONE, 7 Art. No. e38794, JUN 14 2012
abstract, full text, DOI:10.1371/journal.pone.0038794

Chen, Ke; Eargle, John; Lai, Jonathan; Kim, Hajin; Abeysirigunawardena, Sanjaya; Mayerle, Megan; Woodson, Sarah; Ha, Taekjip; Luthey-Schulten, Zaida
Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6819-6831, JUN 14 2012
abstract, full text, DOI:10.1021/jp212614b

Salsbury, Freddie R., Jr.; Yuan, Ye; Knaggs, Michael H.; Poole, Leslie B.; Fetrow, Jacquelyn S.
Structural and Electrostatic Asymmetry at the Active Site in Typical and Atypical Peroxiredoxin Dimers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6832-6843, JUN 14 2012
abstract, full text, DOI:10.1021/jp212606k

Lee, One-Sun; Cho, Vince Y.; Schatz, George C.
A- to B-Form Transition in DNA Between Gold Surfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 116:7000-7005, JUN 14 2012
abstract, full text, DOI:10.1021/jp300877e

Soekmadji, Carolina; Angkawidjaja, Clement; Kelly, Leonard E.
Ca2+ Regulates the Drosophila Stoned-A and Stoned-B Proteins Interaction with the C2B Domain of Synaptotagmin-1
PLOS ONE, 7 Art. No. e38822, JUN 12 2012
abstract, full text, DOI:10.1371/journal.pone.0038822

Hsin, Jen; Gopinathan, Ajay; Huang, Kerwyn C.
Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:9432-9437, JUN 12 2012
abstract, full text, DOI:10.1073/pnas.1120761109

Bussiere, Cyril; Hashem, Yaser; Arora, Sucheta; Frank, Joachim; Johnson, Arlen W.
Integrity of the P-site is probed during maturation of the 60S ribosomal subunit
JOURNAL OF CELL BIOLOGY, 197:747-759, JUN 11 2012
abstract, full text, DOI:10.1083/jcb.201112131

Richards, Laura A.; Schaefer, Andrea I.; Richards, Bryce S.; Corry, Ben
The Importance of Dehydration in Determining Ion Transport in Narrow Pores
SMALL, 8:1701-1709, JUN 11 2012
abstract, full text, DOI:10.1002/smll.201102056

Kireeva, Maria L.; Opron, Kristopher; Seibold, Steve A.; Domecq, Celine; Cukier, Robert I.; Coulombe, Benoit; Kashlev, Mikhail; Burton, Zachary F.
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
BMC BIOPHYSICS, 5 Art. No. 11, JUN 7 2012
abstract, full text, DOI:10.1186/2046-1682-5-11

Anisimov, Victor M.; Bliznyuk, Andrey A.
Charge Transfer Effects in the GroEL-GroES Chaperonin Tetramer in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6261-6268, JUN 7 2012
abstract, full text, DOI:10.1021/jp211385e

Yu, Tao; Wang, Xiao-Qing; Sang, Jian-Ping; Pan, Chun-Xu; Zou, Xian-Wu; Chen, Tsung-Yu; Zou, Xiaoqin
Influences of Mutations on the Electrostatic Binding Free Energies of Chloride Ions in Escherichia coli CIC
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6431-6438, JUN 7 2012
abstract, full text, DOI:10.1021/jp300430f

Priya, M. Hamsa; Merchant, Safir; Asthagiri, Dilip; Paulaitis, Michael E.
Quasi-Chemical Theory of Cosolvent Hydrophobic Preferential Interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6506-6513, JUN 7 2012
abstract, full text, DOI:10.1021/jp301629j

Ozer, Gungor; Quirk, Stephen; Hernandez, Rigoberto
Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 215104, JUN 7 2012
abstract, full text, DOI:10.1063/1.4725183

Huggins, David J.
Benchmarking the thermodynamic analysis of water molecules around a model beta sheet
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1383-1392, JUN 5 2012
abstract, full text, DOI:10.1002/jcc.22971

Xiong, Wei; Cui, Tanxing; Cheng, Kejun; Yang, Fei; Chen, Shao-Rui; Willenbring, Dan; Guan, Yun; Pan, Hui-Lin; Ren, Ke; Xu, Yan; Zhang, Li
Cannabinoids suppress inflammatory and neuropathic pain by targeting alpha 3 glycine receptors
JOURNAL OF EXPERIMENTAL MEDICINE, 209:1121-1134, JUN 4 2012
abstract, full text, DOI:10.1084/jem.20120242

Ricci, Antonio; Anthopoulos, Athanasios; Massarotti, Alberto; Grimstead, Ian; Brancale, Andrea
Haptic-driven applications to molecular modeling: state-of-the-art and perspectives
FUTURE MEDICINAL CHEMISTRY, 4:1219-1228, JUN 2012
abstract, full text, DOI:10.4155/FMC.12.60

Sim, Adelene Y. L.; Minary, Peter; Levitt, Michael
Modeling nucleic acids
CURRENT OPINION IN STRUCTURAL BIOLOGY, 22:273-278, JUN 2012
abstract, full text, DOI:10.1016/j.sbi.2012.03.012

Lee, Whasil; Struempfer, Johan; Bennett, Vann; Schulten, Klaus; Marszalek, Piotr E.
Mutation of Conserved Histidines Alters Tertiary Structure and Nanomechanics of Consensus Ankyrin Repeats
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:19115-19121, JUN 1 2012
abstract, full text, TCBG publications, DOI:10.1074/jbc.M112.365569

Osipiuk, Jerzy; Mulligan, Rory; Bargassa, Monireh; Hamilton, John E.; Cunningham, Mark A.; Joachimiak, Andrzej
Characterization of Member of DUF1888 Protein Family, Self-cleaving and Self-assembling Endopeptidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:19452-19461, JUN 1 2012
abstract, full text, DOI:10.1074/jbc.M112.358069

Chakrabarty, Kuheli; Gupta, Sampad Narayan; Das, Gourab Kanti; Roy, Sukhendu
Theoretical studies on the pyridoxal-5 '-phosphate dependent enzyme dopa decarboxylase: Effect of Thr 246 residue on the co-factor-enzyme binding and reaction mechanism
INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS, 49:155-164, JUN 2012
abstract, full text

Dunstan, Mark S.; Barkauskaite, Eva; Lafite, Pierre; Knezevic, Claire E.; Brassington, Amy; Ahel, Marijan; Hergenrother, Paul J.; Leys, David; Ahel, Ivan
Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase
NATURE COMMUNICATIONS, 3 Art. No. 878, JUN 2012
abstract, full text, DOI:10.1038/ncomms1889

Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua
Crystal structure of a plectonemic RNA supercoil
NATURE COMMUNICATIONS, 3 Art. No. 901, JUN 2012
abstract, full text, DOI:10.1038/ncomms1903

Reboul, C. F.; Porebski, B. T.; Griffin, M. D. W.; Dobson, R. C. J.; Perugini, M. A.; Gerrard, J. A.; Buckle, A. M.
Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002537, JUN 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002537

Pina, Jason E.; Lee, Kuo Hao; Ytreberg, F. Marty
Effects of the binding of calcium ions on the structure and dynamics of the I broken vertical bar X174 virus investigated using molecular dynamics
JOURNAL OF BIOLOGICAL PHYSICS, 38:397-404, JUN 2012
abstract, full text, DOI:10.1007/s10867-011-9260-6

Guo, Wei Wei; Wan, Dun; Liao, Li Fu; Lin, Ying Wu
Unusual peroxidase activity of a myoglobin mutant with two distal histidines
CHINESE CHEMICAL LETTERS, 23:741-744, JUN 2012
abstract, full text, DOI:10.1016/j.cclet.2012.03.025

Martin, Daniel R.; Ozkan, S. Banu; Matyushov, Dmitry V.
Dissipative electro-elastic network model of protein electrostatics
PHYSICAL BIOLOGY, 9 Art. No. 036004, JUN 2012
abstract, full text, DOI:10.1088/1478-3975/9/3/036004

Librando, Vito; Pappalardo, Matteo
Engineered enzyme interactions with polycyclic aromatic hydrocarbons: A theoretical approach
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 36:30-35, JUN 2012
abstract, full text, DOI:10.1016/j.jmgm.2012.02.005

Prevost, Marie S.; Sauguet, Ludovic; Nury, Hugues; Van Renterghem, Catherine; Huon, Christele; Poitevin, Frederic; Baaden, Marc; Delarue, Marc; Corringer, Pierre-Jean
A locally closed conformation of a bacterial pentameric proton-gated ion channel
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 19:642-+, JUN 2012
abstract, full text, DOI:10.1038/nsmb.2307

Sgrignani, Jacopo; Magistrato, Alessandra
Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1595-1606, JUN 2012
abstract, full text, DOI:10.1021/ci300151h

Akbal-Delibas, Bahar; Hashmi, Irina; Shehu, Amarda; Haspel, Nurit
AN EVOLUTIONARY CONSERVATION-BASED METHOD FOR REFINING AND RERANKING PROTEIN COMPLEX STRUCTURES
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 10 Art. No. 1242002, JUN 2012
abstract, full text, DOI:10.1142/S0219720012420024

Puhl, Ana C.; Bernardes, Amanda; Silveira, Rodrigo L.; Yuan, Jing; Campos, Jessica L. O.; Saidemberg, Daniel M.; Palma, Mario S.; Cvoro, Aleksandra; Ayers, Stephen D.; Webb, Paul; Reinach, Peter S.; Skaf, Munir S.; Polikarpov, Igor
Mode of Peroxisome Proliferator-Activated Receptor gamma Activation by Luteolin
MOLECULAR PHARMACOLOGY, 81:788-799, JUN 2012
abstract, full text, DOI:10.1124/mol.111.076216

Pietra, Francesco
Molecular-Dynamics Simulation of Dioxygen Egress from 12/15-Lipoxygenase?Arachidonic Acid Complex
CHEMISTRY & BIODIVERSITY, 9:1019-1032, JUN 2012
abstract, full text, DOI:10.1002/cbdv.201100305

Mihajlovic, Tijana; Kachrimanis, Kyriakos; Graovac, Adrijana; Djuric, Zorica; Ibric, Svetlana
Improvement of Aripiprazole Solubility by Complexation with (2-Hydroxy)propyl-beta-cyclodextrin Using Spray Drying Technique
AAPS PHARMSCITECH, 13:623-631, JUN 2012
abstract, full text, DOI:10.1208/s12249-012-9786-3

Antonio Bermudez-Lugo, Jorge; Perez-Gonzalez, Oscar; Cecilia Rosales-Hernandez, Martha; Ilizaliturri-Flores, Ian; Trujillo-Ferrara, Jose; Correa-Basurto, Jose
Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations
JOURNAL OF MOLECULAR MODELING, 18:2301-2310, JUN 2012
abstract, full text, DOI:10.1007/s00894-011-1240-z

Nandi, Tapas K.; Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Mallik, Payel; Sukul, Dipankar; Bera, Asim K.
Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid-base coupled mechanism in plant thiol protease
JOURNAL OF MOLECULAR MODELING, 18:2633-2644, JUN 2012
abstract, full text, DOI:10.1007/s00894-011-1277-z

Bung, Navneet; Priyakumar, U. Deva
Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27
JOURNAL OF MOLECULAR MODELING, 18:2823-2829, JUN 2012
abstract, full text, DOI:10.1007/s00894-011-1298-7

Colletier, Jacques-Philippe; Aleksandrov, Alexey; Coquelle, Nicolas; Mraihi, Sonia; Mendoza-Barbera, Elena; Field, Martin; Madern, Dominique
Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions
MOLECULAR BIOLOGY AND EVOLUTION, 29:1683-1694, JUN 2012
abstract, full text, DOI:10.1093/molbev/mss015

Ponmurugan, M.; Vemparala, Satyavani
Studies on structural and average unfolding behaviours of FNIII domain of Contactin-1 protein by molecular dynamics simulation
FRONTIERS IN LIFE SCIENCE, 6:33-45, JUN 1 2012
abstract, full text, DOI:10.1080/21553769.2013.776995

Baker, Joseph; Wright, Stephen H.; Tama, Florence
Simulations of substrate transport in the multidrug transporter EmrD
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1620-1632, JUN 2012
abstract, full text, DOI:10.1002/prot.24056

Holland, Bryan W.; Vafaei, Shaghayegh; Tomberli, Bruno
Computer data analysis of the oscillating forward-reverse method
JOURNAL OF COMPUTATIONAL PHYSICS, 231:4355-4364, JUN 1 2012
abstract, full text, DOI:10.1016/j.jcp.2012.02.018

Yu, Rilei; Kaas, Quentin; Craik, David J.
Delineation of the Unbinding Pathway of alpha-Conotoxin Iml from the alpha 7 Nicotinic Acetylcholine Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6097-6105, MAY 31 2012
abstract, full text, DOI:10.1021/jp301352d

Akcapinar, Gunseli Bayram; Gul, Ozgur; Sezerman, Ugur O.
From in silico to in vitro: Modelling and production of Trichoderma reesei endoglucanase 1 and its mutant in Pichia pastoris
JOURNAL OF BIOTECHNOLOGY, 159:61-68, MAY 31 2012
abstract, full text, DOI:10.1016/j.jbiotec.2012.01.001

Gomes, Thiago C. F.; Skaf, Munir S.
Cellulose-Builder: A toolkit for building crystalline structures of cellulose
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1338-1346, MAY 30 2012
abstract, full text, DOI:10.1002/jcc.22959

Querol-Audi, Jordi; Yan, Chunli; Xu, Xiaojun; Tsutakawa, Susan E.; Tsai, Miaw-Sheue; Tainer, John A.; Cooper, Priscilla K.; Nogales, Eva; Ivanov, Ivaylo
Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:8528-8533, MAY 29 2012
abstract, full text, DOI:10.1073/pnas.1121116109

Rivalta, Ivan; Sultan, Mohammad M.; Lee, Ning-Shiuan; Manley, Gregory A.; Loria, J. Patrick; Batista, Victor S.
Allosteric pathways in imidazole glycerol phosphate synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1428-E1436, MAY 29 2012
abstract, full text, DOI:10.1073/pnas.1120536109

Kuo, An-Tsung; Chang, Chien-Hsiang; Shinoda, Wataru
Molecular Dynamics Study of Catanionic Bilayers Composed of Ion Pair Amphiphile with Double-Tailed Cationic Surfactant
LANGMUIR, 28:8156-8164, MAY 29 2012
abstract, full text, DOI:10.1021/la300651u

Sura, Lucie; Zima, Vlastimil; Marsakova, Lenka; Hynkova, Anna; Barvik, Ivan; Vlachova, Viktorie
C-terminal Acidic Cluster Is Involved in Ca2+-induced Regulation of Human Transient Receptor Potential Ankyrin 1 Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:18067-18077, MAY 25 2012
abstract, full text, DOI:10.1074/jbc.M112.341859

Zayner, Josiah P.; Antoniou, Chloe; Sosnick, Tobin R.
The Amino-Terminal Helix Modulates Light-Activated Conformational Changes in AsLOV2
JOURNAL OF MOLECULAR BIOLOGY, 419:61-74, MAY 25 2012
abstract, full text, DOI:10.1016/j.jmb.2012.02.037

Apgar, James; Ross, Mary; Zuo, Xiao; Dohle, Sarah; Sturtevant, Derek; Shen, Binzhang; de la Vega, Humberto; Lessard, Philip; Lazar, Gabor; Raab, R. Michael
A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches
PLOS ONE, 7 Art. No. e37355, MAY 23 2012
abstract, full text, DOI:10.1371/journal.pone.0037355

Liberato, Marcelo Vizona; Nascimento, Alessandro S.; Ayers, Steven D.; Lin, Jean Z.; Cvoro, Aleksandra; Silveira, Rodrigo L.; Martinez, Leandro; Souza, Paulo C. T.; Saidemberg, Daniel; Deng, Tuo; Amato, Angela Angelica; Togashi, Marie; Hsueh, Willa A.; Phillips, Kevin; Palma, Mario Sergio; Neves, Francisco A. R.; Skaf, Munir S.; Webb, Paul; Polikarpov, Igor
Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) gamma Activators and Pan-PPAR Partial Agonists
PLOS ONE, 7 Art. No. e36297, MAY 23 2012
abstract, full text, DOI:10.1371/journal.pone.0036297

Brunk, Elizabeth; Arey, J. Samuel; Rothlisberger, Ursula
Role of Environment for Catalysis of the DNA Repair Enzyme MutY
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:8608-8616, MAY 23 2012
abstract, full text, DOI:10.1021/ja301714j

Maiti, Atanu; Noon, Muhammad S.; MacKerell, Alexander D., Jr.; Pozharski, Edwin; Drohat, Alexander C.
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:8091-8096, MAY 22 2012
abstract, full text, DOI:10.1073/pnas.1201010109

Herrou, Julien; Rotskoff, Grant; Luo, Yun; Roux, Benoit; Crosson, Sean
Structural basis of a protein partner switch that regulates the general stress response of alpha-proteobacteria
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1415-E1423, MAY 22 2012
abstract, full text, DOI:10.1073/pnas.1116887109

Kneller, Gerald R.; Hinsen, Konrad; Calligari, Paolo
Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 191101, MAY 21 2012
abstract, full text, DOI:10.1063/1.4718380

Dixit, Anshuman; Verkhivker, Gennady M.
Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics
PLOS ONE, 7 Art. No. e37605, MAY 18 2012
abstract, full text, DOI:10.1371/journal.pone.0037605

Silveira, Rodrigo L.; Martinez, Julian; Skaf, Munir S.; Martinez, Leandro
Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5671-5678, MAY 17 2012
abstract, full text, DOI:10.1021/jp3017858

Legare, Sebastien; Laguee, Patrick
The Influenza Fusion Peptide Adopts a Flexible Flat V Conformation in Membranes
BIOPHYSICAL JOURNAL, 102:2270-2278, MAY 16 2012
abstract, full text, DOI:10.1016/j.bpj.2012.04.003

Elder, Robert M.; Jayaraman, Arthi
Sequence-Specific Recognition of Cancer Drug-DNA Adducts by HMGB1a Repair Protein
BIOPHYSICAL JOURNAL, 102:2331-2338, MAY 16 2012
abstract, full text, DOI:10.1016/j.bpj.2012.04.013

Sander, Wolfram; Roy, Saonli; Polyak, Iakov; Ramirez-Anguita, Juan Manuel; Sanchez-Garcia, Elsa
The Phenoxyl Radical-Water Complex-A Matrix Isolation and Computational Study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:8222-8230, MAY 16 2012
abstract, full text, DOI:10.1021/ja301528w

Reboul, Cyril F.; Mahmood, Khalid; Whisstock, James C.; Dunstone, Michelle A.
Predicting giant transmembrane beta-barrel architecture
BIOINFORMATICS, 28:1299-1302, MAY 15 2012
abstract, full text, DOI:10.1093/bioinformatics/bts152

Wereszczynski, Jeff; McCammon, J. Andrew
Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:7759-7764, MAY 15 2012
abstract, full text, DOI:10.1073/pnas.1117441109

Yakubovich, Alexander V.; Surdutovich, Eugene; Soloy'yov, Andrey V.
Thermomechanical damage of nucleosome by the shock wave initiated by ion passing through liquid water
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS, 279:135-139, MAY 15 2012
abstract, full text, DOI:10.1016/j.nimb.2011.10.069

da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical analysis of the color tuning mechanism of oxyluciferin and 5-hydroxyoxyluciferin
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 988:56-62, MAY 15 2012
abstract, full text, DOI:10.1016/j.comptc.2012.02.029

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Polar solvation dynamics of lysozyme from molecular dynamics studies
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 185102, MAY 14 2012
abstract, full text, DOI:10.1063/1.4712036

Stolzenberg, Sebastian; Khelashvili, George; Weinstein, Harel
Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5372-5383, MAY 10 2012
abstract, full text, DOI:10.1021/jp301726s

Li, Xiaoyi; Shi, Yanchao; Miao, Bing; Zhao, Yuliang
Effects of Embedded Carbon Nanotube on Properties of Biomembrane
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5391-5397, MAY 10 2012
abstract, full text, DOI:10.1021/jp301864z

Zhang, Miao; Abrams, Cameron; Wang, Liping; Gizzi, Anthony; He, Liping; Lin, Ruihe; Chen, Yuan; Loll, Patrick J.; Pascal, John M.; Zhang, Ji-fang
Structural Basis for Calmodulin as a Dynamic Calcium Sensor
STRUCTURE, 20:911-923, MAY 9 2012
abstract, full text, DOI:10.1016/j.str.2012.03.019

Li, Xiaoyi; Shi, Yanchao; Yang, Yuling; Du, Huailiang; Zhou, Ruhong; Zhao, Yuliang
How does water-nanotube interaction influence water flow through the nanochannel?
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 175101, MAY 7 2012
abstract, full text, DOI:10.1063/1.4707346

Weber, Adrian C. J.; Pizzirusso, Antonio; Muccioli, Luca; Zannoni, Claudio; Meerts, W. Leo; de Lange, Cornelis A.; Burnell, E. Elliott
Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 174506, MAY 7 2012
abstract, full text, DOI:10.1063/1.4705271

Kim, Taekyung; Ravilious, Geoffrey E.; Sept, David; Cooper, John A.
Mechanism for CARMIL Protein Inhibition of Heterodimeric Actin-capping Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:15251-15262, MAY 4 2012
abstract, full text, DOI:10.1074/jbc.M112.345447

Mori, Kenichi; Mahmood, Md. Iqbal; Neya, Saburo; Matsuzaki, Katsumi; Hoshino, Tyuji
Formation of GM1 Ganglioside Clusters on the Lipid Membrane Containing Sphingomyeline and Cholesterol
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5111-5121, MAY 3 2012
abstract, full text, DOI:10.1021/jp207881k

Liu, Yanxin; Struempfer, Johan; Freddolino, Peter L.; Gruebele, Martin; Schulten, Klaus
Structural Characterization of lambda-Repressor Folding from All-Atom Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:1117-1123, MAY 3 2012
abstract, full text, TCBG publications, DOI:10.1021/jz300017c

Ohkubo, Y. Zenmei; Pogorelov, Taras V.; Arcario, Mark J.; Christensen, Geoff A.; Tajkhorshid, Emad
Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model
BIOPHYSICAL JOURNAL, 102:2130-2139, MAY 2 2012
abstract, full text, DOI:10.1016/j.bpj.2012.03.015

Palmer, Samantha G.; Porotto, Matteo; Palermo, Laura M.; Cunha, Luis F.; Greengard, Olga; Moscona, Anne
Adaptation of Human Parainfluenza Virus to Airway Epithelium Reveals Fusion Properties Required for Growth in Host Tissue
MBIO, 3 Art. No. e00137-12, MAY-JUN 2012
abstract, full text, DOI:10.1128/mBio.00137-12

LeBard, David N.; Henin, Jerome; Eckenhoff, Roderic G.; Klein, Michael L.; Brannigan, Grace
General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002532, MAY 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002532

Lawrenz, Morgan; Wereszczynski, Jeff; Ortiz-Sanchez, Juan Manuel; Nichols, Sara E.; McCammon, J. Andrew
Thermodynamic integration to predict host-guest binding affinities
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 26:569-576, MAY 2012
abstract, full text, DOI:10.1007/s10822-012-9542-5

Demchuk, O. M.; Karpov, P. A.; Blume, Ya B.
Docking small ligands to molecule of the plant FtsZ protein: Application of the CUDA technology for faster computations
CYTOLOGY AND GENETICS, 46:172-179, MAY 2012
abstract, full text, DOI:10.3103/S0095452712030048

Sahu, Bhavani S.; Obbineni, Jagan M.; Sahu, Giriraj; Singh, Pradeep K.; Sonawane, Parshuram J.; Sasi, Binu K.; Allu, Prasanna K. R.; Maji, Samir K.; Bera, Amal K.; Senapati, Sanjib; Mahapatra, Nitish R.
Molecular interactions of the physiological anti-hypertensive peptide catestatin with the neuronal nicotinic acetylcholine receptor
JOURNAL OF CELL SCIENCE, 125:2323-2337, MAY 1 2012
abstract, full text, DOI:10.1242/jcs.103176

Zapata-Torres, Gerald; Fierro, Angelica; Miranda-Rojas, Sebastian; Guajardo, Carlos; Saez-Briones, Patricio; Cristian Salgado, J.; Celis-Barros, Cristian
Influence of Protonation on Substrate and Inhibitor Interactions at the Active Site of Human Monoamine Oxidase-A
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1213-1221, MAY 2012
abstract, full text, DOI:10.1021/ci300081w

Demir, Oezlem; Amaro, Rommie E.
Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1308-1318, MAY 2012
abstract, full text, DOI:10.1021/ci3001327

Sciacca, Michele F. M.; Chillemi, Rosa; Sciuto, Sebastiano; Pappalardo, Matteo; La Rosa, Carmelo; Grasso, Domenico; Milardi, Danilo
Interactions of two O-phosphorylresveratrol derivatives with model membranes
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 521:111-116, MAY 2012
abstract, full text, DOI:10.1016/j.abb.2012.03.022

Rogacheva, O. N.; Shchegolev, B. F.; Stefanov, V. E.; Zakharov, G. A.; Savvateeva-Popova, E. V.
Initiation of the 3 ':5 '-AMP-Induced Protein Kinase A I alpha Regulatory Subunit Conformational Transition. Part I. A202 and A326 are Critical Residues
BIOCHEMISTRY-MOSCOW, 77:456-464, MAY 2012
abstract, full text, DOI:10.1134/S0006297912050057

Masciocchi, Daniela; Villa, Stefania; Meneghetti, Fiorella; Pedretti, Alessandro; Barlocco, Daniela; Legnani, Laura; Toma, Lucio; Kwon, Byoung-Mog; Nakano, Shintaro; Asai, Akira; Gelain, Arianna
Biological and computational evaluation of an oxadiazole derivative (MD77) as a new lead for direct STAT3 inhibitors
MEDCHEMCOMM, 3:592-599, MAY 2012
abstract, full text, DOI:10.1039/c2md20018j

Maffeo, Christopher; Luan, Binquan; Aksimentiev, Aleksei
End-to-end attraction of duplex DNA
NUCLEIC ACIDS RESEARCH, 40:3812-3821, MAY 2012
abstract, full text, DOI:10.1093/nar/gkr1220

Miyake, Yusuke; Nagata, Toshi; Tanaka, Hirofumi; Yamazaki, Masashi; Ohta, Masahiro; Kokawa, Ryohei; Ogawa, Takuji
Entropy-Controlled 2D Supramolecular Structures of N,N '-Bis(n-alkyl)-naphthalenediimides on a HOPG Surface
ACS NANO, 6:3876-3887, MAY 2012
abstract, full text, DOI:10.1021/nn205006d

Whitby, Raymond L. D.; Gun'ko, Vladimir M.; Korobeinyk, Alina; Busquets, Rosa; Cundy, Andrew B.; Laszlo, Krisztina; Skubiszewska-Zieba, Jadwiga; Leboda, Roman; Tombacz, Etelka; Toth, Ildiko Y.; Kovacs, Krisztina; Mikhalovsky, Sergey V.
Driving Forces of Conformational Changes in Single-Layer Graphene Oxide
ACS NANO, 6:3967-3973, MAY 2012
abstract, full text, DOI:10.1021/nn3002278

Chan, Henry; Demortiere, Arnaud; Vukovic, Lela; Kral, Petr; Petit, Christophe
Colloidal Nanocube Supercrystals Stabilized by Multipolar Coulombic Coupling
ACS NANO, 6:4203-4213, MAY 2012
abstract, full text, DOI:10.1021/nn3007338

Chao, Ying; Makale, Milan; Karmali, Priya Prakash; Sharikov, Yuriy; Tsigelny, Igor; Merkulov, Sergei; Kesari, Santosh; Wrasidlo, Wolf; Ruoslahti, Erkki; Simberg, Dmitri
Recognition of Dextran-Superparamagnetic Iron Oxide Nanoparticle Conjugates (Feridex) via Macrophage Scavenger Receptor Charged Domains
BIOCONJUGATE CHEMISTRY, 23:1003-1009, MAY 2012
abstract, full text, DOI:10.1021/bc200685a

Palermo, Edmund F.; Vemparala, Satyavani; Kuroda, Kenichi
Cationic Spacer Arm Design Strategy for Control of Antimicrobial Activity and Conformation of Amphiphilic Methacrylate Random Copolymers
BIOMACROMOLECULES, 13:1632-1641, MAY 2012
abstract, full text, DOI:10.1021/bm300342u

Kraft, Johan F.; Vestergaard, Mikkel; Schiott, Birgit; Thogersen, Lea
Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1556-1569, MAY 2012
abstract, full text, DOI:10.1021/ct200921u

Aguayo, Daniel; Gonzalez-Nilo, Fernando D.; Chipot, Christophe
Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1765-1773, MAY 2012
abstract, full text, DOI:10.1021/ct200849k

He, Rui; Zhao, Liuyan; Petrone, Nicholas; Kim, Keun Soo; Roth, Michael; Hone, James; Kim, Philip; Pasupathy, Abhay; Pinczuk, Aron
Large Physisorption Strain in Chemical Vapor Deposition of Graphene on Copper Substrates
NANO LETTERS, 12:2408-2413, MAY 2012
abstract, full text, DOI:10.1021/nl300397v

Anbar, Michael; Gul, Ozgur; Lamed, Raphael; Sezerman, Ugur O.; Bayer, Edward A.
Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78:3458-3464, MAY 2012
abstract, full text, DOI:10.1128/AEM.07985-11

Hospital, Adam; Andrio, Pau; Fenollosa, Carles; Cicin-Sain, Damjan; Orozco, Modesto; Lluis Gelpi, Josep
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
BIOINFORMATICS, 28:1278-1279, MAY 1 2012
abstract, full text, DOI:10.1093/bioinformatics/bts139

Cui, Yubao; Bastien, David A.
Molecular dynamics simulations of PfAQP from the malarial parasite Plasmodium falciparum
MOLECULAR MEDICINE REPORTS, 5:1197-1201, MAY 2012
abstract, full text, DOI:10.3892/mmr.2012.822

Sokkar, Pandian; Sathis, Vani; Ramachandran, Murugesan
Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies
JOURNAL OF MOLECULAR MODELING, 18:1691-1700, MAY 2012
abstract, full text, DOI:10.1007/s00894-011-1150-0

Prasad, Nirmal K.; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V.; Kunal, Swaraj Priyaranjan; Srinivas, M.
In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes
JOURNAL OF MOLECULAR MODELING, 18:2013-2019, MAY 2012
abstract, full text, DOI:10.1007/s00894-011-1215-0

Lagos, Carlos F.; Araya-Secchi, Raul; Thomas, Pablo; Perez-Acle, Tomas; Tapia, Ricardo A.; Salas, Cristian O.
Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione
JOURNAL OF MOLECULAR MODELING, 18:2055-2064, MAY 2012
abstract, full text, DOI:10.1007/s00894-011-1224-z

Pandit, Kunal R.; Klauda, Jeffery B.
Membrane models of E-coli containing cyclic moieties in the aliphatic lipid chain
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1205-1210, MAY 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.01.009

Bondarenko, Vasyl; Mowrey, David; Tillman, Tommy; Cui, Tanxing; Liu, Lu Tian; Xu, Yan; Tang, Pei
NMR structures of the transmembrane domains of the alpha 4 beta 2 nAChR
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1261-1268, MAY 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.02.008

Mihajlovic, Maja; Lazaridis, Themis
Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1274-1283, MAY 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.01.016

Wang, Yi; Schlamadinger, Diana E.; Kim, Judy E.; McCammon, J. Andrew
Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1402-1409, MAY 2012
abstract, full text, DOI:10.1016/j.bbamem.2012.02.017

Sharma, Vivek; Wikstrom, Marten; Kaila, Ville R. I.
Dynamic water networks in cytochrome cbb(3) oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:726-734, MAY 2012
abstract, full text, DOI:10.1016/j.bbabio.2011.09.010

Chatterjee, Prathit; Sengupta, Neelanjana
Effect of the A30P mutation on the structural dynamics of micelle-bound alpha Synuclein released in water: a molecular dynamics study
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 41:483-489, MAY 2012
abstract, full text, DOI:10.1007/s00249-012-0803-y

Friesen, Douglas E.; Barakat, Khaled H.; Semenchenko, Valentyna; Perez-Pineiro, Rolando; Fenske, Bruce W.; Mane, Jonathan; Wishart, David S.; Tuszynski, Jack A.
Discovery of Small Molecule Inhibitors that Interact with gamma-Tubulin
CHEMICAL BIOLOGY & DRUG DESIGN, 79:639-652, MAY 2012
abstract, full text, DOI:10.1111/j.1747-0285.2012.01340.x

Chen Cong; Li Weizhong; Song Yongchen; Weng Lindong; Zhang Ning
Effects of Glycerol Concentrations on Self-diffusion Coefficients of Glycerol in Glycerol-Water-Sodium Chloride Ternary Solutions
ACTA CHIMICA SINICA, 70:1043-1046, APR 28 2012
abstract, full text

Perilla, Juan R.; Woolf, Thomas B.
Towards the prediction of order parameters from molecular dynamics simulations in proteins
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 164101, APR 28 2012
abstract, full text, DOI:10.1063/1.3702447

Yu, Xiang; Luo, Yin; Dinkel, Paul; Zheng, Jie; Wei, Guanghong; Margittai, Martin; Nussinov, Ruth; Ma, Buyong
Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:14950-14959, APR 27 2012
abstract, full text, DOI:10.1074/jbc.M112.340794

Chen, Rong; Chung, Shin-Ho
Conserved Functional Surface of Antimammalian Scorpion beta-Toxins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4796-4800, APR 26 2012
abstract, full text, DOI:10.1021/jp300127j

Xu, Yu; Ma, Buyong; Nussinov, Ruth
Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4801-4811, APR 26 2012
abstract, full text, DOI:10.1021/jp300307u

Rashid, M. Harunur; Kuyucak, Serdar
Affinity and Selectivity of ShK Toxin for the Kv1 Potassium Channels from Free Energy Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4812-4822, APR 26 2012
abstract, full text, DOI:10.1021/jp300639x

Yi, Zheng; Miao, Yinglong; Baudry, Jerome; Jain, Nitin; Smith, Jeremy C.
Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5028-5036, APR 26 2012
abstract, full text, DOI:10.1021/jp2102868

Yu, Xiang; Wang, Qiuming; Lin, Yinan; Zhao, Jun; Zhao, Chao; Zheng, Jie
Structure, Orientation, and Surface Interaction of Alzheimer Amyloid-beta Peptides on the Graphite
LANGMUIR, 28:6595-6605, APR 24 2012
abstract, full text, DOI:10.1021/la3002306

Han, Chen; Wang, Jianping
Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides
CHEMPHYSCHEM, 13:1522-1534, APR 23 2012
abstract, full text, DOI:10.1002/cphc.201100995

Matsushita, Shinji; Inoue, Yasuhiro; Adachi, Taiji
Quantitative analysis of extension-torsion coupling of actin filaments
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 420:710-713, APR 20 2012
abstract, full text, DOI:10.1016/j.bbrc.2012.02.048

Zanuy, David; Preat, Julien; Perpete, Eric A.; Aleman, Carlos
Response of Crown Ether Functionalized Polythiophenes to Alkaline Ions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4575-4583, APR 19 2012
abstract, full text, DOI:10.1021/jp209959a

Long, Feng; Su, Chih-Chia; Lei, Hsiang-Ting; Bolla, Jani Reddy; Do, Sylvia V.; Yu, Edward W.
Structure and mechanism of the tripartite CusCBA heavy-metal efflux complex
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 367:1047-1058, APR 19 2012
abstract, full text, DOI:10.1098/rstb.2011.0203

Jana, Asis K.; Sengupta, Neelanjana
Adsorption Mechanism and Collapse Propensities of the Full-Length, Monomeric A beta(1-42) on the Surface of a Single-Walled Carbon Nanotube: A Molecular Dynamics Simulation Study
BIOPHYSICAL JOURNAL, 102:1889-1896, APR 18 2012
abstract, full text, DOI:10.1016/j.bpj.2012.03.036

Papamokos, George V.; Tziatzos, George; Papageorgiou, Dimitrios G.; Georgatos, Spyros D.; Politou, Anastasia S.; Kaxiras, Efthimios
Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail
BIOPHYSICAL JOURNAL, 102:1926-1933, APR 18 2012
abstract, full text, DOI:10.1016/j.bpj.2012.03.030

Lv, Chunmei; Tan, Cheng; Qin, Meng; Zou, Dawei; Cao, Yi; Wang, Wei
Low Folding Cooperativity of Hp35 Revealed by Single-Molecule Force Spectroscopy and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 102:1944-1951, APR 18 2012
abstract, full text, DOI:10.1016/j.bpj.2012.03.028

Vashisth, Harish; Maragliano, Luca; Abrams, Cameron F.
"DFG-Flip" in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop
BIOPHYSICAL JOURNAL, 102:1979-1987, APR 18 2012
abstract, full text, DOI:10.1016/j.bpj.2012.03.031

Moss, Christopher L.; Turecek, Frantisek
Protonation sites in peptide dications and cation-radicalls containing beta-amino acid residues
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 316:57-67, APR 15 2012
abstract, full text, DOI:10.1016/j.ijms.2011.11.017

Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan
Exploring the inter-molecular interactions in amyloid-beta protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 145101, APR 14 2012
abstract, full text, DOI:10.1063/1.3702195

Krishnan, Marimuthu; Smith, Jeremy C.
Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4124-4133, APR 12 2012
abstract, full text, DOI:10.1021/jp2104853

Connelly, Laura; Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh
Effects of Point Substitutions on the Structure of Toxic Alzheimer's beta-Amyloid Channels: Atomic Force Microscopy and Molecular Dynamics Simulations
BIOCHEMISTRY, 51:3031-3038, APR 10 2012
abstract, full text, DOI:10.1021/bi300257e

Sen, Kakali; Hackett, John C.
Coupled Electron Transfer and Proton Hopping in the Final Step of CYP19-Catalyzed Androgen Aromatization
BIOCHEMISTRY, 51:3039-3049, APR 10 2012
abstract, full text, DOI:10.1021/bi300017p

Feng, Jie; Slocik, Joseph M.; Sarikaya, Mehmet; Naik, Rajesh R.; Farmer, Barry L.; Heinz, Hendrik
Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution
SMALL, 8:1049-1059, APR 10 2012
abstract, full text, DOI:10.1002/smll.201102066

Sarver, Jessica L.; Townsend, Jacqueline E.; Rajapakse, Gayathri; Jen-Jacobson, Linda; Saxena, Sunil
Simulating the Dynamics and Orientations of Spin-Labeled Side Chains in a Protein-DNA Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4024-4033, APR 5 2012
abstract, full text, DOI:10.1021/jp211094n

Lakkaraju, Asvin K. K.; Abrami, Laurence; Lemmin, Thomas; Blaskovic, Sanja; Kunz, Beatrice; Kihara, Akio; Dal Peraro, Matteo; van der Goot, Francoise Gisou
Palmitoylated calnexin is a key component of the ribosome-translocon complex
EMBO JOURNAL, 31:1823-1835, APR 4 2012
abstract, full text, DOI:10.1038/emboj.2012.15

Saunders, Marissa G.; Voth, Gregory A.
Comparison between Actin Filament Models: Coarse-Graining Reveals Essential Differences
STRUCTURE, 20:641-653, APR 4 2012
abstract, full text, DOI:10.1016/j.str.2012.02.008

Utesch, Tillmann; Sezer, Murat; Weidinger, Inez M.; Mroginski, Maria Andrea
Adsorption of Sulfite Oxidase on Self-Assembled Mono layers from Molecular Dynamics Simulations
LANGMUIR, 28:5761-5769, APR 3 2012
abstract, full text, DOI:10.1021/la205055g

Selvin, Jeyasigamani F. A.; Priyadarzini, Thanu R. K.; Veluraja, Kasinadar
Sialyldisaccharide conformations: a molecular dynamics perspective
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 26:375-385, APR 2012
abstract, full text, DOI:10.1007/s10822-012-9563-0

Lee, Kuo Hao; Ytreberg, F. Marty
Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure
ENTROPY, 14:630-641, APR 2012
abstract, full text, DOI:10.3390/e14040630

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Studies on the Interactions between beta(2) Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1005-1014, APR 2012
abstract, full text, DOI:10.1021/ci200594d

Furini, Simone; Domene, Carmen
On Conduction in a Bacterial Sodium Channel
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002476, APR 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002476

Shan, Jufang; Khelashvili, George; Mondal, Sayan; Mehler, Ernest L.; Weinstein, Harel
Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002473, APR 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002473

Thompson, Damien; Hermes, Jens P.; Quinn, Aidan J.; Mayor, Marcel
Scanning the Potential Energy Surface for Synthesis of Dendrimer-Wrapped Gold Clusters: Design Rules for True Single-Molecule Nanostructures
ACS NANO, 6:3007-3017, APR 2012
abstract, full text, DOI:10.1021/nn204470g

Lu, Shih-Jen; Chong, Fok-Ching
Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 13:4496-4507, APR 2012
abstract, full text, DOI:10.3390/ijms13044496

Lin, Ying-Wu; Wu, Yi-Mou; Liao, Li-Fu; Nie, Chang-Ming
Molecular modeling of cytochrome b(5) with a single cytochrome c-like thioether linkage
JOURNAL OF MOLECULAR MODELING, 18:1553-1560, APR 2012
abstract, full text, DOI:10.1007/s00894-011-1189-y

Lin, Ying-Wu; Wu, Yi-Mou; Liao, Li-Fu
Dynamics comparison of two myoglobins with a distinct heme active site
JOURNAL OF MOLECULAR MODELING, 18:1591-1596, APR 2012
abstract, full text, DOI:10.1007/s00894-011-1192-3

Hernandez, Griselda; Anderson, Janet S.; LeMaster, David M.
Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution
BIOPHYSICAL CHEMISTRY, 163:21-34, APR 2012
abstract, full text, DOI:10.1016/j.bpc.2012.02.002

Aktulga, H. M.; Fogarty, J. C.; Pandit, S. A.; Grama, A. Y.
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques
PARALLEL COMPUTING, 38:245-259, APR-MAY 2012
abstract, full text, DOI:10.1016/j.parco.2011.08.005

Espinoza-Moraga, Marlene; Caballero, Julio; Gaube, Friedemann; Winckler, Thomas; Santos, Leonardo S.
1-Benzyl-1,2,3,4-Tetrahydro-ss-Carboline as Channel Blocker of N-Methyl-d-Aspartate Receptors
CHEMICAL BIOLOGY & DRUG DESIGN, 79:594-599, APR 2012
abstract, full text, DOI:10.1111/j.1747-0285.2012.01317.x

Saladino, G.; Gauthier, L.; Bianciotto, M.; Gervasio, F. L.
Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1165-1170, APR 2012
abstract, full text, DOI:10.1021/ct3001377

Sieradzan, Adam K.; Scheraga, Harold A.; Liwo, Adam
Determination of Effective Potentials for the Stretching of C-alpha center dot center dot center dot C-alpha Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1334-1343, APR 2012
abstract, full text, DOI:10.1021/ct2008439

Singharoy, Abhishek; Sereda, Yuriy; Ortoleva, Peter J.
Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1379-1392, APR 2012
abstract, full text, DOI:10.1021/ct200574x

Bukovnik, U.; Gao, J.; Cook, G. A.; Shank, L. P.; Seabra, M. B.; Schultz, B. D.; Iwamoto, T.; Chen, J.; Tomich, J. M.
Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1039-1048, APR 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.07.037

Zhang, Lei; Yan, Feng; Zhang, Shengli; Lei, Dongsheng; Charles, M. Arthur; Cavigiolio, Giorgio; Oda, Michael; Krauss, Ronald M.; Weisgraber, Karl H.; Rye, Kerry-Anne; Pownall, Henry J.; Qiu, Xiayang; Ren, Gang
Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein
NATURE CHEMICAL BIOLOGY, 8:342-349, APR 2012
abstract, full text, DOI:10.1038/NCHEMBIO.796

Li, Yan; Hao, Ming; Ren, Hong; Zhang, Shuwei; Wang, Xia; Ma, Ming; Li, Guohui; Yang, Ling
Exploring the structure requirement for KC theta inhibitory activity of pyridinecarbonitrile derivatives: an in silico analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 34:76-88, APR 2012
abstract, full text, DOI:10.1016/j.jmgm.2011.12.010

Wereszczynski, Jeff; McCammon, J. Andrew
Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates
PROTEIN SCIENCE, 21:475-486, APR 2012
abstract, full text, DOI:10.1002/pro.2024

Calligari, Paolo A.; Salgado, Gilmar F.; Pelupessy, Philippe; Lopes, Philippe; Ouazzani, Jamal; Bodenhausen, Geoffrey; Abergel, Daniel
Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1196-1210, APR 2012
abstract, full text, DOI:10.1002/prot.24019

Asses, Yasmine; Venkatraman, Vishwesh; Leroux, Vincent; Ritchie, David W.; Maigret, Bernard
Exploring c-Met kinase flexibility by sampling and clustering its conformational space
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1227-1238, APR 2012
abstract, full text, DOI:10.1002/prot.24021

Gonnet, Pedro
A short note on the fast evaluation of dihedral angle potentials and their derivatives
JOURNAL OF COMPUTATIONAL PHYSICS, 231:2691-2694, APR 1 2012
full text, DOI:10.1016/j.jcp.2011.12.022

Priyadarzini, Thanu R. K.; Subashini, Balakrishnan; Selvin, Jeyasigamani F. A.; Veluraja, Kasinadar
Molecular dynamics simulation and quantum mechanical calculations on alpha-D-N-acetylneuraminic acid
CARBOHYDRATE RESEARCH, 351:93-97, APR 1 2012
abstract, full text, DOI:10.1016/j.carres.2012.01.015

Oakley, Aaron J.; Bhatia, Surabhi; Ecroyd, Heath; Garner, Brett
Molecular Dynamics Analysis of Apolipoprotein-D - Lipid Hydroperoxide Interactions: Mechanism for Selective Oxidation of Met-93
PLOS ONE, 7 Art. No. e34057, MAR 30 2012
abstract, full text, DOI:10.1371/journal.pone.0034057

Werner, Tim; Morris, Michael B.; Dastmalchi, Siavoush; Church, W. Bret
Structural modelling and dynamics of proteins for insights into drug interactions
ADVANCED DRUG DELIVERY REVIEWS, 64:323-343, MAR 30 2012
abstract, full text, DOI:10.1016/j.addr.2011.11.011

Clare, Daniel K.; Vasishtan, Daven; Stagg, Scott; Quispe, Joel; Farr, George W.; Topf, Maya; Horwich, Arthur L.; Saibil, Helen R.
ATP-Triggered Conformational Changes Delineate Substrate-Binding and -Folding Mechanics of the GroEL Chaperonin
CELL, 149:113-123, MAR 30 2012
abstract, full text, DOI:10.1016/j.cell.2012.02.047

Zhao, Ying; De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe
Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:868-880, MAR 30 2012
abstract, full text, DOI:10.1002/jcc.22883

Pizzirusso, A.; Di Cicco, M. B.; Tiberio, G.; Muccioli, L.; Berardi, R.; Zannoni, C.
Alignment of Small Organic Solutes in a Nematic Solvent: The Effect of Electrostatic Interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3760-3771, MAR 29 2012
abstract, full text, DOI:10.1021/jp3003799

Giussani, Lara; Tabacchi, Gloria; Gianotti, Enrica; Coluccia, Salvatore; Fois, Ettore
Disentangling protein-silica interactions
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 370:1463-1477, MAR 28 2012
abstract, full text, DOI:10.1098/rsta.2011.0267

Huang, Yulin; Rizzo, Robert C.
A Water-Based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases
BIOCHEMISTRY, 51:2390-2406, MAR 27 2012
abstract, full text, DOI:10.1021/bi2016553

Jeong, Woog-Jin; Ha, Man Yeong; Yoon, Hyun Sik; Ambrosia, Matthew
Dynamic Behavior of Water Droplets on Solid Surfaces with Pillar-Type Nanostructures
LANGMUIR, 28:5360-5371, MAR 27 2012
abstract, full text, DOI:10.1021/la205106v

Craddock, Travis J. A.; Tuszynski, Jack A.; Chopra, Deepak; Casey, Noel; Goldstein, Lee E.; Hameroff, Stuart R.; Tanzi, Rudolph E.
The Zinc Dyshomeostasis Hypothesis of Alzheimer's Disease
PLOS ONE, 7 Art. No. e33552, MAR 23 2012
abstract, full text, DOI:10.1371/journal.pone.0033552

Helbing, Jan; Devereux, Michael; Nienhaus, Karin; Nienhaus, G. Ulrich; Hamm, Peter; Meuwly, Markus
Temperature Dependence of the Heat Diffusivity of Proteins
JOURNAL OF PHYSICAL CHEMISTRY A, 116:2620-2628, MAR 22 2012
abstract, full text, DOI:10.1021/jp2061877

Jones, Peter M.; George, Anthony M.
Role of the D-Loops in Allosteric Control of ATP Hydrolysis in an ABC Transporter
JOURNAL OF PHYSICAL CHEMISTRY A, 116:3004-3013, MAR 22 2012
abstract, full text, DOI:10.1021/jp211139s

Kwon, Taekyung; Roux, Benoit; Jo, Sunhwan; Klauda, Jeffery B.; Harris, Andrew L.; Bargiello, Thaddeus A.
Molecular Dynamics Simulations of the Cx26 Hemichannel: Insights into Voltage-Dependent Loop-Gating
BIOPHYSICAL JOURNAL, 102:1341-1351, MAR 21 2012
abstract, full text, DOI:10.1016/j.bpj.2012.02.009

Cheng, Mary Hongying; Coalson, Rob D.
Molecular Dynamics Investigation of Cl- and Water Transport through a Eukaryotic CLC Transporter
BIOPHYSICAL JOURNAL, 102:1363-1371, MAR 21 2012
abstract, full text, DOI:10.1016/j.bpj.2012.01.056

Choi, Kyu-Min; Kwon, Chan Ho; Kim, Hong Lae; Hwang, Hyonseok
Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 33:911-916, MAR 20 2012
abstract, full text, DOI:10.5012/bkcs.2012.33.3.911

Wilkins, Sarah E.; Karttunen, Sarah; Hampton-Smith, Rachel J.; Murchland, Iain; Chapman-Smith, Anne; Peet, Daniel J.
Factor Inhibiting HIF (FIH) Recognizes Distinct Molecular Features within Hypoxia-inducible Factor-alpha (HIF-alpha) versus Ankyrin Repeat Substrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:8769-8781, MAR 16 2012
abstract, full text, DOI:10.1074/jbc.M111.294678

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning
Formation of water and glucose clusters by hydrogen bonds in glucose aqueous solutions
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 984:85-92, MAR 15 2012
abstract, full text, DOI:10.1016/j.comptc.2012.01.013

Falvo, Cyril; Zhuang, Wei; Kim, Yung Sam; Axelsen, Paul H.; Hochstrasser, Robin M.; Mukamel, Shaul
Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3322-3330, MAR 15 2012
abstract, full text, DOI:10.1021/jp2096423

Yeh, In-Chul; Ripoll, Daniel R.; Wallqvist, Anders
Free Energy Difference in Indolicidin Attraction to Eukaryotic and Prokaryotic Model Cell Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3387-3396, MAR 15 2012
abstract, full text, DOI:10.1021/jp211883u

Wang, Beibei; Weng, Jingwei; Fan, Kangnian; Wang, Wenning
Interdomain Flexibility and pH-Induced Conformational Changes of AcrA Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3411-3420, MAR 15 2012
abstract, full text, DOI:10.1021/jp212221v

Moss, Christopher L.; Chamot-Rooke, Julia; Nicol, Edith; Brown, Jeffery; Campuzano, Iain; Richardson, Keith; Williams, Jonathan P.; Bush, Matthew F.; Bythell, Benjamin; Paizs, Bela; Turecek, Frantisek
Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3445-3456, MAR 15 2012
abstract, full text, DOI:10.1021/jp3000784

McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.
Defects in DNA: Lessons from Molecular Motor Design
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:689-693, MAR 15 2012
abstract, full text, DOI:10.1021/jz201649k

Zobnina, Valentina G.; Kosevich, Marina V.; Chagovets, Vitaliy V.; Boryak, Oleg A.; Vekey, Karoly; Goemoery, Agnes; Kulyk, Anna N.
Interactions of oligomers of organic polyethers with histidine amino acid
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 26:532-540, MAR 15 2012
abstract, full text, DOI:10.1002/rcm.5342

Harada, Ryuhei; Sugita, Yuji; Feig, Michael
Protein Crowding Affects Hydration Structure and Dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:4842-4849, MAR 14 2012
abstract, full text, DOI:10.1021/ja211115q

Bastug, Turgut; Heinzelmann, Germano; Kuyucak, Serdar; Salim, Marietta; Vandenberg, Robert J.; Ryan, Renae M.
Position of the Third Na+ Site in the Aspartate Transporter Glt(Ph) and the Human Glutamate Transporter, EAAT1
PLOS ONE, 7 Art. No. e33058, MAR 13 2012
abstract, full text, DOI:10.1371/journal.pone.0033058

Ngo, Van A.
Parallel-pulling protocol for free-energy evaluation
PHYSICAL REVIEW E, 85 Art. No. 036702, MAR 13 2012
abstract, full text, DOI:10.1103/PhysRevE.85.036702

Sanford, Brianne; Cao, Bach; Johnson, James M.; Zimmerman, Kurt; Strom, Alexander M.; Mueller, Robyn M.; Bhattacharyya, Sudeep; Musier-Forsyth, Karin; Hati, Sanchita
Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases
BIOCHEMISTRY, 51:2146-2156, MAR 13 2012
abstract, full text, DOI:10.1021/bi300097g

Du, Juan; Dong, Hao; Zhou, Huan-Xiang
Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:4140-4145, MAR 13 2012
abstract, full text, DOI:10.1073/pnas.1119546109

Diaz, Natalia; Suarez, Dimas
Alternative Interdomain Configurations of the Full-Length MMP-2 Enzyme Explored by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2677-2686, MAR 8 2012
abstract, full text, DOI:10.1021/jp211088d

Rodriguez, Javier; Elola, M. Dolores; Laria, D.
Ionic Liquid Aqueous Solutions under Nanoconfinement
JOURNAL OF PHYSICAL CHEMISTRY C, 116:5394-5400, MAR 8 2012
abstract, full text, DOI:10.1021/jp211101a

Chen, Rong; Chung, Shin-Ho
Engineering a Potent and Specific Blocker of Voltage-Gated Potassium Channel Kv1.3, a Target for Autoimmune Diseases
BIOCHEMISTRY, 51:1976-1982, MAR 6 2012
abstract, full text, DOI:10.1021/bi201811j

Ranganathan, Srivastav; Singh, Pradeep K.; Singh, Uday; Singru, Praful S.; Padinhateeri, Ranjith; Maji, Samir K.
Molecular Interpretation of ACTH-beta-Endorphin Coaggregation: Relevance to Secretory Granule Biogenesis
PLOS ONE, 7 Art. No. e31924, MAR 5 2012
abstract, full text, DOI:10.1371/journal.pone.0031924

Huang, Qiang; Herrmann, Andreas
Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues
PROTEIN & CELL, 3:230-238, MAR 2012
abstract, full text, DOI:10.1007/s13238-012-2035-4

Ghodsi, Hossein; Kazemi, M. T.
Elastic Properties of Actin Assemblies in Different States of Nucleotide Binding
CELLULAR AND MOLECULAR BIOENGINEERING, 5:1-13, MAR 2012
abstract, full text, DOI:10.1007/s12195-011-0181-z

Gorham, Ronald D., Jr.; Kieslich, Chris A.; Morikis, Dimitrios
Complement Inhibition by Staphylococcus aureus: Electrostatics of C3d-EfbC and C3d-Ehp Association
CELLULAR AND MOLECULAR BIOENGINEERING, 5:32-43, MAR 2012
abstract, full text, DOI:10.1007/s12195-011-0195-6

Wan, Dun; Liao, Li-Fu; Zhao, Min-Min; Wu, Min-Long; Wu, Yi-Mou; Lin, Ying-Wu
Interactions of uranyl ion with cytochrome b(5) and its His39Ser variant as revealed by molecular simulation in combination with experimental methods
JOURNAL OF MOLECULAR MODELING, 18:1009-1013, MAR 2012
abstract, full text, DOI:10.1007/s00894-011-1097-1

Gabrielsen, Mari; Ravna, Aina Westrheim; Kristiansen, Kurt; Sylte, Ingebrigt
Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 18:1073-1085, MAR 2012
abstract, full text, DOI:10.1007/s00894-011-1133-1

Moreno-Vargas, Liliana; Correa-Basurto, Jose; Maroun, Rachid C.; Fernandez, Francisco J.
Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking
JOURNAL OF MOLECULAR MODELING, 18:1189-1205, MAR 2012
abstract, full text, DOI:10.1007/s00894-011-1143-z

Xia Dong-hui; Ren Xu-dong; Jiao Long; Li Hua
Inclusion Modes of Berberine with beta-Cyclodextrin in Aqueous Solution
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 28:282-286, MAR 2012
abstract, full text

Tsigelny, Igor F.; Sharikov, Yuriy; Wrasidlo, Wolfgang; Gonzalez, Tania; Desplats, Paula A.; Crews, Leslie; Spencer, Brian; Masliah, Eliezer
Role of alpha-synuclein penetration into the membrane in the mechanisms of oligomer pore formation
FEBS JOURNAL, 279:1000-1013, MAR 2012
abstract, full text, DOI:10.1111/j.1742-4658.2012.08489.x

Pan, Jianjun; Chen, Qiang; Willenbring, Dan; Yoshida, Ken; Tillman, Tommy; Kashlan, Ossama B.; Cohen, Aina; Kong, Xiang-Peng; Xu, Yan; Tang, Pei
Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine
NATURE COMMUNICATIONS, 3 Art. No. 714, MAR 2012
abstract, full text, DOI:10.1038/ncomms1703

Zou, Xueqing; Ma, Wen; Solov'yov, Ilia A.; Chipot, Christophe; Schulten, Klaus
Recognition of methylated DNA through methyl-CpG binding domain proteins
NUCLEIC ACIDS RESEARCH, 40:2747-2758, MAR 2012
abstract, full text, TCBG publications, DOI:10.1093/nar/gkr1057

Craddock, Travis J. A.; Tuszynski, Jack A.; Hameroff, Stuart
Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002421, MAR 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002421

Reboul, Cyril F.; Meyer, Grischa R.; Porebski, Benjamin T.; Borg, Natalie A.; Buckle, Ashley M.
Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002404, MAR 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002404

Satpati, Priyadarshi; Simonson, Thomas
Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1264-1282, MAR 2012
abstract, full text, DOI:10.1002/prot.24023

Lu, Wenzhe; Negi, Surendra S.; Oberhauser, Andres F.; Braun, Werner
Engineering proteins with enhanced mechanical stability by force-specific sequence motifs
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1308-1315, MAR 2012
abstract, full text, DOI:10.1002/prot.24027

Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke
Structural features that predict real-value fluctuations of globular proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1425-1435, MAR 2012
abstract, full text, DOI:10.1002/prot.24040

Bernini, Caterina; Pogni, Rebecca; Basosi, Riccardo; Sinicropi, Adalgisa
The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1476-1483, MAR 2012
abstract, full text, DOI:10.1002/prot.24046

Moss, Christopher L.; Liang, Wenkel; Li, Xiaosong; Turecek, Frantisek
The Early Life of a Peptide Cation-Radical. Ground and Excited-State Trajectories of Electron-Based Peptide Dissociations During the First 330 Femtoseconds
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 23:446-459, MAR 2012
abstract, full text, DOI:10.1007/s13361-011-0283-9

Denisov, I. G.; Shih, A. Y.; Sligar, S. G.
Structural differences between soluble and membrane bound cytochrome P450s
JOURNAL OF INORGANIC BIOCHEMISTRY, 108:150-158, MAR 2012
abstract, full text, DOI:10.1016/j.jinorgbio.2011.11.026

Saiz-Poseu, Javier; Faraudo, Jordi; Figueras, Antoni; Alibes, Ramon; Busque, Felix; Ruiz-Molina, Daniel
Switchable Self-Assembly of a Bioinspired Alkyl Catechol at a Solid/Liquid Interface: Competitive Interfacial, Noncovalent, and Solvent Interactions
CHEMISTRY-A EUROPEAN JOURNAL, 18:3056-3063, MAR 2012
abstract, full text, DOI:10.1002/chem.201101940

Pietra, Francesco
Understanding How H-NOX (Heme Nitric Oxide/Oxygen) Domain Works Needs First Clarifying How Diatomic Gases Are Relocated Inside This Sensing Protein. A Molecular-Mechanics Approach
CHEMISTRY & BIODIVERSITY, 9:606-614, MAR 2012
abstract, full text, DOI:10.1002/cbdv.201100382

Ballenegger, V.; Cerda, J. J.; Holm, C.
How to Convert SPME to P3M: Influence Functions and Error Estimates
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:936-947, MAR 2012
abstract, full text, DOI:10.1021/ct2001792

Capone, Ricardo; Jang, Hyunbum; Kotler, Samuel A.; Connelly, Laura; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh
All-D-Enantiomer of beta-Amyloid Peptide Forms Ion Channels in Lipid Bilayers
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1143-1152, MAR 2012
abstract, full text, DOI:10.1021/ct200885r

Yanagita, Hiroshi; Yamamoto, Norio; Fuji, Hideyoshi; Liu, Xinli; Ogata, Masakazu; Yokota, Mizuho; Takaku, Hiroshi; Hasegawa, Hideki; Odagiri, Takato; Tashiro, Masato; Hoshino, Tyuji
Mechanism of Drug Resistance of Hemagglutinin of Influenza Virus and Potent Scaffolds Inhibiting Its Function
ACS CHEMICAL BIOLOGY, 7:552-562, MAR 2012
abstract, full text, DOI:10.1021/cb200332k

Li, Ling; Li, Songlin; Jones, Martin K.; Segrest, Jere P.
Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1821:481-489, MAR 2012
abstract, full text, DOI:10.1016/j.bbalip.2011.10.013

Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Guchhait, Nikhil
Binding interaction between plasma protein bovine serum albumin and flexible charge transfer fluorophore: A spectroscopic study in combination with molecular docking and molecular dynamics simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY, 231:19-27, MAR 1 2012
abstract, full text, DOI:10.1016/j.jphotochem.2011.12.002

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J.
Viscoelastic properties of model segments of collagen molecules
MATRIX BIOLOGY, 31:141-149, MAR 2012
abstract, full text, DOI:10.1016/j.matbio.2011.11.005

Willis, Chris D.; Oashi, Taiji; Busby, Ben; Mackerell, Alexander D., Jr.; Bloch, Robert J.
Hydrophobic residues in small ankyrin 1 participate in binding to obscurin
MOLECULAR MEMBRANE BIOLOGY, 29:36-51, MAR 2012
abstract, full text, DOI:10.3109/09687688.2012.660709

Stober, Spencer T.; Abrams, Cameron F.
Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors
PROTEIN SCIENCE, 21:307-317, MAR 2012
abstract, full text, DOI:10.1002/pro.2016

Morozov, Dmitry; Khrenova, Maria; Andrijchenko, Natalya; Grigorenko, Bella; Nemukhin, Alexander
Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 983:88-94, MAR 1 2012
abstract, full text, DOI:10.1016/j.comptc.2012.01.009

Perez-Siles, Gonzalo; Nunez, Enrique; Morreale, Antonio; Jimenez, Esperanza; Leo-Macias, Alejandra; Pita, Guillermo; Cherubino, Francesca; Sangaletti, Rachele; Bossi, Elena; Ortiz, Angel R.; Aragon, Carmen; Lopez-Corcuera, Beatriz
An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling
BIOCHEMICAL JOURNAL, 442:323-334, MAR 1 2012
abstract, full text, DOI:10.1042/BJ20110247

Sergelius, Christian; Niinivehmas, Sanna; Maula, Terhi; Kurita, Mayuko; Yamaguchi, Shou; Yamamoto, Tetsuya; Katsumura, Shigeo; Pentikainen, Olli T.; Slotte, J. Peter
Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:474-480, MAR 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.10.013

Cui, Tanxing; Mowrey, David; Bondarenko, Vasyl; Tillman, Tommy; Ma, Dejian; Landrum, Elizabeth; Perez-Aguilar, Jose Manuel; He, Jing; Wang, Wei; Saven, Jeffery G.; Eckenhoff, Roderic G.; Tang, Pei; Xu, Yan
NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:617-626, MAR 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.11.021

Kuttel, Michelle; Ravenscroft, Neil; Foschiatti, Michela; Cescutti, Paola; Rizzo, Roberto
Conformational properties of two exopolysaccharides produced by Inquilinus limosus, a cystic fibrosis lung pathogen
CARBOHYDRATE RESEARCH, 350:40-48, MAR 1 2012
abstract, full text, DOI:10.1016/j.carres.2011.12.025

Sun, Chongbo; Tang, Tian; Uludag, Hasan
Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2405-2413, MAR 1 2012
abstract, full text, DOI:10.1021/jp211716v

Wedberg, Rasmus; Abildskov, Jens; Peters, Gunther H.
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2575-2585, MAR 1 2012
abstract, full text, DOI:10.1021/jp211054u

Vanni, S.; Rothlisberger, U.
A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations
CURRENT MEDICINAL CHEMISTRY, 19:1135-1145, MAR 2012
abstract, full text

Noinaj, Nicholas; Easley, Nicole C.; Oke, Muse; Mizuno, Naoko; Gumbart, James; Boura, Evzen; Steere, Ashley N.; Zak, Olga; Aisen, Philip; Tajkhorshid, Emad; Evans, Robert W.; Gorringe, Andrew R.; Mason, Anne B.; Steven, Alasdair C.; Buchanan, Susan K.
Structural basis for iron piracy by pathogenic Neisseria
NATURE, 483:53-U92, MAR 1 2012
abstract, full text, DOI:10.1038/nature10823

Domene, Carmen; Illingworth, Christopher J. R.
Effects of point mutations in pVHL on the binding of HIF-1 alpha
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:733-746, MAR 2012
abstract, full text, DOI:10.1002/prot.23230

Girolami, Antonio; Scarparo, Pamela; Bonamigo, Emanuela; Santarossa, Liliana; Cristiani, Andrea; Moro, Stefano; Lombardi, Anna Maria
A cluster of factor XI-deficient patients due to a new mutation (Ile 436 Lys) in northeastern Italy
EUROPEAN JOURNAL OF HAEMATOLOGY, 88:229-236, MAR 2012
abstract, full text, DOI:10.1111/j.1600-0609.2011.01723.x

Enlow, Mark A.
Binding of TNT to amplifying fluorescent polymers: An ab initio and molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 33:12-18, MAR 2012
abstract, full text, DOI:10.1016/j.jmgm.2011.09.001

Norris, Scott E.; Landstrom, Jens; Weintraub, Andrej; Bull, Thomas E.; Widmalm, Goran; Freedberg, Daron I.
Transient hydrogen bonding in uniformly 13C,15N-Labeled Carbohydrates in Water
BIOPOLYMERS, 97:145-154, MAR 2012
abstract, full text, DOI:10.1002/bip.21710

Ramya, L.; Gautham, N.
Conformational space exploration of met- and Leu-enkephalin using the mols method, molecular dynamics, and Monte Carlo simulation-a comparative study
BIOPOLYMERS, 97:165-176, MAR 2012
abstract, full text, DOI:10.1002/bip.21721

Domene, Carmen; Furini, Simone
Molecular Dynamics Simulations of the TrkH Membrane Protein
BIOCHEMISTRY, 51:1559-1565, FEB 28 2012
abstract, full text, DOI:10.1021/bi201586n

Ishikawa, Takao; Krzysko, Krystiana A.; Kowalska-Loth, Barbara; Skrajna, Aleksandra M.; Czubaty, Alicja; Girstun, Agnieszka; Cieplak, Maja K.; Lesyng, Bogdan; Staron, Krzysztof
Activities of Topoisomerase I in Its Complex with SRSF1
BIOCHEMISTRY, 51:1803-1816, FEB 28 2012
abstract, full text, DOI:10.1021/bi300043t

Wang, Hai-Long; Cheng, Xiaolin; Sine, Steven M.
Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6482-6489, FEB 24 2012
abstract, full text, DOI:10.1074/jbc.M111.305839

Zhou, Ke; Gao, Yang; Hoy, Julie A.; Mann, Francis M.; Honzatko, Richard B.; Peters, Reuben J.
Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6840-6850, FEB 24 2012
abstract, full text, DOI:10.1074/jbc.M111.337592

Avila-Salas, Fabian; Sandoval, Claudia; Caballero, Julio; Guinez-Molinos, Sergio; Santos, Leonardo S.; Cachau, Raul E.; Gonzalez-Nilo, Fernando D.
Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2031-2039, FEB 23 2012
abstract, full text, DOI:10.1021/jp2069122

Sgrignani, Jacopo; Magistrato, Alessandra
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2259-2268, FEB 23 2012
abstract, full text, DOI:10.1021/jp206475d

Hilder, Tamsyn A.; Yang, Rui; Gordon, Dan; Rendell, Alistair P.; Chung, Shin-Ho
Silicon Carbide Nanotube as a Chloride-Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4465-4470, FEB 23 2012
abstract, full text, DOI:10.1021/jp2113335

Liu, Peng; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Solvent-Controlled Shuttling in a Molecular Switch
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4471-4476, FEB 23 2012
abstract, full text, DOI:10.1021/jp2114169

Becker, Thomas; Franckenberg, Sibylle; Wickles, Stephan; Shoemaker, Christopher J.; Anger, Andreas M.; Armache, Jean-Paul; Sieber, Heidemarie; Ungewickell, Charlotte; Berninghausen, Otto; Daberkow, Ingo; Karcher, Annette; Thomm, Michael; Hopfner, Karl-Peter; Green, Rachel; Beckmann, Roland
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea
NATURE, 482:501-U221, FEB 23 2012
abstract, full text, DOI:10.1038/nature10829

Gumbart, James; Roux, Benoit
Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 102:795-801, FEB 22 2012
abstract, full text, DOI:10.1016/j.bpj.2012.01.021

Nong, Eva X.; DeVience, Stephen J.; Herschbach, Dudley
Minimalist Model for Force-Dependent DNA Replication
BIOPHYSICAL JOURNAL, 102:810-818, FEB 22 2012
abstract, full text, DOI:10.1016/j.bpj.2012.01.020

Smith, Natalie E.; Vrielink, Alice; Attwood, Paul V.; Corry, Ben
Biological Channeling of a Reactive Intermediate in the Bifunctional Enzyme DmpFG
BIOPHYSICAL JOURNAL, 102:868-877, FEB 22 2012
abstract, full text, DOI:10.1016/j.bpj.2012.01.029

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping
Discovery of Intramolecular Signal Transduction Network Based on a New Protein Dynamics Model of Energy Dissipation
PLOS ONE, 7 Art. No. e31529, FEB 20 2012
abstract, full text, DOI:10.1371/journal.pone.0031529

Qiu, Hu; Guo, Wanlin
Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study
APPLIED PHYSICS LETTERS, 100 Art. No. 083106, FEB 20 2012
abstract, full text, DOI:10.1063/1.3686921

Das, Rahul K.; Crick, Scott L.; Pappu, Rohit V.
N-Terminal Segments Modulate the alpha-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins
JOURNAL OF MOLECULAR BIOLOGY, 416:287-299, FEB 17 2012
abstract, full text, DOI:10.1016/j.jmb.2011.12.043

Tipmanee, Varomyalin; Blumberger, Jochen
Kinetics of the Terminal Electron Transfer Step in Cytochrome c Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1876-1883, FEB 16 2012
abstract, full text, DOI:10.1021/jp209175j

Ravi, Harish Kumar; Simona, Fabio; Hulliger, Juerg; Cascella, Michele
Molecular Origin of Piezo- and Pyroelectric Properties in Collagen Investigated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1901-1907, FEB 16 2012
abstract, full text, DOI:10.1021/jp208436j

Gordon, Dan; Chen, Rong; Ho, Junming; Coote, Michelle L.; Chung, Shin-Ho
Rigid Body Brownian Dynamics as a Tool for Studying Ion Channel Blockers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1933-1941, FEB 16 2012
abstract, full text, DOI:10.1021/jp210105f

da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
TD-DFT/Molecular Mechanics Study of the Photinus pyralis Bioluminescence System
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2008-2013, FEB 16 2012
abstract, full text, DOI:10.1021/jp2120059

Cakir, Bilal; Dagliyan, Onur; Dagyildiz, Ezgi; Baris, Ibrahim; Kavakli, Ibrahim Halil; Kizilel, Seda; Turkay, Metin
Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme
PLOS ONE, 7 Art. No. e31787, FEB 15 2012
abstract, full text, DOI:10.1371/journal.pone.0031787

Gao, Chen; Pan, Ming-Ming; Lei, Yan-Jun; Tian, Li-Qing; Jiang, Hui-Ying; Li, Xiao-Li; Shi, Qi; Tian, Chan; Yuan, Yu-Kang; Fan, Gui-Xiang; Dong, Xiao-Ping
A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter
BMC MOLECULAR BIOLOGY, 13 Art. No. 5, FEB 15 2012
abstract, full text, DOI:10.1186/1471-2199-13-5

Gonzalez, Wendy; Riedelsberger, Janin; Morales-Navarro, Samuel E.; Caballero, Julio; Alzate-Morales, Jans H.; Gonzalez-Nilo, Fernando D.; Dreyer, Ingo
The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids
BIOCHEMICAL JOURNAL, 442:57-63, FEB 15 2012
abstract, full text, DOI:10.1042/BJ20111498

Rao, Francesco; Spichty, Martin
Thermodynamics and kinetics of large-time-step molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:475-483, FEB 15 2012
abstract, full text, DOI:10.1002/jcc.21990

Huggins, David J.
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 064518, FEB 14 2012
abstract, full text, DOI:10.1063/1.3683447

Pfaendtner, Jim; Volkmann, Niels; Hanein, Dorit; Dalhaimer, Paul; Pollard, Thomas D.; Voth, Gregory A.
Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation
JOURNAL OF MOLECULAR BIOLOGY, 416:148-161, FEB 10 2012
abstract, full text, DOI:10.1016/j.jmb.2011.12.025

Potoyan, Davit A.; Zhuravlev, Pavel I.; Papoian, Garegin A.
Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1709-1715, FEB 9 2012
abstract, full text, DOI:10.1021/jp209980b

Connelly, Laura; Jang, Hyunbum; Arce, Fernando Teran; Capone, Ricardo; Kotler, Samuel A.; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh
Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's beta-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1728-1735, FEB 9 2012
abstract, full text, DOI:10.1021/jp2108126

Comer, Jeffrey; Aksimentiev, Aleksei
Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 116:3376-3393, FEB 9 2012
abstract, full text, DOI:10.1021/jp210641j

Cheung, Luthur Siu-Lun; Kanwar, Manu; Ostermeier, Marc; Konstantopoulos, Konstantinos
A Hot-Spot Motif Characterizes the Interface between a Designed Ankyrin-Repeat Protein and Its Target Ligand
BIOPHYSICAL JOURNAL, 102:407-416, FEB 8 2012
abstract, full text, DOI:10.1016/j.bpj.2012.01.004

Chen, Rong; Chung, Shin-Ho
Binding Modes of mu-Conotoxin to the Bacterial Sodium Channel (Na(v)Ab)
BIOPHYSICAL JOURNAL, 102:483-488, FEB 8 2012
abstract, full text, DOI:10.1016/j.bpj.2011.12.041

Ndlovu, Hlengisizwe; Ashcroft, Alison E.; Radford, Sheena E.; Harris, Sarah A.
Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 102:587-596, FEB 8 2012
abstract, full text, DOI:10.1016/j.bpj.2011.12.047

Selvaratnam, Rajeevan; VanSchouwen, Bryan; Fogolari, Federico; Mazhab-Jafari, Mohammad T.; Das, Rahul; Melacini, Giuseppe
The Projection Analysis of NMR Chemical Shifts Reveals Extended EPAC Autoinhibition Determinants
BIOPHYSICAL JOURNAL, 102:630-639, FEB 8 2012
abstract, full text, DOI:10.1016/j.bpj.2011.12.030

Basilio, Nuno; Garcia-Rio, Luis; Martin-Pastor, Manuel
Calixarene-Based Surfactants: Evidence of Structural Reorganization upon Micellization
LANGMUIR, 28:2404-2414, FEB 7 2012
abstract, full text, DOI:10.1021/la204004h

Russell, John T.; Wang, Boyang; Kral, Petr
Nanodroplet Transport on Vibrated Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:353-357, FEB 2 2012
abstract, full text, DOI:10.1021/jz201614m

Chen, Po-Chia; Kuyucak, Serdar
Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins
TOXINS, 4:110-138, FEB 2012
abstract, full text, DOI:10.3390/toxins4020110

Stewart, Alastair G.; Lee, Lawrence K.; Donohoe, Mhairi; Chaston, Jessica J.; Stock, Daniela
The dynamic stator stalk of rotary ATPases
NATURE COMMUNICATIONS, 3 Art. No. 687, FEB 2012
abstract, full text, DOI:10.1038/ncomms1693

Pietra, Francesco
Putative Binding Sites, and Pathways to Them, for Amidine and Guanidine Current Inhibitors on Acid-Sensing Ion Channels (ASIC). A Theoretical Approach with hASIC1a Homology Model
CHEMISTRY & BIODIVERSITY, 9:331-351, FEB 2012
abstract, full text, DOI:10.1002/cbdv.201100260

Raghunathan, Devanathan; Gayen, Shovanlal; Kumar, Anil; Hunke, Cornelia; Grueber, Gerhard; Verma, Chandra S.
Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Go1
JOURNAL OF BIOENERGETICS AND BIOMEMBRANES, 44:213-224, FEB 2012
abstract, full text, DOI:10.1007/s10863-012-9410-y

Merino, Felipe; Andres Rivas-Pardo, Jaime; Caniuguir, Andres; Garcia, Ivonne; Guixe, Victoria
Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea
BIOCHIMIE, 94:516-524, FEB 2012
abstract, full text, DOI:10.1016/j.biochi.2011.08.021

Best, Robert B.
Atomistic molecular simulations of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 22:52-61, FEB 2012
abstract, full text, DOI:10.1016/j.sbi.2011.12.001

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:589-603, FEB 2012
abstract, full text, DOI:10.1021/ci200584f

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
PLOS COMPUTATIONAL BIOLOGY, 8 Art. No. e1002394, FEB 2012
abstract, full text, DOI:10.1371/journal.pcbi.1002394

Kowalczyk, Stefan W.; Wells, David B.; Aksimentiev, Aleksei; Dekker, Cees
Slowing down DNA Translocation through a Nanopore in Lithium Chloride
NANO LETTERS, 12:1038-1044, FEB 2012
abstract, full text, DOI:10.1021/nl204273h

Fleming, Patrick J.; Freites, J. Alfredo; Moon, C. Preston; Tobias, Douglas J.; Fleming, Karen G.
Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:126-134, FEB 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.07.016

Li, Jing; Tajkhorshid, Emad
A gate-free pathway for substrate release from the inward-facing state of the Na+-galactose transporter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:263-271, FEB 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.09.011

Wood, Mona L.; Schow, Eric V.; Freites, J. Alfredo; White, Stephen H.; Tombola, Francesco; Tobias, Douglas J.
Water wires in atomistic models of the Hvl proton channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:286-293, FEB 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.07.045

Gumbart, James; Khalili-Araghi, Fatemeh; Sotomayor, Marcos; Roux, Benoit
Constant electric field simulations of the membrane potential illustrated with simple systems
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:294-302, FEB 2012
abstract, full text, DOI:10.1016/j.bbamem.2011.09.030

Ihle, Nathan T.; Byers, Lauren A.; Kim, Edward S.; Saintigny, Pierre; Lee, J. Jack; Blumenschein, George R.; Tsao, Anne; Liu, Suyu; Larsen, Jill E.; Wang, Jing; Diao, Lixia; Coombes, Kevin R.; Chen, Lu; Zhang, Shuxing; Abdelmelek, Mena F.; Tang, Ximing; Papadimitrakopoulou, Vassiliki; Minna, John D.; Lippman, Scott M.; Hong, Waun K.; Herbst, Roy S.; Wistuba, Ignacio I.; Heymach, John V.; Powis, Garth
Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome
JOURNAL OF THE NATIONAL CANCER INSTITUTE, 104:228-239, FEB 2012
abstract, full text, DOI:10.1093/jnci/djr523

Receveur-Brechot, Veronique; Durand, Dominique
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective
CURRENT PROTEIN & PEPTIDE SCIENCE, 13:55-75, FEB 2012
abstract, full text

Do, Trang N.; Ippoliti, Emiliano; Carloni, Paolo; Varani, Gabriele; Parrinello, Michele
Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:688-694, FEB 2012
abstract, full text, DOI:10.1021/ct2005769

Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D., Jr.
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:759-776, FEB 2012
abstract, full text, DOI:10.1021/ct200792v

Drakulic, Branko J.; Marinkovic, Aleksandar D.; Juranic, Ivan O.
On the choice of optimal conformation in linear free-energy relationships. Reactivity of 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbutanoic acids with diphenyldiazomethane
TETRAHEDRON LETTERS, 53:553-556, FEB 1 2012
abstract, full text, DOI:10.1016/j.tetlet.2011.11.097

Liu, Lin; Gronenborn, Angela M.; Bahar, Ivet
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:616-625, FEB 2012
abstract, full text, DOI:10.1002/prot.23225

Negureanu, Lacramioara; Salsbury, Freddie R.
Insights into Protein - DNA Interactions, Stability and Allosteric Communications: A Computational Study of Muts alpha-DNA Recognition Complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:757-776, FEB 2012
abstract, full text

Uchida, Masaki; Morris, David S.; Kang, Sebyung; Jolley, Craig C.; Lucon, Janice; Liepold, Lars O.; LaFrance, Ben; Prevelige, Peter E., Jr.; Douglas, Trevor
Site-Directed Coordination Chemistry with P22 Virus-like Particles
LANGMUIR, 28:1998-2006, JAN 31 2012
abstract, full text, DOI:10.1021/la203866c

Limongelli, Vittorio; Marinelli, Luciana; Cosconati, Sandro; La Motta, Concettina; Sartini, Stefania; Mugnaini, Laura; Da Settimo, Federico; Novellino, Ettore; Parrinello, Michele
Sampling protein motion and solvent effect during ligand binding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1467-1472, JAN 31 2012
abstract, full text, DOI:10.1073/pnas.1112181108

Lettieri, Steven; Zuckerman, Daniel M.
Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:268-275, JAN 30 2012
abstract, full text, DOI:10.1002/jcc.21970

Mori, Takaharu; Ogushi, Fumiko; Sugita, Yuji
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:286-293, JAN 30 2012
abstract, full text, DOI:10.1002/jcc.21973

Kamath, Ganesh; Ketko, MaryBeth; Baker, Gary A.; Potoff, Jeffrey J.
Monte Carlo predictions of phase equilibria and structure for dimethyl ether plus sulfur dioxide and dimethyl ether plus carbon dioxide
JOURNAL OF CHEMICAL PHYSICS, 136 Art. No. 044514, JAN 28 2012
abstract, full text, DOI:10.1063/1.3677880

Taylor, Courtney B.; Talib, M. Faiz; McCabe, Clare; Bu, Lintao; Adney, William S.; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.
Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-binding Module
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:3147-3155, JAN 27 2012
abstract, full text, DOI:10.1074/jbc.M111.270389

Jiao, Wanting; Hutton, Richard D.; Cross, Penelope J.; Jameson, Geoffrey B.; Parker, Emily J.
Dynamic Cross-Talk among Remote Binding Sites: The Molecular Basis for Unusual Synergistic Allostery
JOURNAL OF MOLECULAR BIOLOGY, 415:716-726, JAN 27 2012
abstract, full text, DOI:10.1016/j.jmb.2011.11.037

Wiliam Hernandez-Rodriguez, Erix; Sanchez-Garcia, Elsa; Crespo-Otero, Rachel; Lilian Montero-Alejo, Ana; Alberto Montero, Luis; Thiel, Walter
Understanding Rhodopsin Mutations Linked to the Retinitis pigmentosa Disease: a QM/MM and DFT/MRCI Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1060-1076, JAN 26 2012
abstract, full text, DOI:10.1021/jp2037334

Jing, Yuanyuan; Zheng, Renhui; Li, Hui-Xue; Shi, Qiang
Theoretical Study of the Electronic-Vibrational Coupling in the Q(y) States of the Photosynthetic Reaction Center in Purple Bacteria
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1164-1171, JAN 26 2012
abstract, full text, DOI:10.1021/jp209575q

Naveed, Hammad; Xu, Yun; Jackups, Ronald, Jr.; Liang, Jie
Predicting Three-Dimensional Structures of Transmembrane Domains of beta-Barrel Membrane Proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1775-1781, JAN 25 2012
abstract, full text, DOI:10.1021/ja209895m

Corry, Ben; Thomas, Michael
Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1840-1846, JAN 25 2012
abstract, full text, DOI:10.1021/ja210020h

Volkov, Sergey N.; Paramonova, Ekaterina V.; Yakubovich, Alexander V.; Solov'yov, Andrey V.
Micromechanics of base pair unzipping in the DNA duplex
JOURNAL OF PHYSICS-CONDENSED MATTER, 24 Art. No. 035104, JAN 25 2012
abstract, full text, DOI:10.1088/0953-8984/24/3/035104

Capone, Ricardo; Jang, Hyunbum; Kotler, Samuel A.; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh
Probing Structural Features of Alzheimer's Amyloid-beta Pores in Bilayers Using Site-Specific Amino Acid Substitutions
BIOCHEMISTRY, 51:776-785, JAN 24 2012
abstract, full text, DOI:10.1021/bi2017427

Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L.
Strandwise translocation of a DNA glycosylase on undamaged DNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1086-1091, JAN 24 2012
abstract, full text, DOI:10.1073/pnas.1111237108

Spudich, Elena N.; Ozorowski, Gabriel; Schow, Eric V.; Tobias, Douglas J.; Spudich, John L.; Luecke, Hartmut
A Transporter Converted into a Sensor, a Phototaxis Signaling Mutant of Bacteriorhodopsin at 3.0 angstrom
JOURNAL OF MOLECULAR BIOLOGY, 415:455-463, JAN 20 2012
abstract, full text, DOI:10.1016/j.jmb.2011.11.025

Musgaard, Maria; Thogersen, Lea; Schiott, Birgit; Tajkhorshid, Emad
Tracing Cytoplasmic Ca2+ Ion and Water Access Points in the Ca2+-ATPase
BIOPHYSICAL JOURNAL, 102:268-277, JAN 18 2012
abstract, full text, DOI:10.1016/j.bpj.2011.12.009

Stadler, Andreas Maximilian; Pellegrini, Eric; Johnson, Mark; Fitter, Joerg; Zaccai, Giuseppe
Dynamics-Stability Relationships in Apo- and Holomyoglobin: A Combined Neutron Scattering and Molecular Dynamics Simulations Study
BIOPHYSICAL JOURNAL, 102:351-359, JAN 18 2012
abstract, full text, DOI:10.1016/j.bpj.2011.12.031

Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J.
Learning generative models of molecular dynamics
BMC GENOMICS, 13 Art. No. S5, JAN 17 2012
abstract, full text, DOI:10.1186/1471-2164-13-S1-S5

Tarus, Bogdan; Chevalier, Christophe; Richard, Charles-Adrien; Delmas, Bernard; Di Primo, Carmelo; Slama-Schwok, Anny
Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding
PLOS ONE, 7 Art. No. e30038, JAN 17 2012
abstract, full text, DOI:10.1371/journal.pone.0030038

Weng, Jingwei; Fan, Kangnian; Wang, Wenning
The Conformational Transition Pathways of ATP-Binding Cassette Transporter BtuCD Revealed by Targeted Molecular Dynamics Simulation
PLOS ONE, 7 Art. No. e30465, JAN 17 2012
abstract, full text, DOI:10.1371/journal.pone.0030465

Kuttner, Yosef Y.; Engel, Stanislav
Protein Hot Spots: The Islands of Stability
JOURNAL OF MOLECULAR BIOLOGY, 415:419-428, JAN 13 2012
abstract, full text, DOI:10.1016/j.jmb.2011.11.009

Zheng, Bin; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Force Field for Molecular Dynamics Computations in Flexible ZIF-8 Framework
JOURNAL OF PHYSICAL CHEMISTRY C, 116:933-938, JAN 12 2012
abstract, full text, DOI:10.1021/jp209463a

Lim, Joseph B.; Rogaski, Brent; Klauda, Jeffery B.
Update of the Cholesterol Force Field Parameters in CHARMM
JOURNAL OF PHYSICAL CHEMISTRY B, 116:203-210, JAN 12 2012
abstract, full text, DOI:10.1021/jp207925m

Kucerka, Norbert; Holland, Bryan W.; Gray, Chris G.; Tomberli, Bruno; Katsaras, John
Scattering Density Profile Model of POPG Bilayers As Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 116:232-239, JAN 12 2012
abstract, full text, DOI:10.1021/jp208920h

Huang, Bo; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan
Molecular Mechanism of the Effects of Salt and pH on the Affinity between Protein A and Human lmmunoglobulin G1 Revealed by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:424-433, JAN 12 2012
abstract, full text, DOI:10.1021/jp205770p

Lee, Hyeong J.; Hota, Prasanta K.; Chugha, Preeti; Guo, Hong; Miao, Hui; Zhang, Liqun; Kim, Soon-Jeung; Stetzik, Lukas; Wang, Bing-Cheng; Buck, Matthias
NMR Structure of a Heterodimeric SAM:SAM Complex: Characterization and Manipulation of EphA2 Binding Reveal New Cellular Functions of SHIP2
STRUCTURE, 20:41-55, JAN 11 2012
abstract, full text, DOI:10.1016/j.str.2011.11.013

Satpati, Priyadarshi; Simonson, Thomas
Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways
BIOCHEMISTRY, 51:353-361, JAN 10 2012
abstract, full text, DOI:10.1021/bi201675n

Arkun, Yaman; Gur, Mert
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
PLOS ONE, 7 Art. No. e29628, JAN 6 2012
abstract, full text, DOI:10.1371/journal.pone.0029628

Mastrangelo, Eloise; Bolognesi, Martino; Milani, Mario
Flaviviral helicase: Insights into the mechanism of action of a motor protein
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:84-87, JAN 6 2012
abstract, full text, DOI:10.1016/j.bbrc.2011.11.060

Makiya, Michelle; Dolan, Michael; Agulto, Liane; Purcell, Robert; Chen, Zhaochun
Structural basis of anthrax edema factor neutralization by a neutralizing antibody
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:324-329, JAN 6 2012
abstract, full text, DOI:10.1016/j.bbrc.2011.11.108

Barnard, Travis J.; Gumbart, James; Peterson, Janine H.; Noinaj, Nicholas; Easley, Nicole C.; Dautin, Nathalie; Kuszak, Adam J.; Tajkhorshid, Emad; Bernstein, Harris D.; Buchanan, Susan K.
Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter
JOURNAL OF MOLECULAR BIOLOGY, 415:128-142, JAN 6 2012
abstract, full text, DOI:10.1016/j.jmb.2011.10.049

Gonnet, Pedro
Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:76-81, JAN 5 2012
abstract, full text, DOI:10.1002/jcc.21945

Kang, Yingyong; Lu, Shouqin; Ren, Peng; Huo, Bo; Long, Mian
Molecular Dynamics Simulation of Shear- and Stretch-Induced Dissociation of P-Selectin/PSGL-1 Complex
BIOPHYSICAL JOURNAL, 102:112-120, JAN 4 2012
abstract, full text, DOI:10.1016/j.bpj.2011.11.4002

Morris, Garrett M.
Docking and Virtual Screening
PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY, Issue 23, 171-194, 2012
full text, DOI:10.1039/9781849735377-00171

van Gunsteren, Wilfred F.; Dolenc, Jozica
Thirty-five years of biomolecular simulation: development of methodology, force fields and software
MOLECULAR SIMULATION, 38:1271-1281, 2012
abstract, full text, DOI:10.1080/08927022.2012.701744

Vasile, Ionut T.; Ciobanu-Zabet, Dragos
Integrated System for Modeling and data Analysis of complex Biomolecules (ISyMAB)
2012 5TH ROMANIA TIER 2 FEDERATION GRID, CLOUD & HIGH PERFORMANCE COMPUTING SCIENCE (RO-LCG), 100-102, 2012
abstract, full text

Krol, M.; Konieczny, L.; Stapor, K.; Wisniowski, Z.; Ziajka, W.; Szoniec, G.; Roterman-Konieczna, I.
Misfolded proteins
PROTEIN FOLDING IN SILICO: PROTEIN FOLDING VERSUS PROTEIN STRUCTURE PREDICTION, Issue 22, 141-164, 2012
abstract, full text

Zhang, Ning; Li, Weizhong; Cui, Jing
Molecular Dynamics Simulation of Water Transporting through Nanotube Driven by Concentration Difference
PROCEEDINGS OF THE ASME 9TH INTERNATIONAL CONFERENCE ON NANOCHANNELS, MICROCHANNELS AND MINICHANNELS 2011, VOL 2, 209-213, 2012
abstract, full text

Chen, Xin; Chen, Xiliang; Wu, Tao; Wang, Qi
Simulation of steered molecular dynamics on the exploration of the dynamic structure of HIV-1 protease
MOLECULAR SIMULATION, 38:293-299, 2012
abstract, full text, DOI:10.1080/08927022.2011.621951

Yin, Qian; Luo, Ruiyi; Guo, Ping
Parallelization and Optimization of Molecular Dynamics Simulation on Many Integrated Core
PROCEEDINGS OF THE 2012 EIGHTH INTERNATIONAL CONFERENCE ON COMPUTATIONAL INTELLIGENCE AND SECURITY (CIS 2012), 209-213, 2012
abstract, full text, DOI:10.1109/CIS.2012.54

Fjell, Christopher D.; Hiss, Jan A.; Hancock, Robert E. W.; Schneider, Gisbert
Designing antimicrobial peptides: form follows function
NATURE REVIEWS DRUG DISCOVERY, 11:37-51, JAN 2012
abstract, full text, DOI:10.1038/nrd3591

Bellucci, L.; Brancolini, G.; Calzolari, A.; Parramon, O. Carrillo; Corni, S.; Di Felice, R.
Proteins and Peptides at Gold Surfaces: Insights from Atomistic Simulations
PROTEINS AT INTERFACES III: STATE OF THE ART, 1120:229-250, 2012
abstract, full text

Edelkamp, S.; Schrodl, S.
Heuristic Search: Theory and Applications
HEURISTIC SEARCH: THEORY AND APPLICATIONS, 1-836, 2012
full text

Szuts, Viktoria; Oetvoes, Ferenc; Dezsi, Laszlo; Vagvoelgyi, Csaba; Szalontai, Balazs; Dobrzynski, Halina; Boyett, Mark; Zhang, Henggui; Papp, Julius G.; Varro, Andras; Benyhe, Sandor; Erdelyi, Lajos
What have we learned from two-pore potassium channels? Their molecular configuration and function in the human heart
Acta Biologica Szegediensis, 56:93-107, 2012
abstract, full text

Gkeka, Paraskevi; Athanasiadis, Emmanouil; Spyrou, George; Cournia, Zoe
Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3K alpha inhibitors
IEEE 12TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS & BIOENGINEERING, 266-269, 2012
abstract, full text

Negi, Sunita; Atilgan, Ali Rana; Atilgan, Canan
Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues
IUPAP C20 CONFERENCE ON COMPUTATIONAL PHYSICS (CCP 2011), 402 Art. No. 012047, 2012
abstract, full text, DOI:10.1088/1742-6596/402/1/012047

Nemukhin, A. V.; Grigorenko, B. L.; Lushchekina, S. V.; Varfolomeev, S. D.
Quantum chemical modelling in the research of molecular mechanisms of enzymatic catalysis
RUSSIAN CHEMICAL REVIEWS, 81:1011-1025, 2012
abstract, full text, DOI:10.1070/RC2012v081n11ABEH004311

Dimitrijevic, Blagoje P.; Borozan, Suncica Z.; Stojanovic, Srdan D.
pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures
RSC ADVANCES, 2:12963-12972, 2012
abstract, full text, DOI:10.1039/c2ra21937a

Ionescu, Alina; Mernea, Maria; Vasile, Ionut; Brandus, Catalina Alice; Barbinta-Patrascu, Marcela Elisabeta; Tugulea, Laura; Mihailescu, Dan; Dascalu, Traian
Study of supported phospholipid bilayers by THz-TDS
TERAHERTZ EMITTERS, RECEIVERS, AND APPLICATIONS III, 8496 Art. No. 849614, 2012
abstract, full text, DOI:10.1117/12.981603

Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Unidirectional peristaltic movement in multisite drug binding pockets of AcrB from molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 8:2699-2709, 2012
abstract, full text, DOI:10.1039/c2mb25184a

Shi, Wei; Damodaran, Krishnan; Nulwala, Hunaid B.; Luebke, David R.
Theoretical and experimental studies of water interaction in acetate based ionic liquids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:15897-15908, 2012
abstract, full text, DOI:10.1039/c2cp42975f

Sellers, Michael; Hurley, Margaret M.
In Silico Design of Smart Binders to Anthrax PA
CHEMICAL, BIOLOGICAL, RADIOLOGICAL, NUCLEAR, AND EXPLOSIVES (CBRNE) SENSING XIII, 8358 Art. No. 835807, 2012
abstract, full text, DOI:10.1117/12.918424

Wang, Kefeng; Leng, Yang; Lu, Xiong; Ren, Fuzeng; Ge, Xiang; Ding, Yonghui
Theoretical analysis of protein effects on calcium phosphate precipitation in simulated body fluid
CRYSTENGCOMM, 14:5870-5878, 2012
abstract, full text, DOI:10.1039/c2ce25216c

Zhang, Mingming; Wang, Beibei; Jiang, Tao; Jiang, Meijuan; Yi, Tao
From nano ribbon to fibre by concentration control
CRYSTENGCOMM, 14:8057-8062, 2012
abstract, full text, DOI:10.1039/c2ce25599e

Wan, Dun; Liao, Li-fu; Lin, Ying-Wu
Impacts of Uranyl Ion on the Structure and Function of Cytochrome b(5) His39Ser Mutant
FUTURE MATERIAL RESEARCH AND INDUSTRY APPLICATION, PTS 1 AND 2, 455-456:1204-1209, 2012
abstract, full text, DOI:10.4028/www.scientific.net/AMR.455-456.1204

Huggins, David J.
Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:15106-15117, 2012
abstract, full text, DOI:10.1039/c2cp42631e

Wu, Qiang; Yang, Canqun; Wang, Feng; Xue, Jingling
A Fast Parallel Implementation of Molecular Dynamics with the Morse Potential on a Heterogeneous Petascale Supercomputer
2012 IEEE 26TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS & PHD FORUM (IPDPSW), 140-149, 2012
abstract, full text, DOI:10.1109/IPDPSW.2012.13

Rajachandrasekar, Raghunath; Besseron, Xavier; Panda, Dhabaleswar K.
Monitoring and Predicting Hardware Failures in HPC Clusters with FTB-IPMI
2012 IEEE 26TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS & PHD FORUM (IPDPSW), 1136-1143, 2012
abstract, full text, DOI:10.1109/IPDPSW.2012.139

Lu, Xiuli; Chen, Shuchao; Zhang, Yong; Zhang, Li; Liu, Hongsheng; Gao, Bing
The Discovery of Direct Noncovalent Bonded Interaction between Keap1 and Diethyl Maleate through Molecular Dynamics Simulations
ADVANCED MECHANICAL ENGINEERING II, 192:260-265, 2012
abstract, full text, DOI:10.4028/www.scientific.net/AMM.192.260

Correa-Basurto, J.; Ramos-Morales, F. R.; Matus, M. H.; Rosales-Hernandez, M. C.; Mancilla-Percino, T.; Trujillo-Ferrara, J.; Ilizaliturri-Flores, I.
Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design
MOLECULAR SIMULATION, 38:1072-1084, 2012
abstract, full text, DOI:10.1080/08927022.2012.690877

Shintani, Megumi; Matsuo, Yushi; Sakuraba, Shun; Matubayasi, Nobuyuki
Interaction of naphthalene derivatives with lipids in membranes studied by the H-1-nuclear Overhauser effect and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:14049-14060, 2012
abstract, full text, DOI:10.1039/c2cp41984j

Singh, Sadanand; Chopra, Manan; de Pablo, Juan J.
Density of States-Based Molecular Simulations
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 3, 3:369-394, 2012
abstract, full text, DOI:10.1146/annurev-chembioeng-062011-081032

Dror, Ron O.; Dirks, Robert M.; Grossman, J. P.; Xu, Huafeng; Shaw, David E.
Biomolecular Simulation: A Computational Microscope for Molecular Biology
ANNUAL REVIEW OF BIOPHYSICS, VOL 41, 41:429-452, 2012
abstract, full text, DOI:10.1146/annurev-biophys-042910-155245

Wang, Dongqi; van Gunsteren, Wilfred F.; Chai, Zhifang
Recent advances in computational actinoid chemistry
CHEMICAL SOCIETY REVIEWS, 41:5836-5865, 2012
abstract, full text, DOI:10.1039/c2cs15354h

Yakubovich, Alexander V.; Surdutovich, Eugene; Solov'yov, Andrey V.
Damage of DNA backbone by nanoscale shock waves
1ST NANO-IBCT CONFERENCE 2011 - RADIATION DAMAGE OF BIOMOLECULAR SYSTEMS: NANOSCALE INSIGHTS INTO ION BEAM CANCER THERAPY, 373 Art. No. 012014, 2012
abstract, full text, DOI:10.1088/1742-6596/373/1/012014

Cui, Yubao; Bastien, David A.
Molecular Dynamics Simulation and Bioinformatics Study on Yeast Aquaporin Aqy1 from Pichia pastoris
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES, 8:1026-1035, 2012
abstract, full text, DOI:10.7150/ijbs.4703

Alijanianzadeh, Mahdi; Saboury, Ali Akbar; Ganjali, Mohammad Reza; Hadi-Alijanvand, Hamid; Moosavi-Movahedi, Ali Akbar
Inhibition of mushroom tyrosinase by a newly synthesized ligand: inhibition kinetics and computational simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:448-459, 2012
abstract, full text, DOI:10.1080/07391102.2012.682210

Munteanu, Cristian V. A.; Alexandru, Petruta; Spiridon, Laurentiu N.; Petrescu, Andrei-Jose; Milac, Adina-Luminita
INSIGHTS INTO CECROPIN-MEMBRANE INTERACTION MECHANISM GIVEN BY MOLECULAR DYNAMICS SIMULATIONS
Romanian Journal of Biochemistry, 49:21-31, JAN-JUN 2012
abstract, full text

Morales-Quintana, Luis; Alejandra Moya-Leon, Maria; Herrera, Raul
Molecular docking simulation analysis of alcohol acyltransferases from two related fruit species explains their different substrate selectivities
MOLECULAR SIMULATION, 38:912-921, 2012
abstract, full text, DOI:10.1080/08927022.2012.672738

Saiz-Poseu, Javier; Martinez-Otero, Alberto; Roussel, Thomas; Hui, Joseph K. -H.; Montero, Mavis L.; Urcuyo, Roberto; MacLachlan, Mark J.; Faraudo, Jordi; Ruiz-Molina, Daniel
Self-assembly of a catechol-based macrocycle at the liquid-solid interface: experiments and molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:11937-11943, 2012
abstract, full text, DOI:10.1039/c2cp41407d

Pietropaolo, Adriana
Exploring metal-driven stereoselectivity of glycopeptides by free-energy calculations
PURE AND APPLIED CHEMISTRY, 84:1919-1930, 2012
abstract, full text, DOI:10.1351/PAC-CON-11-09-33

Pandey, R. B.; Kuang, Zhifeng; Farmer, B. L.; Kim, Steve S.; Naik, Rajesh R.
Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach
SOFT MATTER, 8:9101-9109, 2012
abstract, full text, DOI:10.1039/c2sm25870f

Coveney, Peter V.; Swadling, Jacob B.; Wattis, Jonathan A. D.; Greenwell, H. Christopher
Theory, modelling and simulation in origins of life studies
CHEMICAL SOCIETY REVIEWS, 41:5430-5446, 2012
abstract, full text, DOI:10.1039/c2cs35018a

Elder, Robert M.; Jayaraman, Arthi
Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a
MOLECULAR SIMULATION, 38:793-808, 2012
abstract, full text, DOI:10.1080/08927022.2011.654208

Richards, Laura A.; Schaefer, Andrea I.; Richards, Bryce S.; Corry, Ben
Quantifying barriers to monovalent anion transport in narrow non-polar pores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:11633-11638, 2012
abstract, full text, DOI:10.1039/c2cp41641g

Wang, Yi; McCammon, J. Andrew
Accelerated Molecular Dynamics: Theory, Implementation and Applications
THEORY AND APPLICATIONS IN COMPUTATIONAL CHEMISTRY: THE FIRST DECADE OF THE SECOND MILLENNIUM, 1456:165-172, 2012
abstract, full text, DOI:10.1063/1.4730656

Panecka, Joanna; Trylska, Joanna
Molecular Dynamics Techniques in the Studies of the Bacterial Ribosome
THEORY AND APPLICATIONS IN COMPUTATIONAL CHEMISTRY: THE FIRST DECADE OF THE SECOND MILLENNIUM, 1456:207-214, 2012
abstract, full text, DOI:10.1063/1.4730661

Jia, Yun-Fang; Gao, Chun-Ying; He, Jia; Feng, Dao-Fu; Xing, Ke-Li; Wu, Ming; Liu, Yang; Cai, Wen-Sheng; Feng, Xi-Zeng
Unlabeled multi tumor marker detection system based on bioinitiated light addressable potentiometric sensor
ANALYST, 137:3806-3813, 2012
abstract, full text, DOI:10.1039/c2an35188a

Venkateshwari, Sureshkumar; Veluraja, Kasinadar
Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:255-268, 2012
abstract, full text, DOI:10.1080/07391102.2012.680027

Negureanu, Lacramioara; Salsbury, Freddie R., Jr.
The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutS alpha-DNA complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:347-361, 2012
abstract, full text, DOI:10.1080/07391102.2012.680034

Katti, Dinesh R.; Katti, Kalpana S.; Raviprasad, M.; Gu, Chunju
Role of Polymer Interactions with Clays and Modifiers on Nanomechanical Properties and Crystallinity in Polymer Clay Nanocomposites
JOURNAL OF NANOMATERIALS, Art. No. 341056, 2012
abstract, full text, DOI:10.1155/2012/341056

Lopez-Perez, Daniel E.; Revilla-Lopez, Guillermo; Jacquemin, Denis; Zanuy, David; Palys, Barbara; Sek, Slawomir; Aleman, Carlos
Intermolecular interactions in electron transfer through stretched helical peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:10332-10344, 2012
abstract, full text, DOI:10.1039/c2cp40761b

Phan Van Cuong; Kvamme, Bjorn; Kuznetsova, Tatiana; Jensen, Bjornar
Molecular dynamics study of calcite, hydrate and the temperature effect on CO2 transport and adsorption stability in geological formations
MOLECULAR PHYSICS, 110:1097-1106, 2012
abstract, full text, DOI:10.1080/00268976.2012.679629

Androulaki, Eleni; Vergadou, Niki; Ramos, Javier; Economou, Ioannis G.
Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations
MOLECULAR PHYSICS, 110:1139-1152, 2012
abstract, full text, DOI:10.1080/00268976.2012.670280

Peskin, Uri
Quantum mechanical averaging over fluctuating rates
MOLECULAR PHYSICS, 110:729-734, 2012
abstract, full text, DOI:10.1080/00268976.2012.663103

Zhang, Liqun; Bouguet-Bonnet, Sabine; Buck, Matthias
Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase-Protein Interactions
ALLOSTERY: METHODS AND PROTOCOLS, 796:235-259, 2012
abstract, full text, DOI:10.1007/978-1-61779-334-9_13

Savitsky, Alexander P.; Rusanov, Alexander L.; Zherdeva, Victoria V.; Gorodnicheva, Tatiana V.; Khrenova, Maria G.; Nemukhin, Alexander V.
FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins
THERANOSTICS, 2:215-226, 2012
abstract, full text, DOI:10.7150/thno.3885

Saito, Hiroaki; Mizukami, Taku; Kawamoto, Shuhei; Miyakawa, Takeshi; Iwayama, Masashi; Takasu, Masako; Nagao, Hidemi
Molecular Dynamics Studies of Lipid Bilayer With Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:161-170, JAN 2012
abstract, full text, DOI:10.1002/qua.23252

Gao, Chun-Ying; Guo, Yuan-Yuan; He, Jia; Wu, Ming; Liu, Yang; Chen, Zhong-Liang; Cai, Wen-Sheng; Yang, Yan-Lian; Wang, Chen; Feng, Xi-Zeng
L-3,4-dihydroxyphenylalanine-collagen modified PDMS surface for controlled cell culture
JOURNAL OF MATERIALS CHEMISTRY, 22:10763-10770, 2012
abstract, full text, DOI:10.1039/c2jm00104g

Zarudnev, Eugen S.; Plokhotnichenko, Alexander M.; Leontiev, Victor S.; Levitsky, Igor A.; Karachevtsev, Victor A.
Unusual aggregation of poly(rC)-wrapped carbon nanotubes in aqueous suspension induced by cationic porphyrin
JOURNAL OF MATERIALS CHEMISTRY, 22:10795-10804, 2012
abstract, full text, DOI:10.1039/c2jm30645j

Gross, Adam S.; Bell, Alexis T.; Chu, Jhih-Wei
Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:8425-8430, 2012
abstract, full text, DOI:10.1039/c2cp40417f

Keil, F. J.
Multiscale Modelling in Computational Heterogeneous Catalysis
MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY, 307:69-107, 2012
abstract, full text, DOI:10.1007/128_2011_128

Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran
Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields
MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY, 307:201-249, 2012
abstract, full text, DOI:10.1007/128_2011_164

Kamath, Ganesh; Baker, Gary A.
In silico free energy predictions for ionic liquid-assisted exfoliation of a graphene bilayer into individual graphene nanosheets
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:7929-7933, 2012
abstract, full text, DOI:10.1039/c2cp40824d

Hughes, Meghan; Frederix, Pim W. J. M.; Raeburn, Jaclyn; Birchall, Louise S.; Sadownik, Jan; Coomer, Fiona C.; Lin, I-Hsin; Cussen, Edmund J.; Hunt, Neil T.; Tuttle, Tell; Webb, Simon J.; Adams, Dave J.; Ulijn, Rein V.
Sequence/structure relationships in aromatic dipeptide hydrogels formed under thermodynamic control by enzyme-assisted self-assembly
SOFT MATTER, 8:5595-5602, 2012
abstract, full text, DOI:10.1039/c2sm25224d

Gruber, Christian C.; Pleiss, Juergen
Molecular Modeling of Lipase Binding to a Substrate-Water Interface
LIPASES AND PHOSPHOLIPASES: METHODS AND PROTOCOLS, 861:313-327, 2012
abstract, full text, DOI:10.1007/978-1-61779-600-5_19

Espinoza-Fonseca, L. Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, Jose
Backbone conformational preferences of an intrinsically disordered protein in solution
MOLECULAR BIOSYSTEMS, 8:1798-1805, 2012
abstract, full text, DOI:10.1039/c2mb00004k

Desai, Salil; Kaware, Ravindra
Computational modeling of nanodroplet evaporation for scalable micro-/nano-manufacturing
IIE TRANSACTIONS, 44:568-579, 2012
abstract, full text, DOI:10.1080/0740817X.2011.635181

Jana, Madhurima; Bandyopadhyay, Sanjoy
Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:6628-6638, 2012
abstract, full text, DOI:10.1039/c2cp24104h

Xie, Lei; Xie, Li; Kinnings, Sarah L.; Bourne, Philip E.
Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs
ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 52, 52:361-+, 2012
abstract, full text, DOI:10.1146/annurev-pharmtox-010611-134630

Liu, Yingzhe; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Edge effects control helical wrapping of carbon nanotubes by polysaccharides
NANOSCALE, 4:2584-2589, 2012
abstract, full text, DOI:10.1039/C2NR11979J

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J.
Osteogenesis imperfecta mutations lead to local tropocollagen unfolding and disruption of H-bond network
RSC ADVANCES, 2:3890-3896, 2012
abstract, full text, DOI:10.1039/c2ra01047j

Heinke, Florian; Labudde, Dirk
Membrane Protein Stability Analyses by Means of Protein Energy Profiles in Case of Nephrogenic Diabetes Insipidus
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 790281, 2012
abstract, full text, DOI:10.1155/2012/790281

Akhshi, Parisa; Mosey, Nicholas J.; Wu, Gang
Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 51:2850-2854, 2012
full text, DOI:10.1002/anie.201107700

Landstrom, Jens; Bergstrom, Maria; Hamark, Christoffer; Ohlson, Sten; Widmalm, Goran
Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies
ORGANIC & BIOMOLECULAR CHEMISTRY, 10:3019-3032, 2012
abstract, full text, DOI:10.1039/c2ob07066a

Zhang, Jingfen; He, Zhiquan; Wang, Qingguo; Barz, Bogdan; Kosztin, Ioan; Shang, Yi; Xu, Dong
Prediction of Protein Tertiary Structures Using MUFOLD
FUNCTIONAL GENOMICS: METHODS AND PROTOCOLS, SECOND EDITION, 815:3-13, 2012
abstract, full text, DOI:10.1007/978-1-61779-424-7_1

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning
Concentration dependence of water self-diffusion coefficients in dilute glycerol-water binary and glycerol-water-sodium chloride ternary solutions and the insights from hydrogen bonds
MOLECULAR PHYSICS, 110:283-291, 2012
abstract, full text, DOI:10.1080/00268976.2011.641602

Fogolari, Federico; Corazza, Alessandra; Toppo, Stefano; Tosatto, Silvio C. E.; Viglino, Paolo; Ursini, Fulvio; Esposito, Gennaro
Studying Interactions by Molecular Dynamics Simulations at High Concentration
JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, Art. No. 303190, 2012
abstract, full text, DOI:10.1155/2012/303190

Cheng, Chang-Li; Zhao, Guang-Jiu
Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene
NANOSCALE, 4:2301-2305, 2012
abstract, full text, DOI:10.1039/c2nr12112c

Kamath, Ganesh; Bhatnagar, Navendu; Baker, Gary A.; Baker, Sheila N.; Potoff, Jeffrey J.
Computational prediction of ionic liquid 1-octanol/water partition coefficients
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:4339-4342, 2012
abstract, full text, DOI:10.1039/c2cp40122c

Anandarajah, A.; Amarasinghe, Priyanthi M.
Microstructural Investigation of Soil Suction and Hysteresis of Fine-Grained Soils
JOURNAL OF GEOTECHNICAL AND GEOENVIRONMENTAL ENGINEERING, 138:38-46, JAN 2012
abstract, full text, DOI:10.1061/(ASCE)GT.1943-5606.0000555

Anand, Resmi; Ottani, Stefano; Manoli, Francesco; Manet, Ilse; Monti, Sandra
A close-up on doxorubicin binding to gamma-cyclodextrin: an elucidating spectroscopic, photophysical and conformational study
RSC ADVANCES, 2:2346-2357, 2012
abstract, full text, DOI:10.1039/c2ra01221a

Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J. Andrew
Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:469-486, 2012
abstract, full text, DOI:10.1007/978-1-61779-465-0_27

Besker, Neva; Gervasio, Francesco L.
Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:501-513, 2012
abstract, full text, DOI:10.1007/978-1-61779-465-0_29

Amaro, Rommie E.; Li, Wilfred W.
Molecular-Level Simulation of Pandemic Influenza Glycoproteins
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:575-594, 2012
abstract, full text, DOI:10.1007/978-1-61779-465-0_34

Chang, Chia-en A.; Ai, Rizi; Gutierrez, Michael; Marsella, Michael J.
Homology Modeling of Cannabinoid Receptors: Discovery of Cannabinoid Analogues for Therapeutic Use
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:595-613, 2012
abstract, full text, DOI:10.1007/978-1-61779-465-0_35

Feng, Rui; Xenos, Michalis; Girdhar, Gaurav; Kang, Wei; Davenport, James W.; Deng, Yuefan; Bluestein, Danny
Viscous flow simulation in a stenosis model using discrete particle dynamics: a comparison between DPD and CFD
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 11:119-129, JAN 2012
abstract, full text, DOI:10.1007/s10237-011-0297-z

Liu Jian; Fan Jian-Fen
Relationship between the Permeation-Diffusion Parameters of a Single-File Channel
CHINESE PHYSICS LETTERS, 29 Art. No. 010502, JAN 2012
abstract, full text, DOI:10.1088/0256-307X/29/1/010502

Saiz-Poseu, Javier; Alcon, Isaac; Alibes, Ramon; Busque, Felix; Faraudo, Jordi; Ruiz-Molina, Daniel
Self-assembly of alkylcatechols on HOPG investigated by scanning tunneling microscopy and molecular dynamics simulations
CRYSTENGCOMM, 14:264-271, 2012
abstract, full text, DOI:10.1039/c1ce06010d

Orts, Julien; Bartoschek, Stefan; Griesinger, Christian; Monecke, Peter; Carlomagno, Teresa
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
JOURNAL OF BIOMOLECULAR NMR, 52:23-30, JAN 2012
abstract, full text, DOI:10.1007/s10858-011-9590-5

Xu, Xue; Li, Ruibin; Ma, Ming; Wang, Xia; Wang, Yonghua; Zou, Hanfa
Multidrug resistance protein P-glycoprotein does not recognize nanoparticle C-60: experiment and modeling
SOFT MATTER, 8:2915-2923, 2012
abstract, full text, DOI:10.1039/c2sm06811g

Czajkowsky, Daniel M.; Li, Lin; Sun, Jielin; Hu, Jun; Shao, Zhifeng
Heteroepitaxial Streptavidin Nanocrystals Reveal Critical Role of Proton "Fingers" and Subsurface Atoms in Determining Adsorbed Protein Orientation
ACS NANO, 6:190-198, JAN 2012
abstract, full text, DOI:10.1021/nn203356p

Schmid, Maurus; Nogueira, Elisa S.; Monnard, Fabien W.; Ward, Thomas R.; Meuwly, Markus
Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation
CHEMICAL SCIENCE, 3:690-700, 2012
abstract, full text, DOI:10.1039/c1sc00628b

Giannozzi, Paolo; Jansen, Karl; La Penna, Giovanni; Minicozzi, Velia; Morante, Silvia; Rossi, Giancarlo; Stellato, Francesco
Zn induced structural aggregation patterns of beta-amyloid peptides by first-principle simulations and XAS measurements
METALLOMICS, 4:156-165, 2012
abstract, full text, DOI:10.1039/c2mt00148a

Luan, Binquan; Stolovitzky, Gustavo; Martyna, Glenn
Slowing and controlling the translocation of DNA in a solid-state nanopore
NANOSCALE, 4:1068-1077, 2012
abstract, full text, DOI:10.1039/c1nr11201e

Jana, Sankar; Ghosh, Shalini; Dalapati, Sasanka; Guchhait, Nikhil
Exploring structural change of protein bovine serum albumin by external perturbation using extrinsic fluorescence probe: spectroscopic measurement, molecular docking and molecular dynamics simulation
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 11:323-332, 2012
abstract, full text, DOI:10.1039/c1pp05180f

Muenz, Marton; Biggin, Philip C.
JGromacs: A Java Package for Analyzing Protein Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:255-259, JAN 2012
abstract, full text, DOI:10.1021/ci200289s

Lauer, Timothy M.; Agrawal, Neeraj J.; Chennamsetty, Naresh; Egodage, Kamal; Helk, Bernhard; Trout, Bernhardt L.
Developability index: A rapid in silico tool for the screening of antibody aggregation propensity
JOURNAL OF PHARMACEUTICAL SCIENCES, 101:102-115, JAN 2012
abstract, full text, DOI:10.1002/jps.22758

Barr, Daniel; van der Vaart, Arjan
The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:2070-2077, 2012
abstract, full text, DOI:10.1039/c2cp23780f

Sanderson, Joseph P.; Waldburger-Hauri, Kathrin; Garzon, Diana; Matulis, Gediminas; Mansour, Salah; Pumphrey, Nicholas J.; Lissin, Nikolai; Villiger, Peter M.; Jakobsen, Bent; Faraldo-Gomez, Jose D.; Gadola, Stephan D.
Natural variations at position 93 of the invariant Va24-Ja18 a chain of human iNKT-cell TCRs strongly impact on CD1d binding
EUROPEAN JOURNAL OF IMMUNOLOGY, 42:248-255, JAN 2012
abstract, full text, DOI:10.1002/eji.201141956

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Local heterogeneous dynamics of water around lysozyme: a computer simulation study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:899-913, 2012
abstract, full text, DOI:10.1039/c1cp22575h

Fedoseyenko, Dmytro; Raghuraman, Arjun; Ko, Eunhwa; Burgess, Kevin
Omegatides: constrained analogs of peptide primary sequence
ORGANIC & BIOMOLECULAR CHEMISTRY, 10:921-924, 2012
full text, DOI:10.1039/c2ob06692k

Agnew, Christopher R. J.; Warrilow, Andrew G. S.; Burton, Nicholas M.; Lamb, David C.; Kelly, Steven L.; Brady, R. Leo
An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium leprae
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56:391-402, JAN 2012
abstract, full text, DOI:10.1128/AAC.05227-11

Pizzirusso, A.; Berardi, R.; Muccioli, L.; Ricci, M.; Zannoni, C.
Predicting surface anchoring: molecular organization across a thin film of 5CB liquid crystal on silicon
CHEMICAL SCIENCE, 3:573-579, 2012
abstract, full text, DOI:10.1039/c1sc00696g

Hart, Katarina; Foloppe, Nicolas; Baker, Christopher M.; Denning, Elizabeth J.; Nilsson, Lennart; MacKerell, Alexander D., Jr.
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:348-362, JAN 2012
abstract, full text, DOI:10.1021/ct200723y

Figueras, Luis; Faraudo, Jordi
Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes
MOLECULAR SIMULATION, 38:23-25, 2012
abstract, full text, DOI:10.1080/08927022.2011.599032

Fu, Jin; Bottegoni, Giovanni; Sasso, Oscar; Bertorelli, Rosalia; Rocchia, Walter; Masetti, Matteo; Guijarro, Ana; Lodola, Alessio; Armirotti, Andrea; Garau, Gianpiero; Bandiera, Tiziano; Reggiani, Angelo; Mor, Marco; Cavalli, Andrea; Piomelli, Daniele
A catalytically silent FAAH-1 variant drives anandamide transport in neurons
NATURE NEUROSCIENCE, 15:64-U82, JAN 2012
abstract, full text, DOI:10.1038/nn.2986

Gorny, K.; Dendzik, Z.; Raczynski, P.; Gburski, Z.
Dynamic properties of propylene glycol confined in ZSM-5 zeolite matrix-A computer simulation study
SOLID STATE COMMUNICATIONS, 152:8-12, JAN 2012
abstract, full text, DOI:10.1016/j.ssc.2011.10.020

Zhu, Xiao; Lopes, Pedro E. M.; MacKerell, Alexander D., Jr.
Recent developments and applications of the CHARMM force fields
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:167-185, JAN-FEB 2012
abstract, full text, DOI:10.1002/wcms.74

Zhang, Yubo; Cui, Yubao; Chen, L. Y.
Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel
BIOPHYSICAL CHEMISTRY, 160:69-74, JAN 2012
abstract, full text, DOI:10.1016/j.bpc.2011.07.006

Espinoza-Fonseca, L. Michel
Aromatic residues link binding and function of intrinsically disordered proteins
MOLECULAR BIOSYSTEMS, 8:237-246, 2012
abstract, full text, DOI:10.1039/c1mb05239j

Rogacheva, O.N.; Shchegolev, B.F.; Stefanov, V.E.; Zakharov, G.A.; SavvateevaPopova, E.V.
A202 AND A326 ARE CRITICAL RESIDUES FOR INITIATION OF 3':5'-AMP-INDUCED PROTEIN KINASE A Ialpha REGULATORY SUBUNIT CONFORMATIONAL TRANSITION. Part I
BIOCHEMISTRY (MOSCOW), 77:568-577, 2012
abstract, full text

Cardinali, Angela; D'Antuono, Isabella; Belviso, Benny Danilo; Caliandro, Rocco
Computational studies on a new cationic peroxidase isoenzyme from artichoke leaves (vol 49, pg 395, 2011)
BIOENGINEERED, 3:60-66, JAN-FEB 2012
abstract, full text, DOI:10.4161/bbug.3.1.17937

Lawrence, Sara L.; Feil, Susanne C.; Holien, Jessica K.; Kuiper, Michael J.; Doughty, Larissa; Dolezal, Olan; Mulhern, Terrence D.; Tweten, Rodney K.; Parker, Michael W.
Manipulating the Lewis antigen specificity of the cholesterol-dependent cytolysin lectinolysin
FRONTIERS IN IMMUNOLOGY, 3 Art. No. 330, 2012
abstract, full text, DOI:10.3389/fimmu.2012.00330

Baker, C. M.; Darian, E.; Mackerell, A. D., Jr.
Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model
INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS, VOL 1, Issue 23, 23-50, 2012
full text, DOI:10.1039/9781849735049-00023

Cheng, Xiaolin; Parks, Jerry M.; Petridis, Loukas; Lindner, Benjamin; Schulz, Roland; Guo, Hao-Bo; Srinivas, Goundla; Smith, Jeremy C.
Molecular Simulation in the Energy Biosciences
INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS, VOL 1, Issue 23, 87-114, 2012
full text, DOI:10.1039/9781849735049-00087

Foley, Meredith C.; Arora, Karunesh; Schlick, Tamar
Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism
INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS, VOL 2, Issue 24, 81-110, 2012
full text, DOI:10.1039/9781849735056-00081

Swift, Robert V.; Amaro, Rommie E.
Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications
INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS, VOL 2, Issue 24, 281-315, 2012
full text, DOI:10.1039/9781849735056-00281

Lee, Whasil; Marszalek, Piotr E.; Zeng, Xiancheng; Yang, Weitao
Mechanics of Polysaccharides
MOLECULAR MANIPULATION WITH ATOMIC FORCE MICROSCOPY, 83-128, 2012
full text

Amaravani, M.; Prasad, Nirmal K.; Ramakrishna, Vadde
COX-2 structural analysis and docking studies with gallic acid structural analogues
SPRINGERPLUS, 1 Art. No. 58, 2012
abstract, full text, DOI:10.1186/2193-1801-1-58

Muszala, Stefan P.; Alaghband, Gita; Hack, James; Connors, Daniel
Natural Load Indices (NLI) for scientific simulation
JOURNAL OF SUPERCOMPUTING, 59:392-413, JAN 2012
abstract, full text, DOI:10.1007/s11227-010-0442-y

Sapay, Nicolas; Cabannes, Eric; Petitou, Maurice; Imberty, Anne
Molecular Model of Human Heparanase with Proposed Binding Mode of a Heparan Sulfate Oligosaccharide and Catalytic Amino Acids
BIOPOLYMERS, 97:21-34, JAN 2012
abstract, full text, DOI:10.1002/bip.21696

Golebiowska, Monika; Roth, Michael; Firlej, Lucyna; Kuchta, Bogdan; Wexler, Carlos
The reversibility of the adsorption of methane-methyl mercaptan mixtures in nanoporous carbon
CARBON, 50:225-234, JAN 2012
abstract, full text, DOI:10.1016/j.carbon.2011.08.039

Georgoulia, Panagiota S.; Glykos, Nicholas M.
Using J-Coupling Constants for Force Field Validation: Application to Hepta-alanine
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15221-15227, DEC 29 2011
abstract, full text, DOI:10.1021/jp209597e

Faro, Tatiana M. C.; Skaf, Munir S.; Coluci, Vitor R.
Mechanisms of the rotational dynamics of C-70 in C-70-cubane heteromolecular crystals
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 244510, DEC 28 2011
abstract, full text, DOI:10.1063/1.3671948

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 245104, DEC 28 2011
abstract, full text, DOI:10.1063/1.3670877

Musgaard, Maria; Thogersen, Lea; Schiott, Birgit
Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study
BIOCHEMISTRY, 50:11109-11120, DEC 27 2011
abstract, full text, DOI:10.1021/bi201164b

Araya-Secchi, Raul; Garate, J. A.; Holmes, David S.; Perez-Acle, Tomas
Molecular dynamics study of the archaeal aquaporin AqpM
BMC GENOMICS, 12 Art. No. S8, DEC 22 2011
abstract, full text, DOI:10.1186/1471-2164-12-S4-S8

Jones, Peter M.; Robinson, Mark W.; Dalton, John P.; George, Anthony M.
The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations
PLOS ONE, 6 Art. No. e28589, DEC 21 2011
abstract, full text, DOI:10.1371/journal.pone.0028589

Krueger, S.; Shin, J. -H.; Raghunandan, S.; Curtis, J. E.; Kelman, Z.
Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein
BIOPHYSICAL JOURNAL, 101:2999-3007, DEC 21 2011
abstract, full text, DOI:10.1016/j.bpj.2011.11.006

Zhao, Jun; Wang, Qiuming; Liang, Guizhao; Zheng, Jie
Molecular Dynamics Simulations of Low-Ordered Alzheimer beta-Amyloid Oligomers from Dimer to Hexamer on Self-Assembled Monolayers
LANGMUIR, 27:14876-14887, DEC 20 2011
abstract, full text, DOI:10.1021/la2027913

Puri, Anu; Jang, Hyunbum; Yavlovich, Amichai; Masood, M. Athar; Veenstra, Timothy D.; Luna, Carlos; Aranda-Espinoza, Helim; Nussinov, Ruth; Blumenthal, Robert
Material Properties of Matrix Lipids Determine the Conformation and Intermolecular Reactivity of Diacetylenic Phosphatidylcholine in the Lipid Bilayer
LANGMUIR, 27:15120-15128, DEC 20 2011
abstract, full text, DOI:10.1021/la203453x

Gannon, G.; O'Dwyer, C.; Larsson, J. A.; Thompson, D.
Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14518-14525, DEC 15 2011
abstract, full text, DOI:10.1021/jp207709c

Vivcharuk, Victor; Kaznessis, Yiannis N.
Thermodynamic Analysis of Protegrin-1 Insertion and Permeation through a Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14704-14712, DEC 15 2011
abstract, full text, DOI:10.1021/jp205153y

Matysiak, Silvina; Debenedetti, Pablo G.; Rossky, Peter J.
Dissecting the Energetics of Hydrophobic Hydration of Polypeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14859-14865, DEC 15 2011
abstract, full text, DOI:10.1021/jp2079633

Christelle, Bidouil; Eduardo, Basilio De Oliveira; Latifa, Chebil; Elaine-Rose, Maia; Bernard, Maigret; Evelyne, Ronat-Heidt; Mohamed, Ghoul; Jean-Marc, Engasser; Catherine, Humeau
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation
JOURNAL OF BIOTECHNOLOGY, 156:203-210, DEC 10 2011
abstract, full text, DOI:10.1016/j.jbiotec.2011.09.007

Vargas, Ernesto; Bezanilla, Francisco; Roux, Benoit
In Search of a Consensus Model of the Resting State of a Voltage-Sensing Domain
NEURON, 72:713-720, DEC 8 2011
abstract, full text, DOI:10.1016/j.neuron.2011.09.024

Rudzinski, Joseph F.; Noid, W. G.
Coarse-graining entropy, forces, and structures
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 214101, DEC 7 2011
abstract, full text, DOI:10.1063/1.3663709

Chen, Rong; Robinson, Anna; Gordon, Dan; Chung, Shin-Ho
Modeling the Binding of Three Toxins to the Voltage-Gated Potassium Channel (Kv1.3)
BIOPHYSICAL JOURNAL, 101:2652-2660, DEC 7 2011
abstract, full text, DOI:10.1016/j.bpj.2011.10.029

Gordon, Dan; Chung, Shin-Ho
Permeation and Block of the Kv1.2 Channel Examined Using Brownian and Molecular Dynamics
BIOPHYSICAL JOURNAL, 101:2671-2678, DEC 7 2011
abstract, full text, DOI:10.1016/j.bpj.2011.10.045

Marinelli, Fabrizio; Kuhlmann, Sonja I.; Grell, Ernst; Kunte, Hans-Joerg; Ziegler, Christine; Faraldo-Gomez, Jose D.
Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:E1285-E1292, DEC 6 2011
abstract, full text, DOI:10.1073/pnas.1112534108

Bucher, Denis; Grant, Barry J.; McCammon, J. Andrew
Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
BIOCHEMISTRY, 50:10530-10539, DEC 6 2011
abstract, full text, DOI:10.1021/bi201481a

Lin, Ying-Wu; Nie, Chang-Ming; Liao, Li-Fu
Insights into Uranyl Ion Binding to Ubiquitin from Molecular Modeling and Dynamics Simulations
CHEMISTRY LETTERS, 40:1330-1331, DEC 5 2011
abstract, full text, DOI:10.1246/cl.2011.1330

Castro-Nallar, Eduardo; Cortez-San Martin, Marcelo; Mascayano, Carolina; Molina, Cristian; Crandall, Keith A.
Molecular Phylodynamics and Protein Modeling of Infectious Salmon Anemia Virus (ISAV)
BMC EVOLUTIONARY BIOLOGY, 11 Art. No. 349, DEC 2 2011
abstract, full text, DOI:10.1186/1471-2148-11-349

Krammer, Eva-Maria; Homble, Fabrice; Prevost, Martine
Concentration Dependent Ion Selectivity in VDAC: A Molecular Dynamics Simulation Study
PLOS ONE, 6 Art. No. e27994, DEC 2 2011
abstract, full text, DOI:10.1371/journal.pone.0027994

Biswas, Mithun; Voltz, Karine; Smith, Jeremy C.; Langowski, Joerg
Role of Histone Tails in Structural Stability of the Nucleosome
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002279, DEC 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002279

Ruiz, Luis; Keten, Sinan
ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES
INTERNATIONAL JOURNAL OF APPLIED MECHANICS, 3:667-684, DEC 2011
abstract, full text, DOI:10.1142/S1758825111001184

Tordesillas, Leticia; Gamboa, Pedro; Sanz, Maria L.; Palacin, Arantxa; Gomez-Casado, Cristina; Cuesta-Herranz, Javier; Pacios, Luis F.; Salcedo, Gabriel; Diaz-Perales, Araceli
A mutant of the major melon allergen, Cuc m 2, with reduced IgE binding capacity is a good candidate for specific immunotherapy
MOLECULAR IMMUNOLOGY, 49:504-511, DEC 2011
abstract, full text, DOI:10.1016/j.molimm.2011.09.020

Wanunu, Meni; Bhattacharya, Swati; Xie, Yun; Tor, Yitzhak; Aksimentiev, Aleksei; Drndic, Marija
Nanopore Analysis of Individual RNA/Antibiotic Complexes
ACS NANO, 5:9345-9353, DEC 2011
abstract, full text, DOI:10.1021/nn203764j

Kurkcuoglu, Zeynep; Ural, Gulgun; Akten, E. Demet; Doruker, Pemra
Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human
MOLECULAR INFORMATICS, 30:986-995, DEC 2011
abstract, full text, DOI:10.1002/minf.201100109

Mrinal, Nirotpal; Tomar, Archana; Nagaraju, Javaregowda
Role of sequence encoded kappa B DNA geometry in gene regulation by Dorsal
NUCLEIC ACIDS RESEARCH, 39:9574-9591, DEC 2011
abstract, full text, DOI:10.1093/nar/gkr672

Colpitts, Che C.; Kim, Sung Soo; Posehn, Sarah E.; Jepson, Christina; Kim, Sun Young; Wiedemann, Gertrud; Reski, Ralf; Wee, Andrew G. H.; Douglas, Carl J.; Suh, Dae-Yeon
PpASCL, a moss ortholog of anther-specific chalcone synthase-like enzymes, is a hydroxyalkylpyrone synthase involved in an evolutionarily conserved sporopollenin biosynthesis pathway
NEW PHYTOLOGIST, 192:855-868, DEC 2011
abstract, full text, DOI:10.1111/j.1469-8137.2011.03858.x

Wang, Xiaoling; Kumar, Sandeep; Singh, Satish K.
Disulfide Scrambling in IgG2 Monoclonal Antibodies: Insights from Molecular Dynamics Simulations
PHARMACEUTICAL RESEARCH, 28:3128-3144, DEC 2011
abstract, full text, DOI:10.1007/s11095-011-0503-9

Sanli, Deniz; Keskin, Ozlem; Gursoy, Attila; Erman, Burak
Structural cooperativity in histone H3 tail modifications
PROTEIN SCIENCE, 20:1982-1990, DEC 2011
abstract, full text, DOI:10.1002/pro.745

Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.; Kulik, A. N.; Gomory, A.
Stable associates of polyether oligomers with chlorine anion as revealed by the data of electrospray mass spectrometry and molecular dynamics
JOURNAL OF ANALYTICAL CHEMISTRY, 66:1341-1347, DEC 2011
abstract, full text, DOI:10.1134/S1061934811130107

Melillo, Matthew; Zhu, Fangqiang; Snyder, Mark A.; Mittal, Jeetain
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2978-2983, DEC 1 2011
abstract, full text, DOI:10.1021/jz2012319

Matthai, C. C.; March, N. H.
The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes
THEORETICAL CHEMISTRY ACCOUNTS, 130:1155-1167, DEC 2011
abstract, full text, DOI:10.1007/s00214-011-1022-9

Schmidtke, Peter; Bidon-Chanal, Axel; Javier Luque, F.; Barril, Xavier
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
BIOINFORMATICS, 27:3276-3285, DEC 1 2011
abstract, full text, DOI:10.1093/bioinformatics/btr550

Skjaerven, Lars; Reuter, Nathalie; Martinez, Aurora
Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach
FUTURE MEDICINAL CHEMISTRY, 3:2079-2100, DEC 2011
abstract, full text, DOI:10.4155/FMC.11.159

Ren, Hao; Jiang, Jun; Mukamel, Shaul
Deep UV Resonance Raman Spectroscopy of beta-Sheet Amyloid Fibrils: A QM/MM Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13955-13962, DEC 1 2011
abstract, full text, DOI:10.1021/jp207849u

Du, Huailiang; Li, Jingyuan; Zhang, Jing; Su, Gang; Li, Xiaoyi; Zhao, Yuliang
Separation of Hydrogen and Nitrogen Gases with Porous Graphene Membrane
JOURNAL OF PHYSICAL CHEMISTRY C, 115:23261-23266, DEC 1 2011
abstract, full text, DOI:10.1021/jp206258u

Lin, Ying-Wu; Liao, Li-Fu
Probing interactions between uranyl ions and lipid membrane by molecular dynamics simulation
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 976:130-134, DEC 1 2011
abstract, full text, DOI:10.1016/j.comptc.2011.08.016

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Bera, Asim K.
Role of Salt Bridge Dynamics in Inter Domain Recognition of Human IMPDH Isoforms: An Insight to Inhibitor Topology for Isoform-II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:441-462, DEC 2011
abstract, full text

Izanloo, C.; Parsafar, G. A.; Abroshan, H.; Akbarzadeh, H.
Denaturation of Drew-Dickerson DNA in a High Salt Concentration Medium: Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3354-3361, DEC 2011
abstract, full text, DOI:10.1002/jcc.21908

Renthal, Robert; Brancaleon, Lorenzo; Pena, Isaac; Silva, Frances; Chen, Liao Y.
Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles
BIOPHYSICAL CHEMISTRY, 159:321-327, DEC 2011
abstract, full text, DOI:10.1016/j.bpc.2011.08.005

Dawid, A.; Gorny, K.; Gburski, Z.
The structural studies of fullerenol C-60(OH)(24) and nitric oxide mixture in water solvent - MD simulation
NITRIC OXIDE-BIOLOGY AND CHEMISTRY, 25:373-380, NOV 30 2011
abstract, full text, DOI:10.1016/j.niox.2011.08.004

Abdel-Azeim, Safwat; Li, Xin; Chung, Lung Wa; Morokuma, Keiji
Zinc-Homocysteine Binding in Cobalamin-Dependent Methionine Synthase and its Role in the Substrate Activation: DFT, ONIOM, and QM/MM Molecular Dynamics Studies
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3154-3167, NOV 30 2011
abstract, full text, DOI:10.1002/jcc.21895

Bannerman, M. N.; Sargant, R.; Lue, L.
DynamO: A Free O(N) General Event-Driven Molecular Dynamics Simulator
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3329-3338, NOV 30 2011
abstract, full text, DOI:10.1002/jcc.21915

Xiang, Xue; Lee, Cho-yin; Li, Tian; Chen, Wei; Lou, Jizhong; Zhu, Cheng
Structural Basis and Kinetics of Force-Induced Conformational Changes of an alpha A Domain-Containing Integrin
PLOS ONE, 6 Art. No. e27946, NOV 28 2011
abstract, full text, DOI:10.1371/journal.pone.0027946

Joshi, Harshad; Cheluvaraja, Srinath; Somogyi, Endre; Brown, Darron R.; Ortoleva, Peter
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity
VACCINE, 29:9423-9430, NOV 28 2011
abstract, full text, DOI:10.1016/j.vaccine.2011.10.039

Fu, Chein-Wei; Lin, Thy-Hou
Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 115:13523-13533, NOV 24 2011
abstract, full text, DOI:10.1021/jp204658w

Gross, Adam S.; Bell, Alexis T.; Chu, Jhih-Wei
Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13433-13440, NOV 24 2011
abstract, full text, DOI:10.1021/jp202415v

Priya, M. Hamsa; Ashbaugh, H. S.; Paulaitis, M. E.
Cosolvent Preferential Molecular Interactions in Aqueous Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13633-13642, NOV 24 2011
abstract, full text, DOI:10.1021/jp2083067

Yuzlenko, Olga; Lazandis, Themis
Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13674-13684, NOV 24 2011
abstract, full text, DOI:10.1021/jp2052213

Shukla, Diwakar; Schneider, Curtiss P.; Trout, Bernhardt L.
Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18713-18718, NOV 23 2011
abstract, full text, DOI:10.1021/ja205215t

Nemkevich, Alexandra; Spackman, Mark A.; Corry, Ben
Mechanism of Concerted Hydrogen Bond Reorientation in Clathrates of Dianin's Compound and Hydroquinone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18880-18888, NOV 23 2011
abstract, full text, DOI:10.1021/ja206962f

Yamaguchi, Shoichi; Watanabe, Hidekazu; Mondal, Sudip Kumar; Kundu, Achintya; Tahara, Tahei
"Up" versus "down" alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 194705, NOV 21 2011
abstract, full text, DOI:10.1063/1.3662136

Schneider, Curtiss P.; Shukla, Diwakar; Trout, Bernhardt L.
Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers
PLOS ONE, 6 Art. No. e27665, NOV 18 2011
abstract, full text, DOI:10.1371/journal.pone.0027665

da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Study on the Effects of Intermolecular Interactions on Firefly Multicolor Bioluminescence
CHEMPHYSCHEM, 12:3002-3008, NOV 18 2011
abstract, full text, DOI:10.1002/cphc.201100389

Dai, Zheng-Wei; Wan, Ling-Shu; Huang, Xiao-Jun; Ling, Jun; Xu, Zhi-Kang
Selective Adsorption of Isopropyl Alcohol Aqueous Solution on Polypropylene Surfaces: A Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 115:22415-22421, NOV 17 2011
abstract, full text, DOI:10.1021/jp206733b

Sun, Sheng; Wong, Joseph T. Y.; Zhang, Tong-Yi
Atomistic Simulations of Electroporation in Water Preembedded Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13355-13359, NOV 17 2011
abstract, full text, DOI:10.1021/jp206607j

Cho, Samuel S.; Reddy, Govardhan; Straub, John E.; Thirumalai, D.
Entropic Stabilization of Proteins by TMAO
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13401-13407, NOV 17 2011
abstract, full text, DOI:10.1021/jp207289b

Heinzelmann, Germano; Bastug, Turgut; Kuyucak, Serdar
Free Energy Simulations of Ligand Binding to the Aspartate Transporter Glt(Ph)
BIOPHYSICAL JOURNAL, 101:2380-2388, NOV 16 2011
abstract, full text, DOI:10.1016/j.bpj.2011.10.010

Re, Suyong; Miyashita, Naoyuki; Yamaguchi, Yoshiki; Sugita, Yuji
Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 101:L44-L46, NOV 16 2011
abstract, full text, DOI:10.1016/j.bpj.2011.10.019

Shekhar, Prabhanshu; Nanda, Hirsh; Loesche, Mathias; Heinrich, Frank
Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques
JOURNAL OF APPLIED PHYSICS, 110 Art. No. 102216, NOV 15 2011
abstract, full text, DOI:10.1063/1.3661986

Lam, A. R.; Jiang, J.; Mukamel, S.
Distinguishing Amyloid Fibril Structures in Alzheimer's Disease (AD) by Two-Dimensional Ultraviolet (2DUV) Spectroscopy
BIOCHEMISTRY, 50:9809-9816, NOV 15 2011
abstract, full text, DOI:10.1021/bi201317c

Luo, Yun; Harder, Edward; Faibish, Ron S.; Roux, Benoit
Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane
JOURNAL OF MEMBRANE SCIENCE, 384:1-9, NOV 15 2011
abstract, full text, DOI:10.1016/j.memsci.2011.08.057

Garate, Jose-Antonio; English, Niall J.; Singh, Ajay; Ryan, Kevin M.; Mooney, Damian A.; MacElroy, J. M. D.
Electrophoretic Deposition of Poly(3-decylthiophene) onto Gold-Mounted Cadmium Selenide Nanorods
LANGMUIR, 27:13506-13513, NOV 15 2011
abstract, full text, DOI:10.1021/la203227k

Ganesan, Narayan; Bauer, Brad A.; Lucas, Timothy R.; Patel, Sandeep; Taufer, Michela
Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2958-2973, NOV 15 2011
abstract, full text, DOI:10.1002/jcc.21871

Borstnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janezic, Dusanka
The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3005-3013, NOV 15 2011
abstract, full text, DOI:10.1002/jcc.21882

Garcia-Risueno, Pablo; Echenique, Pablo; Alonso, J. L.
Exact and Efficient Calculation of Lagrange Multipliers in Biological Polymers with Constrained Bond Lengths and Bond Angles: Proteins and Nucleic Acids as Example Cases
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3039-3046, NOV 15 2011
abstract, full text, DOI:10.1002/jcc.21885

Jo, Sunhwan; Song, Kevin C.; Desaire, Heather; MacKerell, Alexander D., Jr.; Im, Wonpil
Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3135-3141, NOV 15 2011
abstract, full text, DOI:10.1002/jcc.21886

Weber, Valery; Merchant, Safir; Asthagiri, D.
Communication: Regularizing binding energy distributions and thermodynamics of hydration: Theory and application to water modeled with classical and ab initio simulations
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 181101, NOV 14 2011
abstract, full text, DOI:10.1063/1.3660205

Ferrer, Tania; Cordero-Morales, Julio F.; Arias, Marcelo; Ficker, Eckhard; Medovoy, David; Perozo, Eduardo; Tristani-Firouzi, Martin
Molecular Coupling in the Human ether-a-go-go-related gene-1 (hERG1) K+ Channel Inactivation Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39091-39099, NOV 11 2011
abstract, full text, DOI:10.1074/jbc.M111.292060

Li, Minghui; Zheng, Wenjun
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
BIOCHEMISTRY, 50:8645-8655, NOV 11 2011
abstract, full text, DOI:10.1021/bi2008257

Lim, Kok Hong; Huang, Heng; Pralle, Arnd; Park, Sheldon
Engineered Streptavidin Monomer and Dimer with Improved Stability and Function
BIOCHEMISTRY, 50:8682-8691, NOV 11 2011
abstract, full text, DOI:10.1021/bi2010366

Dolores Elola, M.; Rodriguez, Javier; Laria, Daniel
Liquid Methanol Confined within Functionalized Silica Nanopores. 2. Solvation Dynamics of Coumarin 153
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12859-12867, NOV 10 2011
abstract, full text, DOI:10.1021/jp205832y

D'Antonio, Edward L.; D'Antonio, Jennifer; de Serrano, Vesna; Gracz, Hanna; Thompson, Matthew K.; Ghiladi, Reza A.; Bowden, Edmond F.; Franzen, Stefan
Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin
BIOCHEMISTRY, 50:9664-9680, NOV 8 2011
abstract, full text, DOI:10.1021/bi201368u

Calligari, Paolo; Calandrini, Vania; Kneller, Gerald R.; Abergel, Daniel
From NMR Relaxation to Fractional Brownian Dynamics in Proteins: Results from a Virtual Experiment
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12370-12379, NOV 3 2011
abstract, full text, DOI:10.1021/jp205380f

Karachevtsev, Victor A.; Stepanian, Stepan G.; Glamazda, Alexander Yu.; Karachevtsev, Maksym V.; Eremenko, Victor V.; Lytvyn, Oksana S.; Adamowicz, Ludwik
Noncovalent Interaction of Single-Walled Carbon Nanotubes with 1-Pyrenebutanoic Acid Succinimide Ester and Glucoseoxidase
JOURNAL OF PHYSICAL CHEMISTRY C, 115:21072-21082, NOV 3 2011
abstract, full text, DOI:10.1021/jp207916d

Mondal, Sayan; Khelashvili, George; Shan, Jufang; Andersen, Olaf S.; Weinstein, Harel
Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors
BIOPHYSICAL JOURNAL, 101:2092-2101, NOV 2 2011
abstract, full text, DOI:10.1016/j.bpj.2011.09.037

Luan, Binquan; Martyna, Glenn; Stolovitzky, Gustavo
Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore
BIOPHYSICAL JOURNAL, 101:2214-2222, NOV 2 2011
abstract, full text, DOI:10.1016/j.bpj.2011.08.038

Elder, Robert M.; Emrick, Todd; Jayaraman, Arthi
Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 12:3870-3879, NOV 2011
abstract, full text, DOI:10.1021/bm201113y

Anisimov, Victor M.; Ziemys, Arturas; Kizhake, Smitha; Yuan, Ziyan; Natarajan, Amarnath; Cavasotto, Claudio N.
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:1071-1084, NOV 2011
abstract, full text, DOI:10.1007/s10822-011-9484-3

Gao, Xiang; Zhang, Nan; Wei, Tian-Di; Su, Hai-Nan; Xie, Bin-Bin; Dong, Chuang-Chuang; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Wang, Zhi-Xin; Wu, Jia-Wei; Zhang, Yu-Zhong
Crystal structure of the N-terminal domain of linker L-R and the assembly of cyanobacterial phycobilisome rods
MOLECULAR MICROBIOLOGY, 82:698-705, NOV 2011
abstract, full text, DOI:10.1111/j.1365-2958.2011.07844.x

Durrant, Jacob D.; McCammon, J. Andrew
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 31:5-9, NOV 2011
abstract, full text, DOI:10.1016/j.jmgm.2011.07.008

Kraszewski, Sebastian; Tarek, Mounir; Ramseyer, Christophe
Uptake and Translocation Mechanisms of Cationic Amino Derivatives Functionalized on Pristine C-60 by Lipid Membranes: A Molecular Dynamics Simulation Study
ACS NANO, 5:8571-8578, NOV 2011
abstract, full text, DOI:10.1021/nn201952c

Sathe, Chaitanya; Zou, Xueqing; Leburton, Jean-Pierre; Schulten, Klaus
Computational Investigation of DNA Detection Using Graphene Nanopores
ACS NANO, 5:8842-8851, NOV 2011
abstract, full text, TCBG publications, DOI:10.1021/nn202989w

Du, X. N.; Zhang, X.; Qi, J. L.; An, H. L.; Li, J. W.; Wan, Y. M.; Fu, Y.; Gao, H. X.; Gao, Z. B.; Zhan, Y.; Zhang, H. L.
Characteristics and molecular basis of celecoxib modulation on K(v)7 potassium channels
BRITISH JOURNAL OF PHARMACOLOGY, 164:1722-1737, NOV 2011
abstract, full text, DOI:10.1111/j.1476-5381.2011.01483.x

Kwon, Taekyung; Harris, Andrew L.; Rossi, Angelo; Bargiello, Thaddeus A.
Molecular dynamics simulations of the Cx26 hemichannel: Evaluation of structural models with Brownian dynamics
JOURNAL OF GENERAL PHYSIOLOGY, 138:475-493, NOV 2011
abstract, full text, DOI:10.1085/jgp.201110679

Huggins, David J.; Marsh, May; Payne, Mike C.
Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3514-3522, NOV 2011
abstract, full text, DOI:10.1021/ct200465z

Tanner, David E.; Chan, Kwok-Yan; Phillips, James C.; Schulten, Klaus
Parallel Generalized Born Implicit Solvent Calculations with NAMD
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3635-3642, NOV 2011
abstract, full text, TCBG publications, DOI:10.1021/ct200563j

Gilman-Politi, Regina; Harries, Daniel
Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3816-3828, NOV 2011
abstract, full text, DOI:10.1021/ct200455n

Feldmann, Erik A.; Ni, Shuisong; Sahu, Indra D.; Mishler, Clay H.; Risser, Douglas D.; Murakami, Jodi L.; Tom, Sasa K.; McCarrick, Robert M.; Lorigan, Gary A.; Tolbert, Blanton S.; Callahan, Sean M.; Kennedy, Michael A.
Evidence for Direct Binding between HetR from Anabaena sp PCC 7120 and PatS-5
BIOCHEMISTRY, 50:9212-9224, NOV 1 2011
abstract, full text, DOI:10.1021/bi201226e

Mishra, Sabyashachi; Caflisch, Amedeo
Dynamics in the Active Site of beta-Secretase: A Network Analysis of Atomistic Simulations
BIOCHEMISTRY, 50:9328-9339, NOV 1 2011
abstract, full text, DOI:10.1021/bi2011948

Valley, Christopher C.; Perlmutter, Jason D.; Braun, Anthony R.; Sachs, Jonathan N.
NaCl Interactions with Phosphatidylcholine Bilayers Do Not Alter Membrane Structure but Induce Long-Range Ordering of Ions and Water
JOURNAL OF MEMBRANE BIOLOGY, 244:35-42, NOV 2011
abstract, full text, DOI:10.1007/s00232-011-9395-1

Severin, Philip M. D.; Zou, Xueqing; Gaub, Hermann E.; Schulten, Klaus
Cytosine methylation alters DNA mechanical properties
NUCLEIC ACIDS RESEARCH, 39:8740-8751, NOV 2011
abstract, full text, TCBG publications, DOI:10.1093/nar/gkr578

Utesch, Tillmann; Daminelli, Grazia; Mroginski, Maria Andrea
Molecular Dynamics Simulations of the Adsorption of Bone Morphogenetic Protein-2 on Surfaces with Medical Relevance
LANGMUIR, 27:13144-13153, NOV 1 2011
abstract, full text, DOI:10.1021/la202489w

Caulfield, Thomas; Medina-Franco, Jose L.
Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
JOURNAL OF STRUCTURAL BIOLOGY, 176:185-191, NOV 2011
abstract, full text, DOI:10.1016/j.jsb.2011.07.015

Barata, Teresa S.; Brocchini, Steve; Teo, Ian; Shaunak, Sunil; Zloh, Mire
From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers
JOURNAL OF MOLECULAR MODELING, 17:2741-2749, NOV 2011
abstract, full text, DOI:10.1007/s00894-011-0966-y

Mazzucco, Nicolo; Zanconato, Stefano; De Lucrezia, Davide; Argese, Emanuele; Poli, Irene; Minervini, Giovanni
Design and dynamic simulation of minimal metallo-proteins
JOURNAL OF MOLECULAR MODELING, 17:2919-2925, NOV 2011
abstract, full text, DOI:10.1007/s00894-011-0993-8

Sadasivan, Vatsala D.; Narpala, Sandeep R.; Budil, David E.; Sacco, Albert, Jr.; Carrier, Rebecca L.
Modeling the human intestinal Mucin (MUC2) C-terminal cystine knot dimer
JOURNAL OF MOLECULAR MODELING, 17:2953-2963, NOV 2011
abstract, full text, DOI:10.1007/s00894-010-0932-0

Contreras-Torres, Flavio F.; Martinez-Loran, Erick
DNA insertion in and wrapping around carbon nanotubes
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:902-919, NOV-DEC 2011
abstract, full text, DOI:10.1002/wcms.60

Sammond, Deanne W.; Joce, Catherine; Takeshita, Ryan; McQuate, Sarah E.; Ghosh, Nilanjan; Martin, Jennifer M.; Yin, Hang
Transmembrane Peptides Used to Investigate the Homo-Oligomeric Interface and Binding Hotspot of Latent Membrane Protein 1
BIOPOLYMERS, 95:772-784, NOV 2011
abstract, full text, DOI:10.1002/bip.21672

Durrant, Jacob D.; McCammon, J. Andrew
Molecular dynamics simulations and drug discovery
BMC BIOLOGY, 9 Art. No. 71, OCT 28 2011
abstract, full text, DOI:10.1186/1741-7007-9-71

Espinoza-Fonseca, L. Michel; Thomas, David D.
Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium
PLOS ONE, 6 Art. No. e26936, OCT 27 2011
abstract, full text, DOI:10.1371/journal.pone.0026936

Tsutakawa, Susan E.; Van Wynsberghe, Adam W.; Freudenthal, Bret D.; Weinacht, Christopher P.; Gakhar, Lokesh; Washington, M. Todd; Zhuang, Zhihao; Tainer, John A.; Ivanov, Ivaylo
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:17672-17677, OCT 25 2011
abstract, full text, DOI:10.1073/pnas.1110480108

Teh, Aik-Hong; Saito, Jennifer A.; Baharuddin, Aida; Tuckerman, Jason R.; Newhouse, James S.; Kanbe, Masaomi; Newhouse, Elizabeth I.; Rahim, Rashidah Abdul; Favier, Frederique; Didierjean, Claude; Sousa, Eduardo H. S.; Stott, Matthew B.; Dunfield, Peter F.; Gonzalez, Gonzalo; Gilles-Gonzalez, Marie-Alda; Najimudin, Nazalan; Alam, Maqsudul
Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin
FEBS LETTERS, 585:3250-3258, OCT 20 2011
abstract, full text, DOI:10.1016/j.febslet.2011.09.002

Nam, Ky-Youb; Byung Ha Chang; No, Kyoung Tai
Conformational Study of N-terminal Prion Peptides by Molecular Dynamics Simulations
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 32:3553-3554, OCT 20 2011
full text, DOI:10.5012/bkcs.2011.32.10.3553

Lee, Tai-Sung; Giambasu, George M.; Harris, Michael E.; York, Darrin M.
Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2538-2543, OCT 20 2011
abstract, full text, DOI:10.1021/jz201106y

Shukla, Diwakar; Trout, Bernhardt L.
Understanding the Synergistic Effect of Arginine and Glutamic Acid Mixtures on Protein Solubility
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11831-11839, OCT 20 2011
abstract, full text, DOI:10.1021/jp204462t

Willenbring, Dan; Liu, Lu Tian; Mowrey, David; Xu, Yan; Tang, Pei
Isoflurane Alters the Structure and Dynamics of GLIC
BIOPHYSICAL JOURNAL, 101:1905-1912, OCT 19 2011
abstract, full text, DOI:10.1016/j.bpj.2011.09.026

Ettig, Ramona; Kepper, Nick; Stehr, Rene; Wedemann, Gero; Rippe, Karsten
Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping
BIOPHYSICAL JOURNAL, 101:1999-2008, OCT 19 2011
abstract, full text, DOI:10.1016/j.bpj.2011.07.057

Virtanen, Jouko Juhani; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.
Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering
BIOPHYSICAL JOURNAL, 101:2061-2069, OCT 19 2011
abstract, full text, DOI:10.1016/j.bpj.2011.09.021

Lin, Yuchun; Silvestre-Ryan, Jordi; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.; Chu, Jhih-Wei
Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16617-16624, OCT 19 2011
abstract, full text, DOI:10.1021/ja206692g

Mekhaiel, David N. A.; Czajkowsky, Daniel M.; Andersen, Jan Terje; Shi, Jianguo; El-Faham, Marwa; Doenhoff, Michael; McIntosh, Richard S.; Sandlie, Inger; He, Jianfeng; Hu, Jun; Shao, Zhifeng; Pleass, Richard J.
Polymeric human Fc-fusion proteins with modified effector functions
SCIENTIFIC REPORTS, 1 Art. No. 124, OCT 19 2011
abstract, full text, DOI:10.1038/srep00124

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping
A New Concept to Reveal Protein Dynamics Based on Energy Dissipation
PLOS ONE, 6 Art. No. e26453, OCT 17 2011
abstract, full text, DOI:10.1371/journal.pone.0026453

Jackson, Patricia L.; Noerager, Brett D.; Jablonsky, Michael J.; Hardison, Matthew T.; Cox, Bryan D.; Patterson, James C.; Dhanapal, Boopathy; Blalock, J. Edwin; Muccio, Donald D.
A CXCL8 receptor antagonist based on the structure of N-acetyl-proline-glycine-proline
EUROPEAN JOURNAL OF PHARMACOLOGY, 668:435-442, OCT 15 2011
abstract, full text, DOI:10.1016/j.ejphar.2011.02.045

Pedretti, Alessandro; Labozzetta, Alessandra; Lo Monte, Matteo; Beccari, Andrea R.; Moriconi, Alessio; Vistoli, Giulio
Exploring the activation mechanism of TRPM8 channel by targeted MD simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 414:14-19, OCT 14 2011
abstract, full text, DOI:10.1016/j.bbrc.2011.08.134

Saunders, Marissa G.; Voth, Gregory A.
Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis
JOURNAL OF MOLECULAR BIOLOGY, 413:279-291, OCT 14 2011
abstract, full text, DOI:10.1016/j.jmb.2011.07.068

Palermo, Giulia; Branduardi, Davide; Masetti, Matteo; Lodoa, Alessio; Mor, Marco; Piomelli, Daniele; Cavalli, Andrea; De Vivo, Marco
Covalent Inhibitors of Fatty Acid Amide Hydrolase: A Rationale for the Activity of Piperidine and Piperazine Aryl Ureas
JOURNAL OF MEDICINAL CHEMISTRY, 54:6612-6623, OCT 13 2011
abstract, full text, DOI:10.1021/jm2004283

Dlugosz, Maciej; Trylska, Joanna
Secondary Structures of Native and Pathogenic Huntingtin N-Terminal Fragments
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11597-11608, OCT 13 2011
abstract, full text, DOI:10.1021/jp206373g

Souza, Paulo C. T.; Barra, Gustavo B.; Velasco, Lara F. R.; Ribeiro, Isabel C. J.; Simeoni, Luiz A.; Togashi, Marie; Webb, Paul; Neves, Francisco A. R.; Skaf, Munir S.; Martinez, Leandro; Polikarpov, Igor
Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants
JOURNAL OF MOLECULAR BIOLOGY, 412:882-893, OCT 7 2011
abstract, full text, DOI:10.1016/j.jmb.2011.04.014

Duff, Nathan; Peters, Baron
Polymorph specific RMSD local order parameters for molecular crystals and nuclei: alpha-, beta-, and gamma-glycine
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 134101, OCT 7 2011
abstract, full text, DOI:10.1063/1.3638268

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 135101, OCT 7 2011
abstract, full text, DOI:10.1063/1.3634004

Sorensen, Jesper; Periole, Xavier; Skeby, Katrine K.; Marrink, S.i.e.w.e.r.t.-.J.; Schiott, Birgit
Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2385-2390, OCT 6 2011
abstract, full text, DOI:10.1021/jz2010094

Carnevale, Vincenzo; Treptow, Werner; Klein, Michael L.
Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2504-2508, OCT 6 2011
abstract, full text, DOI:10.1021/jz2011379

Dixit, Anshuman; Verkhivker, Gennady M.
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
PLOS ONE, 6 Art. No. e26071, OCT 6 2011
abstract, full text, DOI:10.1371/journal.pone.0026071

Goldsmith, Jacob; Hinds, Bruce J.
Simulation of Steady-State Methanol Flux through a Model Carbon Nanotube Catalyst Support
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19158-19164, OCT 6 2011
abstract, full text, DOI:10.1021/jp201467y

Giangreco, Ilenia; Lattanzi, Gianluca; Nicolotti, Orazio; Catto, Marco; Laghezza, Antonio; Leonetti, Francesco; Stefanachi, Angela; Carotti, Angelo
Insights into the Complex Formed by Matrix Metalloproteinase-2 and Alloxan Inhibitors: Molecular Dynamics Simulations and Free Energy Calculations
PLOS ONE, 6 Art. No. e25597, OCT 5 2011
abstract, full text, DOI:10.1371/journal.pone.0025597

Furini, Simone; Domene, Carmen
Gating at the Selectivity Filter of Ion Channels that Conduct Na+ and K+ Ions
BIOPHYSICAL JOURNAL, 101:1623-1631, OCT 5 2011
abstract, full text, DOI:10.1016/j.bpj.2011.08.035

Sarkar, Anindya; Zhou, Crystal; Meklemburg, Robert; Wintrode, Patrick L.
Local Conformational Flexibility Provides a Basis for Facile Polymer Formation in Human Neuroserpin
BIOPHYSICAL JOURNAL, 101:1758-1765, OCT 5 2011
abstract, full text, DOI:10.1016/j.bpj.2011.08.037

Patapati, Kalliopi K.; Glykos, Nicholas M.
Three Force Fields' Views of the 3(10) Helix
BIOPHYSICAL JOURNAL, 101:1766-1771, OCT 5 2011
abstract, full text, DOI:10.1016/j.bpj.2011.08.044

Bisson, Mauro; Bernaschi, Massimo; Melchionna, Simone
Parallel Molecular Dynamics with Irregular Domain Decomposition
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 10:1071-1088, OCT 2011
abstract, full text, DOI:10.4208/cicp.140810.021210a

Demir, Oezlem; Baronio, Roberta; Salehi, Faezeh; Wassman, Christopher D.; Hall, Linda; Hatfield, G. Wesley; Chamberlin, Richard; Kaiser, Peter; Lathrop, Richard H.; Amaro, Rommie E.
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002238, OCT 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002238

Dixit, Anshuman; Verkhivker, Gennady M.
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002179, OCT 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002179

Koldso, Heidi; Noer, Pernille; Grouleff, Julie; Autzen, Henriette Elisabeth; Sinning, Steffen; Schiott, Birgit
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002246, OCT 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002246

Sethi, Anurag; Goldstein, Byron; Gnanakaran, S.
Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002192, OCT 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002192

Atkinson, Jeffrey; Kapralov, Alexandr A.; Yanamala, Naveena; Tyurina, Yulia Y.; Amoscato, Andrew A.; Pearce, Linda; Peterson, Jim; Huang, Zhentai; Jiang, Jianfei; Samhan-Arias, Alejandro K.; Maeda, Akihiro; Feng, Weihong; Wasserloos, Karla; Belikova, Natalia A.; Tyurin, Vladimir A.; Wang, Hong; Fletcher, Jackie; Wang, Yongsheng; Vlasova, Irina I.; Klein-Seetharaman, Judith; Stoyanovsky, Detcho A.; Bayir, Huelya; Pitt, Bruce R.; Epperly, Michael W.; Greenberger, Joel S.; Kagan, Valerian E.
A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death
NATURE COMMUNICATIONS, 2 Art. No. 497, OCT 2011
abstract, full text, DOI:10.1038/ncomms1499

Ahmed, Ahmed Ashour; Goldsmith, Juliet; Fokt, Izabela; Le, Xiao-Feng; Krzysko, Krystiana A.; Lesyng, Bogdan; Bast, Robert C., Jr.; Priebe, Waldemar
A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer
CANCER CHEMOTHERAPY AND PHARMACOLOGY, 68:1033-1044, OCT 2011
abstract, full text, DOI:10.1007/s00280-011-1575-2

Skillman, Kristen M.; Diraviyam, Karthikeyan; Khan, Asis; Tang, Keliang; Sept, David; Sibley, L. David
Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites
PLOS PATHOGENS, 7 Art. No. e1002280, OCT 2011
abstract, full text, DOI:10.1371/journal.ppat.1002280

Han, Chen; Wang, Jian-ping
Temperature-Dependence of the Amide-I Frequency Map for Peptides Proteins
CHINESE JOURNAL OF CHEMICAL PHYSICS, 24:529-537, OCT 2011
abstract, full text, DOI:10.1088/1674-0068/24/05/529-537

Lindbo, Dag; Tornberg, Anna-Karin
Spectral accuracy in fast Ewald-based methods for particle simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 230:8744-8761, OCT 1 2011
abstract, full text, DOI:10.1016/j.jcp.2011.08.022

Vaitheeswaran, S.; Chen, Jie; Thirumalai, D.
Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins
JOURNAL OF STATISTICAL PHYSICS, 145:276-292, OCT 2011
abstract, full text, DOI:10.1007/s10955-011-0313-9

Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.
Multiscale simulation of microbe structure and dynamics
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 107:200-217, OCT 2011
abstract, full text, DOI:10.1016/j.pbiomolbio.2011.07.006

Volzing, Katherine; Biliouris, Konstantinos; Kaznessis, Yiannis N.
proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression
ACS CHEMICAL BIOLOGY, 6:1107-1116, OCT 2011
abstract, full text, DOI:10.1021/cb200168y

Muixi, L.; Gay, M.; Munoz-Torres, P. M.; Guitart, C.; Cedano, J.; Abian, J.; Alvarez, I.; Jaraquemada, D.
The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles
GENES AND IMMUNITY, 12:504-512, OCT 2011
abstract, full text, DOI:10.1038/gene.2011.26

Vassiliev, Serguei; Mahboob, Abdullah; Bruce, Doug
Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes
PHOTOSYNTHESIS RESEARCH, 110:25-38, OCT 2011
abstract, full text, DOI:10.1007/s11120-011-9689-2

Durrant, Jacob D.; Friedman, Aaron J.; McCammon, J. Andrew
CrystalDock: A Novel Approach to Fragment-Based Drug Design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2573-2580, OCT 2011
abstract, full text, DOI:10.1021/ci200357y

Wright, David W.; Coveney, Peter V.
Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2636-2649, OCT 2011
abstract, full text, DOI:10.1021/ci200308r

Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu; Hatcher, Elizabeth; Vanommeslaeghe, Kenno; Foster, Theresa J.; Jamison, Francis W., I.I.; MacKerell, Alexander D., Jr.
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate-Protein Modeling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3162-3180, OCT 2011
abstract, full text, DOI:10.1021/ct200328p

Wang, Yi; Markwick, Phineus R. L.; de Oliveira, Cesar Augusto F.; McCammon, J. Andrew
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3199-3207, OCT 2011
abstract, full text, DOI:10.1021/ct200430c

Nayar, Divya; Agarwal, Manish; Chakravarty, Charusita
Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3354-3367, OCT 2011
abstract, full text, DOI:10.1021/ct2002732

Patel, Jagdish Suresh; Branduardi, Davide; Masetti, Matteo; Rocchia, Walter; Cavalli, Andrea
Insights into Ligand-Protein Binding from Local Mechanical Response
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3368-3378, OCT 2011
abstract, full text, DOI:10.1021/ct200324j

Eichenberger, Andreas P.; Allison, Jane R.; Dolenc, Jozica; Geerke, Daan P.; Horta, Bruno A. C.; Meier, Katharina; Oostenbrink, Chris; Schmid, Nathan; Steiner, Denise; Wang, Dongqi; van Gunsteren, Wilfred F.
GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3379-3390, OCT 2011
abstract, full text, DOI:10.1021/ct2003622

Sun, Chongbo; T'ang, Tian; Uludag, Hasan
Molecular Dynamics Simulations of PEI Mediated DNA Aggregation
BIOMACROMOLECULES, 12:3698-3707, OCT 2011
abstract, full text, DOI:10.1021/bm2009476

Soriano-Ursua, Marvin A.; Correa-Basurto, Jose; Trujillo-Ferrara, Jose G.; Kaumann, Alberto J.
Homology model and docking studies on porcine beta(2) adrenoceptor: description of two binding sites
JOURNAL OF MOLECULAR MODELING, 17:2525-2538, OCT 2011
abstract, full text, DOI:10.1007/s00894-010-0915-1

Spangberg, Daniel; Larsson, Daniel S. D.; van der Spoel, David
Trajectory NG: portable, compressed, general molecular dynamics trajectories
JOURNAL OF MOLECULAR MODELING, 17:2669-2685, OCT 2011
abstract, full text, DOI:10.1007/s00894-010-0948-5

Blasco, Benjamin; Stenta, Marco; Alonso-Sarduy, Livan; Dietler, Giovanni; Dal Peraro, Matteo; Cole, Stewart T.; Pojer, Florence
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
MOLECULAR MICROBIOLOGY, 82:251-264, OCT 2011
abstract, full text, DOI:10.1111/j.1365-2958.2011.07813.x

Korchowiec, Beata; Korchowiec, Jacek; Hato, Masakatsu; Rogalska, Ewa
Glycolipid-cholesterol monolayers: Towards a better understanding of the interaction between the membrane components
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2466-2476, OCT 2011
abstract, full text, DOI:10.1016/j.bbamem.2011.06.027

Warshaviak, Dora Toledo; Muellner, Michael J.; Chachisvilis, Mirianas
Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2608-2617, OCT 2011
abstract, full text, DOI:10.1016/j.bbamem.2011.06.010

Li, Ping; Liu, Ming; Tan, Jian Jun; Zhang, Xiao Yi; Chen, Wei Zu; Wang, Cun Xin
Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:311-323, OCT 2011
abstract, full text

Fatima Lucas, M.; Rousseau, Denis L.; Guallar, Victor
Electron transfer pathways in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1305-1313, OCT 2011
abstract, full text, DOI:10.1016/j.bbabio.2011.03.003

Liu, Yingzhe; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
The effects of 7-dehydrocholesterol on the structural properties of membranes
PHYSICAL BIOLOGY, 8 Art. No. 056005, OCT 2011
abstract, full text, DOI:10.1088/1478-3975/8/5/056005

Wan, Shunzhou; Coveney, Peter V.
Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations Within the Epidermal Growth Factor Receptor
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2843-2852, OCT 2011
abstract, full text, DOI:10.1002/jcc.21866

Ma, Buyong; Nussinov, Ruth
Polymorphic Triple beta-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid beta 42 Peptide
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:34244-34253, SEP 30 2011
abstract, full text, DOI:10.1074/jbc.M111.241141

Lee, Kuo Hao; Miller, Craig R.; Nagel, Anna C.; Wichman, Holly A.; Joyce, Paul; Ytreberg, F. Marty
First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus
PLOS ONE, 6 Art. No. e25640, SEP 29 2011
abstract, full text, DOI:10.1371/journal.pone.0025640

Slade, Dea; Dunstan, Mark S.; Barkauskaite, Eva; Weston, Ria; Lafite, Pierre; Dixon, Neil; Ahel, Marijan; Leys, David; Ahel, Ivan
The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
NATURE, 477:616-U150, SEP 29 2011
abstract, full text, DOI:10.1038/nature10404

Mallajosyula, Sairam S.; MacKerell, Alexander D., Jr.
Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11215-11229, SEP 29 2011
abstract, full text, DOI:10.1021/jp203695t

Bardhan, Jaydeep P.; Knepley, Matthew G.
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 124107, SEP 28 2011
abstract, full text, DOI:10.1063/1.3641485

Calero, Carles; Faraudo, Jordi; Bastos-Gonzalez, Delfi
Interaction of Monovalent Ions with Hydrophobic and Hydrophilic Colloids: Charge Inversion and Ionic Specificity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:15025-15035, SEP 28 2011
abstract, full text, DOI:10.1021/ja204305b

Torres, Rodrigo; Swift, Robert V.; Chim, Nicholas; Wheatley, Nicole; Lan, Benson; Atwood, Brian R.; Pujol, Celine; Sankaran, Banu; Bliska, James B.; Amaro, Rommie E.; Goulding, Celia W.
Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis
PLOS ONE, 6 Art. No. e25084, SEP 26 2011
abstract, full text, DOI:10.1371/journal.pone.0025084

Monajjemi, M.; Sabaghzadeh, R.; Ilkhani, A. R.; Mollaamin, F.
Nano-modeling of insulin-like growth factor 1 (IGF-1) by computational methods
AFRICAN JOURNAL OF MICROBIOLOGY RESEARCH, 5:2895-2905, SEP 23 2011
abstract, full text

Favia, Angelo D.; Masetti, Matteo; Recanatini, Maurizio; Cavalli, Andrea
Substrate Binding Process and Mechanistic Functioning of Type 1 11 beta-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
PLOS ONE, 6 Art. No. e25375, SEP 23 2011
abstract, full text, DOI:10.1371/journal.pone.0025375

Shim, Joong-Youn; Bertalovitz, Alexander C.; Kendall, Debra A.
Identification of Essential Cannabinoid-binding Domains STRUCTURAL INSIGHTS INTO EARLY DYNAMIC EVENTS IN RECEPTOR ACTIVATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:33422-33435, SEP 23 2011
abstract, full text, DOI:10.1074/jbc.M111.261651

Kim, Sang N.; Kuang, Zhifeng; Slocik, Joseph M.; Jones, Sharon E.; Cui, Yue; Farmer, Barry L.; McAlpine, Michael C.; Naik, Rajesh R.
Preferential Binding of Peptides to Graphene Edges and Planes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14480-14483, SEP 21 2011
abstract, full text, DOI:10.1021/ja2042832

Miao, Yinglong; Baudry, Jerome
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
BIOPHYSICAL JOURNAL, 101:1493-1503, SEP 21 2011
abstract, full text, DOI:10.1016/j.bpj.2011.08.020

Barr, Daniel; Oashi, Taiji; Burkhard, Kimberly; Lucius, Sarah; Samadani, Ramin; Zhang, Jun; Shapiro, Paul; MacKerell, Alexander D., Jr.; van der Vaart, Arjan
Importance of Domain Closure for the Autoactivation of ERK2
BIOCHEMISTRY, 50:8038-8048, SEP 20 2011
abstract, full text, DOI:10.1021/bi200503a

King, Dylan T.; Warren, Dallas B.; Pouton, Colin W.; Chalmers, David K.
Using Molecular Dynamics to Study Liquid Phase Behavior: Simulations of the Ternary Sodium Laurate/Sodium Oleate/Water System
LANGMUIR, 27:11381-11393, SEP 20 2011
abstract, full text, DOI:10.1021/la2022903

Naidu, Mamta D.; Agarwal, Rakhi; Pena, Louis A.; Cunha, Luis; Mezei, Mihaly; Shen, Min; Wilson, David M., I.I.I.; Liu, Yuan; Sanchez, Zina; Chaudhary, Pankaj; Wilson, Samuel H.; Waring, Michael J.
Lucanthone and Its Derivative Hycanthone Inhibit Apurinic Endonuclease-1 (APE1) by Direct Protein Binding
PLOS ONE, 6 Art. No. e23679, SEP 15 2011
abstract, full text, DOI:10.1371/journal.pone.0023679

Modi, Niraj; Singh, Pratik Raj; Mahendran, Kozhinjampara R.; Schulz, Robert; Winterhalter, Mathias; Kleinekathoefer, Ulrich
Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2331-2336, SEP 15 2011
abstract, full text, DOI:10.1021/jz201006b

Singleton, Belinda K.; Lau, Winnie; Fairweather, Victoria S. S.; Burton, Nicholas M.; Wilson, Marieangela C.; Parsons, Steve F.; Richardson, Ben M.; Trakarnsanga, Kongtana; Brady, R. Leo; Anstee, David J.; Frayne, Jan
Mutations in the second zinc finger of human EKLF reduce promoter affinity but give rise to benign and disease phenotypes
BLOOD, 118:3137-3145, SEP 15 2011
abstract, full text, DOI:10.1182/blood-2011-04-349985

Matyushov, Dmitry V.
Nanosecond Stokes Shift Dynamics, Dynamical Transition, and Gigantic Reorganization Energy of Hydrated Heme Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10715-10724, SEP 15 2011
abstract, full text, DOI:10.1021/jp200409z

Videla, Pablo E.; Sala, Jonas; Marti, Jordi; Guardia, Elvira; Laria, Daniel
Aqueous electrolytes confined within functionalized silica nanopores
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 104503, SEP 14 2011
abstract, full text, DOI:10.1063/1.3632050

Ulucan, Ozlem; Keskin, Ozlem; Erman, Burak; Gursoy, Attila
A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A
PLOS ONE, 6 Art. No. e24664, SEP 13 2011
abstract, full text, DOI:10.1371/journal.pone.0024664

Cui, Yubao; Bastien, David A.
Water transport in human aquaporin-4: Molecular dynamics (MD) simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:654-659, SEP 9 2011
abstract, full text, DOI:10.1016/j.bbrc.2011.08.019

Lawrence, Scott A.; Hackett, John C.; Moran, Richard G.
Tetrahydrofolate Recognition by the Mitochondrial Folate Transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:31480-31489, SEP 9 2011
abstract, full text, DOI:10.1074/jbc.M111.272187

Shah, Manas; Santiso, Erik E.; Trout, Bernhardt L.
Computer Simulations of Homogeneous Nucleation of Benzene from the Melt
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10400-10412, SEP 8 2011
abstract, full text, DOI:10.1021/jp203550t

Cho, Hyung Min; Gross, Adam S.; Chu, Jhih-Wei
Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14033-14041, SEP 7 2011
abstract, full text, DOI:10.1021/ja2046155

Hsin, Jen; LaPointe, Loren M.; Kazy, Alla; Chipot, Christophe; Senes, Alessandro; Schulten, Klaus
Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14071-14081, SEP 7 2011
abstract, full text, TCBG publications, DOI:10.1021/ja204869h

Gonzalez, Angel; Perez-Acle, Tomas; Pardo, Leonardo; Deupi, Xavier
Molecular Basis of Ligand Dissociation in beta-Adrenergic Receptors
PLOS ONE, 6 Art. No. e23815, SEP 7 2011
abstract, full text, DOI:10.1371/journal.pone.0023815

Chan, Kwok-Yan; Gumbart, James; McGreevy, Ryan; Watermeyer, Jean M.; Sewell, B. Trevor; Schulten, Klaus
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
STRUCTURE, 19:1211-1218, SEP 7 2011
abstract, full text, TCBG publications, DOI:10.1016/j.str.2011.07.017

McParland, Victoria; Varsano, Giulia; Li, Xun; Thornton, Janet; Baby, Jancy; Aravind, Ajay; Meyer, Christoph; Pavic, Karolina; Rios, Pablo; Koehn, Maja
The Metastasis-Promoting Phosphatase PRL-3 Shows Activity toward Phosphoinositides
BIOCHEMISTRY, 50:7579-7590, SEP 6 2011
abstract, full text, DOI:10.1021/bi201095z

Perlmutter, Jason D.; Drasler, William J., I.I.; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N.
All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
LANGMUIR, 27:10523-10537, SEP 6 2011
abstract, full text, DOI:10.1021/la202103v

Gentilucci, Luca; Tolomelli, Alessandra; De Marco, Rossella; Spampinato, Santi; Bedini, Andrea; Artali, Roberto
The Inverse Type II beta-Turn on D-Trp-Phe, a Pharmacophoric Motif for MOR Agonists
CHEMMEDCHEM, 6:1640-1653, SEP 5 2011
abstract, full text, DOI:10.1002/cmdc.201100169

Henry, L. Keith; Iwamoto, Hideki; Field, Julie R.; Kaufmann, Kristian; Dawson, Eric S.; Jacobs, Miriam T.; Adams, Chelsea; Felts, Bruce; Zdravkovic, Igor; Armstrong, Vanessa; Combs, Steven; Solis, Ernesto; Rudnick, Gary; Noskov, Sergei Y.; DeFelice, Louis J.; Meiler, Jens; Blakely, Randy D.
A Conserved Asparagine Residue in Transmembrane Segment 1 (TM1) of Serotonin Transporter Dictates Chloride-coupled Neurotransmitter Transport
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:30823-30836, SEP 2 2011
abstract, full text, DOI:10.1074/jbc.M111.250308

Long, Mian; Sato, Masaaki; Lim, Chwee Teck; Wu, Jianhua; Adachi, Taiji; Inoue, Yasuhiro
Advances in Experiments and Modeling in Micro- and Nano-Biomechanics: A Mini Review
CELLULAR AND MOLECULAR BIOENGINEERING, 4:327-339, SEP 2011
abstract, full text, DOI:10.1007/s12195-011-0183-x

Huang, Qingsheng; Lou, Jizhong; Wu, Jianhua; Zhu, Cheng
Conformational Transition of Glycoprotein Ib alpha Mutants in Flow Molecular Dynamics Simulation
CELLULAR AND MOLECULAR BIOENGINEERING, 4:495-504, SEP 2011
abstract, full text, DOI:10.1007/s12195-011-0171-1

Pan, Di; Song, Yuhua
Effects of Altered Restraints in beta 1 Integrin on the Force-Regulated Interaction between the Glycosylated I-Like Domain of beta 1 Integrin and Fibronectin III9-10: A Steered Molecular Dynamic Study
Molecular & Cellular Biomechanics, 8:233-252, SEP 2011
abstract, full text

Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele
Metadynamics
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:826-843, SEP-OCT 2011
abstract, full text, DOI:10.1002/wcms.31

Heinrich, Joerg-Christian; Tuukkanen, Anne; Schroeder, Michael; Fahrig, Torsten; Fahrig, Rudolf
RP101 (brivudine) binds to heat shock protein HSP27 (HSPB1) and enhances survival in animals and pancreatic cancer patients
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, 137:1349-1361, SEP 2011
abstract, full text, DOI:10.1007/s00432-011-1005-1

Meredith, Jeremy S.; Roth, Philip C.; Spafford, Kyle L.; Vetter, Jeffrey S.
PERFORMANCE IMPLICATIONS OF NONUNIFORM DEVICE TOPOLOGIES IN SCALABLE HETEROGENEOUS ARCHITECTURES
IEEE MICRO, 31:66-75, SEP-OCT 2011
full text

Phatak, Mukta; Adamczak, Rafal; Cao, Baoqiang; Wagner, Michael; Meller, Jaroslaw
Solvent and Lipid Accessibility Prediction as a Basis for Model Quality Assessment in Soluble and Membrane Proteins
CURRENT PROTEIN & PEPTIDE SCIENCE, 12:563-573, SEP 2011
abstract, full text

Wang, Yeng-Tseng; Lee, Wen-Jay; Su, Zhi-Yuan; Chen, Cheng-Lung
Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 42:724-726, SEP 2011
abstract, full text, DOI:10.1016/j.jtice.2011.02.004

Necula, Gheorghe; Mihai, Maria E.; Sbarcea, Claudiu E.; Dinu, Sorin; Lupulescu, Emilia; Ceausu, Emanoil; Streinu-Cercel, Adrian; Mihailescu, Dan F.; Alexandrescu, Viorel I.
Overview of influenza virus antiviral resistance in Romania in the last four epidemic seasons - phenotyping, genotyping and molecular analysis study
REVISTA ROMANA DE MEDICINA DE LABORATOR, 19:227-240, SEP 2011
abstract, full text

Styrcz, Anna; Mrozek, Janusz; Mazur, Grzegorz
A NEURAL-NETWORK CONTROLLED DYNAMIC EVOLUTIONARY SCHEME FOR GLOBAL MOLECULAR GEOMETRY OPTIMIZATION
INTERNATIONAL JOURNAL OF APPLIED MATHEMATICS AND COMPUTER SCIENCE, 21:559-566, SEP 2011
abstract, full text, DOI:10.2478/v10006-011-0044-8

Vazquez, Nancy; Schmeisser, Hana; Dolan, Michael A.; Bekisz, Joseph; Zoon, Kathryn C.; Wahl, Sharon M.
Structural variants of IFN alpha preferentially promote antiviral functions
BLOOD, 118:2567-2577, SEP 1 2011
abstract, full text, DOI:10.1182/blood-2010-12-325027

Moldovan, Clara; Thompson, Damien
Molecular dynamics of the "hydrophobic patch" that immobilizes hydrophobin protein HFBII on silicon
JOURNAL OF MOLECULAR MODELING, 17:2227-2235, SEP 2011
abstract, full text, DOI:10.1007/s00894-010-0887-1

Mikulska, Karolina; Peplowski, Lukasz; Nowak, Wieslaw
Nanomechanics of Ig-like domains of human contactin (BIG-2)
JOURNAL OF MOLECULAR MODELING, 17:2313-2323, SEP 2011
abstract, full text, DOI:10.1007/s00894-011-1010-y

Izanloo, C.; Parsafar, G. A.; Abroshan, H.; Akbarzade, H.
Calculation of Melting Temperature and Transition Curve for Dickerson DNA Dodecamer on the Basis of Configurational Entropy, Hydrogen Bonding Energy, and Heat Capacity: A Molecular Dynamics Simulation Study
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:708-716, SEP 2011
abstract, full text

Kostyuchenko, Victor A.; Jakana, Joanita; Liu, Xiangan; Haddow, Andrew D.; Aung, Myint; Weaver, Scott C.; Chiu, Wah; Lok, Shee-Mei
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
JOURNAL OF VIROLOGY, 85:9327-9333, SEP 2011
abstract, full text, DOI:10.1128/JVI.05015-11

Robinson, David; Besley, Nicholas A.; O'Shea, Paul; Hirst, Jonathan D.
Water Order Profiles on Phospholipid/Cholesterol Membrane Bilayer Surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2613-2618, SEP 2011
abstract, full text, DOI:10.1002/jcc.21840

Pietropaolo, Adriana; Branduardi, Davide; Bonomi, Massimiliano; Parrinello, Michele
A Chirality-Based Metrics for Free-Energy Calculations in Biomolecular Systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2627-2637, SEP 2011
abstract, full text, DOI:10.1002/jcc.21842

Da Silva, Luis Pinto; Esteves Da Silva, Joaquim C. G.
Theoretical Modulation of the Color of Light Emitted by Firefly Oxyluciferin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2654-2663, SEP 2011
abstract, full text, DOI:10.1002/jcc.21845

Pittala, Valeria; Siracusa, Maria A.; Modica, Maria N.; Salerno, Loredana; Pedretti, Alessandro; Vistoli, Giulio; Cagnotto, Alfredo; Mennini, Tiziana; Romeo, Giuseppe
Synthesis and molecular modeling of 1H-pyrrolopyrimidine-2,4-dione derivatives as ligands for the alpha(1)-adrenoceptors
BIOORGANIC & MEDICINAL CHEMISTRY, 19:5260-5276, SEP 1 2011
abstract, full text, DOI:10.1016/j.bmc.2011.06.043

Vetter, Jeffrey S.; Glassbrook, Richard; Dongarra, Jack; Schwan, Karsten; Loftis, Bruce; McNally, Stephen; Meredith, Jeremy; Rogers, James; Roth, Philip; Spafford, Kyle; Yalamanchili, Sudhakar
KEENELAND: BRINGING HETEROGENEOUS GPU COMPUTING TO THE COMPUTATIONAL SCIENCE COMMUNITY
COMPUTING IN SCIENCE & ENGINEERING, 13:90-95, SEP-OCT 2011
full text

Balaeff, Alexander; Craig, Stephen L.; Beratan, David N.
B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9377-9391, SEP 1 2011
abstract, full text, DOI:10.1021/jp110871g

Oteri, Francesco; Falconi, Mattia; Chillemi, Giovanni; Andersen, Felicie F.; Oliveira, Cristiano L. P.; Pedersen, Jan S.; Knudsen, Birgitta R.; Desideri, Alessandro
Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability
JOURNAL OF PHYSICAL CHEMISTRY C, 115:16819-16827, SEP 1 2011
abstract, full text, DOI:10.1021/jp203999x

Sapay, Nicolas; Cabannes, Eric; Petitou, Maurice; Imberty, Anne
Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together
GLYCOBIOLOGY, 21:1181-1193, SEP 2011
abstract, full text, DOI:10.1093/glycob/cwr052

Montanez, Maria Isabel; Najera, Francisco; Perez-Inestrosa, Ezequiel
NMR Studies and Molecular Dynamic Simulation of Synthetic Dendritic Antigens
POLYMERS, 3:1533-1553, SEP 2011
abstract, full text, DOI:10.3390/polym3031533

Morozov, I. V.; Valuev, I. A.
Automatic distributed workflow generation with GridMD library
COMPUTER PHYSICS COMMUNICATIONS, 182:2052-2058, SEP 2011
abstract, full text, DOI:10.1016/j.cpc.2011.01.005

Caroli Rezende, Marcos; Mascayano, Carolina; Briones, Luis; Aliaga, Carolina
Sensing different micellar microenvironments with solvatochromic dyes of variable lipophilicity
DYES AND PIGMENTS, 90:219-224, SEP 2011
abstract, full text, DOI:10.1016/j.dyepig.2011.01.001

Vukovic, Lela; Khatib, Fatima A.; Drake, Stephanie P.; Madriaga, Antonett; Brandenburg, Kenneth S.; Kral, Petr; Onyuksel, Hayat
Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13481-13488, AUG 31 2011
abstract, full text, DOI:10.1021/ja204043b

Nishima, Wataru; Kanamaru, Shuji; Arisaka, Fumio; Kitao, Akio
Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13571-13576, AUG 31 2011
abstract, full text, DOI:10.1021/ja204451g

Mao, Debin; Lu, Shouqin; Li, Ning; Zhang, Yan; Long, Mian
Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1
PLOS ONE, 6 Art. No. e24188, AUG 31 2011
abstract, full text, DOI:10.1371/journal.pone.0024188

Wedberg, Rasmus; O'Connell, John P.; Peters, Gunther H.; Abildskov, Jens
Pair correlation function integrals: Computation and use
JOURNAL OF CHEMICAL PHYSICS, 135 Art. No. 084113, AUG 28 2011
abstract, full text, DOI:10.1063/1.3626799

Thota, Abhinav; Luckow, Andre; Jha, Shantenu
Efficient large-scale replica-exchange simulations on production infrastructure
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3318-3335, AUG 28 2011
abstract, full text, DOI:10.1098/rsta.2011.0151

Zasada, Stefan J.; Haidar, Ali N.; Coveney, Peter V.
On the usability of grid middleware and security mechanisms
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3413-3428, AUG 28 2011
abstract, full text, DOI:10.1098/rsta.2011.0131

Morishita, Masayo; di Luccio, Eric
Structural insights into the regulation and the recognition of histone marks by the SET domain of NSD1
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:214-219, AUG 26 2011
abstract, full text, DOI:10.1016/j.bbrc.2011.07.061

Legrand, Baptiste; Giudice, Emmanuel; Nicolas, Aurelie; Delalande, Olivier; Le Rumeur, Elisabeth
Computational Study of the Human Dystrophin Repeats: Interaction Properties and Molecular Dynamics
PLOS ONE, 6 Art. No. e23819, AUG 25 2011
abstract, full text, DOI:10.1371/journal.pone.0023819

Anzini, Maurizio; Valenti, Salvatore; Braile, Carlo; Cappelli, Andrea; Vomero, Salvatore; Acaro, Stefano; Ortuso, Francesco; Marinelli, Luciana; Limongelli, Vittorio; Novellino, Ettore; Betti, Laura; Giannaccini, Gino; Lucacchini, Antonio; Daniele, Simona; Martini, Claudia; Ghelardini, Carla; Mannelli, Lorenzo Di Cesare; Giorgi, Gianluca; Mascia, Maria Paola; Biggio, Giovanni
New Insight into the Central Benzodiazepine Receptor-Ligand Interactions: Design, Synthesis, Biological Evaluation, and Molecular Modeling of 3-Substituted 6-Phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and Related Compounds
JOURNAL OF MEDICINAL CHEMISTRY, 54:5694-5711, AUG 25 2011
abstract, full text, DOI:10.1021/jm2001597

van Hoof, Bram; Markvoort, Albert J.; van Santen, Rutger A.; Hilbers, Peter A. J.
The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10001-10012, AUG 25 2011
abstract, full text, DOI:10.1021/jp201975m

Centrone, Andrea; Santiso, Erik E.; Hatton, T. Alan
Separation of Chemical Reaction Intermediates by Metal-Organic Frameworks
SMALL, 7:2356-2364, AUG 22 2011
abstract, full text, DOI:10.1002/smll.201100098

Bellesia, Giovanni; Chundawat, Shishir P. S.; Langan, Paul; Dale, Bruce E.; Gnanakaran, S.
Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9782-9788, AUG 18 2011
abstract, full text, DOI:10.1021/jp2048844

Raghuraman, Arjun; Ko, Eunhwa; Perez, Lisa M.; Ioerger, Thomas R.; Burgess, Kevin
Pyrrolinone-Pyrrolidine Oligomers as Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12350-12353, AUG 17 2011
abstract, full text, DOI:10.1021/ja2033734

Wang, Jun; Ma, Chunlong; Fiorin, Giacomo; Carnevale, Vincenzo; Wang, Tuo; Hu, Fanghao; Lamb, Robert A.; Pinto, Lawrence H.; Hong, Mei; Kein, Michael L.; DeGrado, William F.
Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12834-12841, AUG 17 2011
abstract, full text, DOI:10.1021/ja204969m

Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher
Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling
PLOS ONE, 6 Art. No. e23396, AUG 17 2011
abstract, full text, DOI:10.1371/journal.pone.0023396

ElSawy, Karim M.; Caves, Leo S. D.; Twarock, Reidun
On the Origin of Order in the Genome Organization of ssRNA Viruses
BIOPHYSICAL JOURNAL, 101:774-780, AUG 17 2011
abstract, full text, DOI:10.1016/j.bpj.2011.07.005

Liu, Liping; Ghosh, Nilanjan; Slivka, Peter F.; Fiorini, Zeno; Hutchinson, Mark R.; Watkins, Linda R.; Yin, Hang
An MD2 Hot-Spot-Mimicking Peptide that Suppresses TLR4-Mediated Inflammatory Response in vitro and in vivo
CHEMBIOCHEM, 12:1827-1831, AUG 16 2011
full text, DOI:10.1002/cbic.201100211

Grasso, Giuseppa I.; Arena, Giuseppe; Bellia, Francesco; Maccarrone, Giuseppe; Parrinello, Michele; Pietropaolo, Adriana; Vecchio, Graziella; Rizzarelli, Enrico
Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine-Trehalose Conjugates
CHEMISTRY-A EUROPEAN JOURNAL, 17:9448-9455, AUG 16 2011
abstract, full text, DOI:10.1002/chem.201100313

Chen, Min-Hsuan; Sandberg, Daniel J.; Babu, Kunnel R.; Bubis, Jose; Surya, Arjun; Ramos, Lavoisier S.; Zapata, Heidi J.; Galan, Jhenny F.; Sandberg, Megan N.; Birge, Robert R.; Knox, Barry E.
Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments
BIOCHEMISTRY, 50:6763-6773, AUG 16 2011
abstract, full text, DOI:10.1021/bi101557m

Wan, Shunzhou; Coveney, Peter V.
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8:1114-1127, AUG 7 2011
abstract, full text, DOI:10.1098/rsif.2010.0609

Louet, Maxime; Perahia, David; Martinez, Jean; Floquet, Nicolas
A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins
JOURNAL OF MOLECULAR BIOLOGY, 411:298-312, AUG 5 2011
abstract, full text, DOI:10.1016/j.jmb.2011.05.034

Manji, Shehnaaz S. M.; Miller, Kerry A.; Williams, Louise H.; Andreasen, Lotte; Siboe, Maria; Rose, Elizabeth; Bahlo, Melanie; Kuiper, Michael; Dahl, Hans-Henrik M.
An ENU-Induced Mutation of Cdh23 Causes Congenital Hearing Loss, but No Vestibular Dysfunction, in Mice
AMERICAN JOURNAL OF PATHOLOGY, 179:903-914, AUG 2011
abstract, full text, DOI:10.1016/j.ajpath.2011.04.002

Watanabe, Hiroshi; Suzuki, Masaru; Ito, Nobuyasu
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
PROGRESS OF THEORETICAL PHYSICS, 126:203-235, AUG 2011
abstract, full text

Cojocaru, Vlad; Balali-Mood, Kia; Sansom, Mark S. P.; Wade, Rebecca C.
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002152, AUG 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002152

Matts, Robert L.; Dixit, Anshuman; Peterson, Laura B.; Sun, Liang; Voruganti, Sudhakar; Kalyanaraman, Palgunan; Hartson, Steve D.; Verkhivker, Gennady M.; Blagg, Brian S. J.
Elucidation of the Hsp90 C-Terminal Inhibitor Binding Site
ACS CHEMICAL BIOLOGY, 6:800-807, AUG 2011
abstract, full text, DOI:10.1021/cb200052x

Pietra, Francesco
On the Egress of Carbon Monoxide from Myoglobin
CHEMISTRY & BIODIVERSITY, 8:1410-1421, AUG 2011
abstract, full text

Maeda, Satoshi; Morokuma, Keiji
Finding Reaction Pathways of Type A+B -> X: Toward Systematic Prediction of Reaction Mechanisms
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2335-2345, AUG 2011
abstract, full text, DOI:10.1021/ct200290m

Romo, Tod D.; Grossfield, Alan
Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2464-2472, AUG 2011
abstract, full text, DOI:10.1021/ct2002754

Srinivas, Goundla; Cheng, Xiaolin; Smith, Jeremy C.
A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2539-2548, AUG 2011
abstract, full text, DOI:10.1021/ct200181t

Papadopoulos, Philip M.
Extending clusters to Amazon EC2 using the Rocks toolkit
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 25:317-327, AUG 2011
abstract, full text, DOI:10.1177/1094342011414747

Glykos, Nicholas M.
On the application of structure-specific bulk-solvent models
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:739-741, AUG 2011
abstract, full text, DOI:10.1107/S090744491102258X

Knapp, B.; Frantal, S.; Cibena, M.; Schreiner, W.; Bauer, P.
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?
JOURNAL OF COMPUTATIONAL BIOLOGY, 18:997-1005, AUG 2011
abstract, full text, DOI:10.1089/cmb.2010.0237

Pedretti, Alessandro; De Luca, Laura; Marconi, Cristina; Regazzoni, Luca; Aldini, Giancarlo; Vistoli, Giulio
Fragmental modeling of hPepT2 and analysis of its binding features by docking studies and pharmacophore mapping
BIOORGANIC & MEDICINAL CHEMISTRY, 19:4544-4551, AUG 2011
abstract, full text, DOI:10.1016/j.bmc.2011.06.027

Lin, Tu-Liang; Song, Guang
Efficient mapping of ligand migration channel networks in dynamic proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2475-2490, AUG 2011
abstract, full text, DOI:10.1002/prot.23071

Du, Hongbo; Qian, Xianghong
Molecular Dynamics Simulations of PNIPAM-co-PEGMA Copolymer Hydrophilic to Hydrophobic Transition in NaCl Solution
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 49:1112-1122, AUG 1 2011
abstract, full text, DOI:10.1002/polb.22280

Caulfield, Thomas R.
Inter-ring rotation of apolipoprotein A-I protein monomers for the double-belt model using biased molecular dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:1006-1014, AUG 2011
abstract, full text, DOI:10.1016/j.jmgm.2011.04.005

Klenin, Konstantin; Strode, Birgit; Wales, David J.; Wenzel, Wolfgang
Modelling proteins: Conformational sampling and reconstruction of folding kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:977-1000, AUG 2011
abstract, full text, DOI:10.1016/j.bbapap.2010.09.006

McGeagh, John D.; Ranaghan, Kara E.; Mulholland, Adrian J.
Protein dynamics and enzyme catalysis: Insights from simulations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1077-1092, AUG 2011
abstract, full text, DOI:10.1016/j.bbapap.2010.12.002

Venkatesan, Bala Murali; Polans, James; Comer, Jeffrey; Sridhar, Supriya; Wendell, David; Aksimentiev, Aleksei; Bashir, Rashid
Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore
BIOMEDICAL MICRODEVICES, 13:671-682, AUG 2011
abstract, full text, DOI:10.1007/s10544-011-9537-3

Romo, Tod D.; Bradney, Laura A.; Greathouse, Denise V.; Grossfield, Alan
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2019-2030, AUG 2011
abstract, full text, DOI:10.1016/j.bbamem.2011.03.017

Guerry, Paul; Herrmann, Torsten
Advances in automated NMR protein structure determination
QUARTERLY REVIEWS OF BIOPHYSICS, 44:257-309, AUG 2011
abstract, full text, DOI:10.1017/S0033583510000326

Boresch, Stefan; Bruckner, Stefan
Avoiding the van der Waals Endpoint Problem Using Serial Atomic Insertion
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2449-2458, AUG 2011
abstract, full text, DOI:10.1002/jcc.21829

Makowski, Lee; Gore, David; Mandava, Suneeta; Minh, David; Park, Sanghyun; Rodi, Diane J.; Fischetti, Robert F.
X-ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles
BIOPOLYMERS, 95:531-542, AUG 2011
abstract, full text, DOI:10.1002/bip.21631

Shintani, Megumi; Yoshida, Ken; Sakuraba, Shun; Nakahara, Masaru; Matubayasi, Nobuyuki
NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9106-9115, JUL 28 2011
abstract, full text, DOI:10.1021/jp204051f

Karachevtsev, Maxim V.; Karachevtsev, Victor A.
Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9271-9279, JUL 28 2011
abstract, full text, DOI:10.1021/jp2026362

Chundawat, Shishir P. S.; Bellesia, Giovanni; Uppugundla, Nirmal; Sousa, Leonardo da Costa; Gao, Dahai; Cheh, Albert M.; Agarwal, Umesh P.; Bianchetti, Christopher M.; Phillips, George N., Jr.; Langan, Paul; Balan, Venkatesh; Gnanakaran, S.; Dale, Bruce E.
Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:11163-11174, JUL 27 2011
abstract, full text, DOI:10.1021/ja2011115

Rivalta, Ivan; Amin, Muhamed; Luber, Sandra; Vassiliev, Serguei; Pokhrel, Ravi; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Bruce, Doug; Brudvig, Gary W.; Gunner, M. R.; Batista, Victor S.
Structural-Functional Role of Chloride in Photosystem II
BIOCHEMISTRY, 50:6312-6315, JUL 26 2011
abstract, full text, DOI:10.1021/bi200685w

He, Yuhui; Scheicher, Ralph H.; Grigoriev, Anton; Ahuja, Rajeev; Long, Shibing; Huo, ZongLiang; Liu, Ming
Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes
ADVANCED FUNCTIONAL MATERIALS, 21:2674-2679, JUL 22 2011
abstract, full text, DOI:10.1002/adfm.201002530

Bond, Peter J.; Faraldo-Gomez, Jose D.
Molecular Mechanism of Selective Recruitment of Syk Kinases by the Membrane Antigen-Receptor Complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:25872-25881, JUL 22 2011
abstract, full text, DOI:10.1074/jbc.M111.223321

Ufimtsev, Ivan S.; Luehr, Nathan; Martinez, Todd J.
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1789-1793, JUL 21 2011
abstract, full text, DOI:10.1021/jz200697c

Carr, Rogan; Comer, Jeffrey; Ginsberg, Mark D.; Aksimentiev, Aleksei
Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1804-1807, JUL 21 2011
abstract, full text, DOI:10.1021/jz200749d

Zanuy, David; Hamley, Ian W.; Aleman, Carlos
Modeling the Tetraphenylalanine-PEG Hybrid Amphiphile: From DFT Calculations on the Peptide to Molecular Dynamics Simulations on the Conjugate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8937-8946, JUL 21 2011
abstract, full text, DOI:10.1021/jp2031187

Watt, Eric D.; Rivalta, Ivan; Whittier, Sean K.; Batista, Victor S.; Loria, J. Patrick
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
BIOPHYSICAL JOURNAL, 101:411-420, JUL 20 2011
abstract, full text, DOI:10.1016/j.bpj.2011.05.039

Liu, Jian J.; Stockton, Rebecca A.; Gingras, Alexandre R.; Ablooglu, Ararat J.; Han, Jaewon; Bobkov, Andrey A.; Ginsberg, Mark H.
A mechanism of Rap1-induced stabilization of endothelial cell-cell junctions
MOLECULAR BIOLOGY OF THE CELL, 22:2509-2519, JUL 15 2011
abstract, full text, DOI:10.1091/mbc.E11-02-0157

Beretta, G.; Artali, R.; Facino, R. Maffei; Gelmini, F.
An analytical and theoretical approach for the profiling of the antioxidant activity of essential oils: The case of Rosmarinus officinalis L.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 55:1255-1264, JUL 15 2011
abstract, full text, DOI:10.1016/j.jpba.2011.03.026

Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; Mackerell, Alexander D., Jr.
Impact of 2 '-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1929-1943, JUL 15 2011
abstract, full text, DOI:10.1002/jcc.21777

Andersson, Magnus; Freites, J. Alfredo; Tobias, Douglas J.; White, Stephen H.
Structural Dynamics of the S4 Voltage-Sensor Helix in Lipid Bilayers Lacking Phosphate Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8732-8738, JUL 14 2011
abstract, full text, DOI:10.1021/jp2001964

Banerjee, Rajat; Reynolds, Noah M.; Yadavalli, Srujana S.; Rice, Cory; Roy, Herve; Banerjee, Papri; Alexander, Rebecca W.; Ibba, Michael
Mitochondrial Aminoacyl-tRNA Synthetase Single-Nucleotide Polymorphisms That Lead to Defects in Refolding but Not Aminoacylation
JOURNAL OF MOLECULAR BIOLOGY, 410:280-293, JUL 8 2011
abstract, full text, DOI:10.1016/j.jmb.2011.05.011

Gamini, Ramya; Sotomayor, Marcos; Chipot, Christophe; Schulten, Klaus
Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
BIOPHYSICAL JOURNAL, 101:80-89, JUL 6 2011
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2011.05.042

Hamaneh, Mehdi Bagheri; Zhang, Liqun; Buck, Matthias
A Direct Coupling between Global and Internal Motions in a Single Domain Protein? MD Investigation of Extreme Scenarios
BIOPHYSICAL JOURNAL, 101:196-204, JUL 6 2011
abstract, full text, DOI:10.1016/j.bpj.2011.05.041

Rommel, Judith B.; Kaestner, Johannes
The Fragmentation-Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:10195-10203, JUL 6 2011
abstract, full text, DOI:10.1021/ja202312d

Cristiani, Andrea; Costa, Giorgio; Cozza, Giorgio; Meggio, Flavio; Scapozza, Leonardo; Moro, Stefano
The Role of the N-Terminal Domain in the Regulation of the "Constitutively Active" Conformation of Protein Kinase CK2 alpha: Insight from a Molecular Dynamics Investigation
CHEMMEDCHEM, 6:1207-1216, JUL 4 2011
abstract, full text, DOI:10.1002/cmdc.201100046

Bettinelli, Ilaria; Graziani, Davide; Marconi, Cristina; Pedretti, Alessandro; Vistoli, Giulio
The Approach of Conformational Chimeras to Model the Role of Proline-Containing Helices on GPCR Mobility: the Fertile Case of Cys-LTR1
CHEMMEDCHEM, 6:1217-1227, JUL 4 2011
abstract, full text, DOI:10.1002/cmdc.201100037

Kralikova, Sarka; Budesinsky, Milos; Barvik, Ivan; Masojidkova, Milena; Tocik, Zdenek; Rosenberg, Ivan
SYNTHESIS AND PROPERTIES OF ApA ANALOGUES WITH SHORTENED PHOSPHONATE INTERNUCLEOTIDE LINKAGE
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 30:524-543, JUL-SEP 2011
abstract, full text, DOI:10.1080/15257770.2011.581259

Amarasinghe, Priyanthi M.; Anandarajah, A.
Influence of fabric variables on clay-water-air capillary meniscus
CANADIAN GEOTECHNICAL JOURNAL, 48:987-995, JUL 2011
abstract, full text, DOI:10.1139/T11-018

Wang, Lizhe; Chen, Dan; Deng, Ze; Huang, Fang
Large scale distributed visualization on computational Grids: A review
COMPUTERS & ELECTRICAL ENGINEERING, 37:403-416, JUL 2011
abstract, full text, DOI:10.1016/j.compeleceng.2011.05.010

Romanowska, Julia; McCammon, J. Andrew; Trylska, Joanna
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002099, JUL 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002099

Iacovache, Ioan; Degiacomi, Matteo T.; Pernot, Lucile; Ho, Sylvia; Schiltz, Marc; Dal Peraro, Matteo; van der Goot, F. Gisou
Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLOS PATHOGENS, 7 Art. No. e1002135, JUL 2011
abstract, full text, DOI:10.1371/journal.ppat.1002135

Parker, Lorien J.; Italiano, Louis C.; Morton, Craig J.; Hancock, Nancy C.; Ascher, David B.; Aitken, Jade B.; Harris, Hugh H.; Campomanes, Pablo; Rothlisberger, Ursula; De Luca, Anastasia; Lo Bello, Mario; Ang, Wee Han; Dyson, Paul J.; Parker, Michael W.
Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation
CHEMISTRY-A EUROPEAN JOURNAL, 17:7806-7816, JUL 2011
abstract, full text, DOI:10.1002/chem.201100586

Kim, Sang Kyoon; Huh, June; Kim, Sang Yoon; Byun, Youngro; Lee, Dong Yun; Moon, Hyun Tae
Physicochemical Conjugation with Deoxycholic Acid and Dimethylsulfoxide for Heparin Oral Delivery
BIOCONJUGATE CHEMISTRY, 22:1451-1458, JUL 2011
abstract, full text, DOI:10.1021/bc100594v

Soriano-Ursua, Marvin A.; Ocampo-Lopez, Jorge O.; Ocampo-Mendoza, Karina; Trujillo-Ferrara, Jose G.; Correa-Basurto, Jose
Theoretical study of 3-D molecular similarity and ligand binding modes of orthologous human and rat D-2 dopamine receptors
COMPUTERS IN BIOLOGY AND MEDICINE, 41:537-545, JUL 2011
abstract, full text, DOI:10.1016/j.compbiomed.2011.04.018

Splettstoesser, Thomas; Holmes, Kenneth C.; Noe, Frank; Smith, Jeremy C.
Structural modeling and molecular dynamics simulation of the actin filament
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2033-2043, JUL 2011
abstract, full text, DOI:10.1002/prot.23017

Janosi, Lorant; Keer, Harindar; Cogdell, Richard J.; Ritz, Thorsten; Kosztin, Ioan
In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2306-2315, JUL 2011
abstract, full text, DOI:10.1002/prot.23056

Perez-Siles, Gonzalo; Morreale, Antonio; Leo-Macias, Alejandra; Pita, Guillermo; Ortiz, Angel R.; Aragon, Carmen; Lopez-Corcuera, Beatriz
Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2
JOURNAL OF NEUROCHEMISTRY, 118:195-204, JUL 2011
abstract, full text, DOI:10.1111/j.1471-4159.2011.07309.x

Lawrenz, Morgan; Baron, Riccardo; Wang, Yi; McCammon, J. Andrew
Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2224-2232, JUL 2011
abstract, full text, DOI:10.1021/ct200230v

Palmai, Zoltan; Perahia, David; Lionne, Corinne; Fidy, Judit; Balog, Erika; Chaloin, Laurent
Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: Comparison between D- and L-nucleotides
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 511:88-100, JUL 2011
abstract, full text, DOI:10.1016/j.abb.2011.04.014

Jevnikar, Zala; Obermajer, Natasa; Doljak, Bojan; Turk, Samo; Gobec, Stanislav; Svajger, Urban; Hailfinger, Stephan; Thome, Margot; Kos, Janko
Cathepsin X cleavage of the beta(2) integrin regulates talin-binding and LFA-1 affinity in T cells
JOURNAL OF LEUKOCYTE BIOLOGY, 90:99-109, JUL 2011
abstract, full text, DOI:10.1189/jlb.1110622

Mayo, Daniel; Zhou, Andy; Sahu, Indra; McCarrick, Robert; Walton, Parker; Ring, Adam; Troxel, Kaylee; Coey, Aaron; Hawn, Jaclyn; Emwas, Abdul-Hamid; Lorigan, Gary A.
Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy
PROTEIN SCIENCE, 20:1100-1104, JUL 2011
abstract, full text, DOI:10.1002/pro.656

Savol, Andrej J.; Burger, Virginia M.; Agarwal, Pratul K.; Ramanathan, Arvind; Chennubhotla, Chakra S.
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
BIOINFORMATICS, 27:I52-I60, JUL 1 2011
abstract, full text, DOI:10.1093/bioinformatics/btr248

Raliou, Mariam; Grauso, Marta; Hoffmann, Brice; Schlegel-Le-Poupon, Claire; Nespoulous, Claude; Debat, Helene; Belloir, Christine; Wiencis, Anna; Sigoillot, Maud; Bano, Singh Preet; Trotier, Didier; Pernollet, Jean-Claude; Montmayeur, Jean-Pierre; Faurion, Annick; Briand, Loic
Human Genetic Polymorphisms in T1R1 and T1R3 Taste Receptor Subunits Affect Their Function
CHEMICAL SENSES, 36:527-537, JUL 2011
abstract, full text, DOI:10.1093/chemse/bjr014

Huebner, Melanie; Dixit, Anshuman; Mou, Tung-Chung; Lushington, Gerald H.; Pinto, Cibele; Gille, Andreas; Geduhn, Jens; Koenig, Burkhard; Sprang, Stephen R.; Seifert, Roland
Structural Basis for the High-Affinity Inhibition of Mammalian Membranous Adenylyl Cyclase by 2 ',3 '-O-(N-Methylanthraniloyl)-Inosine 5 '-Triphosphate
MOLECULAR PHARMACOLOGY, 80:87-96, JUL 2011
abstract, full text, DOI:10.1124/mol.111.071894

Beassoni, Paola R.; Otero, Lisandro H.; Boetsch, Cristhian; Domenech, Carlos E.; Gonzalez-Nilo, Fernado D.; Lisa, Angela T.
Site-directed mutations and kinetic studies show key residues involved in alkylammonium interactions and reveal two sites for phosphorylcholine in Pseudomonas aeruginosa phosphorylcholine phosphatase
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:858-863, JUL 2011
abstract, full text, DOI:10.1016/j.bbapap.2011.04.003

Tavoosi, Narjes; Davis-Harrison, Rebecca L.; Pogorelov, Taras V.; Ohkubo, Y. Zenmei; Arcario, Mark J.; Clay, Mary C.; Rienstra, Chad M.; Tajkhorshid, Emad; Morrissey, James H.
Molecular Determinants of Phospholipid Synergy in Blood Clotting
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:23247-23253, JUL 1 2011
abstract, full text, DOI:10.1074/jbc.M111.251769

Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
JOURNAL OF MOLECULAR MODELING, 17:1565-1577, JUL 2011
abstract, full text, DOI:10.1007/s00894-010-0860-z

Khrenova, Maria; Domratcheva, Tatiana; Grigorenko, Bella; Nemukhin, Alexander
Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1
JOURNAL OF MOLECULAR MODELING, 17:1579-1586, JUL 2011
abstract, full text, DOI:10.1007/s00894-010-0842-1

Strunk, Timo; Hamacher, Kay; Hoffgaard, Franziska; Engelhardt, Harald; Zillig, Martina Daniela; Faist, Karin; Wenzel, Wolfgang; Pfeifer, Felicitas
Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo
MOLECULAR MICROBIOLOGY, 81:56-68, JUL 2011
abstract, full text, DOI:10.1111/j.1365-2958.2011.07669.x

Wu, Baojun; Xin, Bo; Jin, Meng; Wei, Tiandi; Bai, Zengliang
Comparative and phylogenetic analyses of three TIR domain-containing adaptors in metazoans: Implications for evolution of TLR signaling pathways
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY, 35:764-773, JUL 2011
abstract, full text, DOI:10.1016/j.dci.2011.02.009

Narayanan, Sai Shyam; Sokkar, Pandian; Ramachandran, Murugesan; Nampoothiri, Kesavan Madhavan
Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis
FEMS MICROBIOLOGY LETTERS, 320:40-47, JUL 2011
abstract, full text, DOI:10.1111/j.1574-6968.2011.02289.x

Kleinekathoefer, Ulrich; Isralewitz, Barry; Dittrich, Markus; Schulten, Klaus
Domain Motion of Individual F-1-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7267-7274, JUN 30 2011
abstract, full text, TCBG publications, DOI:10.1021/jp2005088

Schulz, Robert; Vargiu, Attilio V.; Ruggerone, Paolo; Kleinekathoefer, Ulrich
Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8278-8287, JUN 30 2011
abstract, full text, DOI:10.1021/jp200996x

Bravaya, Ksenia B.; Khrenova, Maria G.; Grigorenko, Bella L.; Nemukhin, Alexander V.; Krylov, Anna I.
Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8296-8303, JUN 30 2011
abstract, full text, DOI:10.1021/jp2020269

White, Katherine H.; Orzechowski, Marek; Fourmy, Dominique; Visscher, Koen
Mechanical Unfolding of the Beet Western Yellow Virus-1 Frameshift Signal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9775-9782, JUN 29 2011
abstract, full text, DOI:10.1021/ja111281f

Kotsikorou, Evangelia; Madrigal, Karla E.; Hurst, Dow P.; Sharir, Haleli; Lynch, Diane L.; Heynen-Genel, Susanne; Milan, Loribelle B.; Chung, Thomas D. Y.; Setzman, Herbert H.; Bai, Yushi; Caron, Marc G.; Barak, Larry; Abood, Mary E.; Reggio, Patricia H.
Identification of the GPR55 Agonist Binding Site Using a Novel Set of High-Potency GPR55 Selective Ligands
BIOCHEMISTRY, 50:5633-5647, JUN 28 2011
abstract, full text, DOI:10.1021/bi200010k

Lee, Wook; Luckner, Sylvia R.; Kisker, Caroline; Tonge, Peter J.; Engels, Bernd
Elucidation of the Protonation States of the Catalytic Residues in mtKasA: Implications for Inhibitor Design
BIOCHEMISTRY, 50:5743-5756, JUN 28 2011
abstract, full text, DOI:10.1021/bi200006t

Truong, Khue; Su, Yang; Song, Jing; Chen, Yuan
Entropy-Driven Mechanism of an E3 Ligase
BIOCHEMISTRY, 50:5757-5766, JUN 28 2011
abstract, full text, DOI:10.1021/bi2001856

Furini, Simone; Domene, Carmen
Selectivity and Permeation of Alkali Metal Ions in K+-channels
JOURNAL OF MOLECULAR BIOLOGY, 409:867-878, JUN 24 2011
abstract, full text, DOI:10.1016/j.jmb.2011.04.043

Bleicher, Lucas; Prates, Erica T.; Gomes, Thiago C. F.; Silveira, Rodrigo L.; Nascimento, Alessandro S.; Rojas, Adriana L.; Golubev, Alexander; Martinez, Leandro; Skaf, Munir S.; Polikarpov, Igor
Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7940-7949, JUN 23 2011
abstract, full text, DOI:10.1021/jp200330z

Liu, Yanxin; Hsin, Jen; Kim, HyeongJun; Selvin, Paul R.; Schulten, Klaus
Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins
BIOPHYSICAL JOURNAL, 100:2964-2973, JUN 22 2011
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2011.05.010

Jones, Peter M.; George, Anthony M.
Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the Asymmetric Occluded State
BIOPHYSICAL JOURNAL, 100:3025-3034, JUN 22 2011
abstract, full text, DOI:10.1016/j.bpj.2011.05.028

Frauer, Carina; Hoffmann, Thomas; Bultmann, Sebastian; Casa, Valentina; Cardoso, M. Cristina; Antes, Iris; Leonhardt, Heinrich
Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain
PLOS ONE, 6 Art. No. e21306, JUN 22 2011
abstract, full text, DOI:10.1371/journal.pone.0021306

Buch, Ignasi; Giorgino, Toni; De Fabritiis, Gianni
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:10184-10189, JUN 21 2011
abstract, full text, DOI:10.1073/pnas.1103547108

Ziemys, A.; Kojic, M.; Milosevic, M.; Kojic, N.; Hussain, F.; Ferrari, M.; Grattoni, A.
Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method
JOURNAL OF COMPUTATIONAL PHYSICS, 230:5722-5731, JUN 20 2011
abstract, full text, DOI:10.1016/j.jcp.2011.03.054

Pan, Zhengzheng; McCullagh, Martin; Schatz, George C.; Lewis, Frederick D.
Conformational Control of Thymine Photodimerization in Purine-Containing Trinucleotides
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1432-1438, JUN 16 2011
abstract, full text, DOI:10.1021/jz200532w

Rose, Frisco; Hodak, Miroslav; Bernholc, Jerzy
Mechanism of copper(II)-induced misfolding of Parkinson's disease protein
SCIENTIFIC REPORTS, 1 Art. No. 11, JUN 14 2011
abstract, full text, DOI:10.1038/srep00011

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Synergistic Interactions between Repeats in Tau Protein and A beta Amyloids May Be Responsible for Accelerated Aggregation via Polymorphic States
BIOCHEMISTRY, 50:5172-5181, JUN 14 2011
abstract, full text, DOI:10.1021/bi200400u

Tian, Jianhui; Garcia, Angel E.
Simulations of the confinement of ubiquitin in self-assembled reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 225101, JUN 14 2011
abstract, full text, DOI:10.1063/1.3592712

Dixit, Purushottam D.; Asthagiri, D.
An Elastic-Network-Based Local Molecular Field Analysis of Zinc Finger Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7374-7382, JUN 9 2011
abstract, full text, DOI:10.1021/jp200244r

Schneider, Curtiss P.; Shukla, Diwakar; Trout, Bernhardt L.
Arginine and the Hofmeister Series: The Role of Ion-Ion Interactions in Protein Aggregation Suppression
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7447-7458, JUN 9 2011
abstract, full text, DOI:10.1021/jp111920y

Serrano, Arnaldo L.; Tucker, Matthew J.; Gai, Feng
Direct Assessment of the alpha-Helix Nucleation Time
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7472-7478, JUN 9 2011
abstract, full text, DOI:10.1021/jp200628b

Tanner, David E.; Ma, Wen; Chen, Zhongzhou; Schulten, Klaus
Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth
BIOPHYSICAL JOURNAL, 100:2548-2556, JUN 8 2011
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2011.04.036

Sun, Chongbo; Tang, Tian; Uludag, Hasan; Cuervo, Javier E.
Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State
BIOPHYSICAL JOURNAL, 100:2754-2763, JUN 8 2011
abstract, full text, DOI:10.1016/j.bpj.2011.04.045

Falvo, Cyril; Meier, Christoph
A fluctuating quantum model of the CO vibration in carboxyhemoglobin
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 214106, JUN 7 2011
abstract, full text, DOI:10.1063/1.3592707

Yu, Xiang; Zheng, Jie
Polymorphic Structures of Alzheimer's beta-Amyloid Globulomers
PLOS ONE, 6 Art. No. e20575, JUN 7 2011
abstract, full text, DOI:10.1371/journal.pone.0020575

Matsushita, Shinji; Inoue, Yasuhiro; Hojo, Masaki; Sokabe, Masahiro; Adachi, Taiji
Effect of tensile force on the mechanical behavior of actin filaments
JOURNAL OF BIOMECHANICS, 44:1776-1781, JUN 3 2011
abstract, full text, DOI:10.1016/j.jbiomech.2011.04.012

Zomot, Elia; Bahar, Ivet
Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:19693-19701, JUN 3 2011
abstract, full text, DOI:10.1074/jbc.M110.202085

Dai, Zheng-Wei; Ling, Jun; Huang, Xiao-Jun; Wan, Ling-Shu; Xu, Zhi-Kang
Molecular Simulation on the Interactions of Water with Polypropylene Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:10702-10708, JUN 2 2011
abstract, full text, DOI:10.1021/jp201040g

Balog, Erika; Perahia, David; Smith, Jeremy C.; Merzel, Franci
Vibrational Softening of a Protein on Ligand Binding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6811-6817, JUN 2 2011
abstract, full text, DOI:10.1021/jp108493g

Madsen, Jesper J.; Linderoth, Lars; Subramanian, Arun K.; Andresen, Thomas L.; Peters, Gunther H.
Secretory Phospholipase A(2) Activity toward Diverse Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6853-6861, JUN 2 2011
abstract, full text, DOI:10.1021/jp112137b

Arcario, Mark J.; Ohkubo, Y. Zenmei; Tajkhorshid, Emad
Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7029-7037, JUN 2 2011
abstract, full text, DOI:10.1021/jp109631y

Verde, Ana Vila; Campen, R. Kramer
Disaccharide Topology Induces Slowdown in Local Water Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7069-7084, JUN 2 2011
abstract, full text, DOI:10.1021/jp112178c

Ivetac, Anthony; McCammon, J. Andrew
Molecular Recognition in the Case of Flexible Targets
CURRENT PHARMACEUTICAL DESIGN, 17:1663-1671, JUN 2011
abstract, full text

Li, Cui; Shen, Jie; Li, Weihua; Lu, Chunhua; Liu, Guixia; Tang, Yun
Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1800-1809, JUN 2011
abstract, full text, DOI:10.1002/prot.23004

Kim, Soo-Kyung; Riley, Lindsay; Abrol, Ravinder; Jacobson, Kenneth A.; Goddard, William A., I.I.I.
Predicted structures of agonist and antagonist bound complexes of adenosine A(3) receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1878-1897, JUN 2011
abstract, full text, DOI:10.1002/prot.23012

Dong, Hao; Zhou, Huan-Xiang
Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor
NATURE COMMUNICATIONS, 2 Art. No. 354, JUN 2011
abstract, full text, DOI:10.1038/ncomms1362

Cristiani, Andrea; Brisotto, Nicola; Cedrati, Fabian Chatwin; Floris, Matteo; Scapozza, Leonardo; Moro, Stefano
ClickMD: an intuitive web-oriented molecular dynamics platform
FUTURE MEDICINAL CHEMISTRY, 3:923-931, JUN 2011
abstract, full text, DOI:10.4155/FMC.11.59

Liao, Chenzhong; Sitzmann, Markus; Pugliese, Angelo; Nicklaus, Marc C.
Software and resources for computational medicinal chemistry
FUTURE MEDICINAL CHEMISTRY, 3:1057-1085, JUN 2011
abstract, full text, DOI:10.4155/FMC.11.63

Bourne, Jonathan W.; Torzilli, Peter A.
Molecular simulations predict novel collagen conformations during cross-link loading
MATRIX BIOLOGY, 30:356-360, JUN 2011
abstract, full text, DOI:10.1016/j.matbio.2011.03.010

Baker, John A.; Hirst, Jonathan D.
Molecular Dynamics Simulations Using Graphics Processing Units
MOLECULAR INFORMATICS, 30:498-504, JUN 2011
abstract, full text, DOI:10.1002/minf.201100042

Pan, Yongping; Nussinov, Ruth
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002077, JUN 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002077

Shin, Andrew J.; Telesco, Shannon E.; Choi, Sung-Hee; Lemmon, Mark A.; Radhakrishnan, Ravi
Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases
BIOCHEMICAL JOURNAL, 436:241-251, JUN 1 2011
abstract, full text, DOI:10.1042/BJ20101791

Hernandez-Ortega, Aitor; Borrelli, Kenneth; Ferreira, Patricia; Medina, Milagros; Martinez, Angel T.; Guallar, Victor
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase
BIOCHEMICAL JOURNAL, 436:341-350, JUN 1 2011
abstract, full text, DOI:10.1042/BJ20102090

Skulachev, M. V.; Antonenko, Y. N.; Anisimov, V. N.; Chernyak, B. V.; Cherepanov, D. A.; Chistyakov, V. A.; Egorov, M. V.; Kolosova, N. G.; Korshunova, G. A.; Lyamzaev, K. G.; Plotnikov, E. Y.; Roginsky, V. A.; Savchenko, A. Y.; Severina, I. I.; Severin, F. F.; Shkurat, T. P.; Tashlitsky, V. N.; Shidlovsky, K. M.; Vyssokikh, M. Y.; Zamyatnin, A. A., Jr.; Zorov, D. B.; Skulachev, V. P.
Mitochondrial-Targeted Plastoquinone Derivatives. Effect on Senescence and Acute Age-Related Pathologies
CURRENT DRUG TARGETS, 12:800-826, JUN 2011
abstract, full text

Librando, Vito; Pappalardo, Matteo
Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:915-919, JUN 2011
abstract, full text, DOI:10.1016/j.jmgm.2011.03.001

Liu, Li; Liu, Xiaofeng; Gong, Jiayu; Jiang, Hualiang; Li, Honglin
Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1595-1603, JUN 2011
abstract, full text, DOI:10.1021/ct100728k

Grouleff, Julie; Jensen, Frank
Searching Peptide Conformational Space
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1783-1790, JUN 2011
abstract, full text, DOI:10.1021/ct200161e

Moya-Garcia, Aurelio A.; Rodriguez-Agudo, Daniel; Hayashi, Hideyuki; Angel Medina, Miguel; Luis Urdiales, Jose; Sanchez-Jimenez, Francisca
Analysis of Mammalian Histidine Decarboxylase Dimerization Interface Reveals an Electrostatic Hotspot Important for Catalytic Site Topology and Function
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1935-1942, JUN 2011
abstract, full text, DOI:10.1021/ct100690p

Giorgino, Toni; De Fabritiis, Gianni
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1943-1950, JUN 2011
abstract, full text, DOI:10.1021/ct100707s

Mangold, Martina; Rolland, Leslie; Costanzo, Francesca; Sprik, Michiel; Sulpizi, Marialore; Blumberger, Jochen
Absolute pK(a) Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1951-1961, JUN 2011
abstract, full text, DOI:10.1021/ct100715x

Kenzaki, Hiroo; Koga, Nobuyasu; Hori, Naoto; Kanada, Ryo; Li, Wenfei; Okazaki, Kei-ichi; Yao, Xin-Qiu; Takada, Shoji
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1979-1989, JUN 2011
abstract, full text, DOI:10.1021/ct2001045

Chen Cong; Li Wei-Zhong; Song Yong-Chen; Weng Lin-Dong
Structure and Kinetics of Hydrogen Bonds in Aqueous Glucose Solutions
ACTA PHYSICO-CHIMICA SINICA, 27:1372-1378, JUN 2011
abstract, full text, DOI:10.3866/PKU.WHXB20110626

Dai, Weimin; You, Zhonglu; Zhou, He; Zhang, Jian; Hu, Yiqiao
Structure-function relationships of the human bitter taste receptor hTAS2R1: insights from molecular modeling studies
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:229-240, JUN 2011
abstract, full text, DOI:10.3109/10799893.2011.578141

Banu, Hussaina; Renuka, N.; Vasanthakumar, Geetha
Reduced catalytic activity of human CYP2C9 natural alleles for gliclazide: Molecular dynamics simulation and docking studies
BIOCHIMIE, 93:1028-1036, JUN 2011
abstract, full text, DOI:10.1016/j.biochi.2011.02.008

Veldhuis, N. A.; Kuiper, M. J.; Dobson, R. C. J.; Pearson, R. B.; Camakaris, J.
In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding
BIOMETALS, 24:477-487, JUN 2011
abstract, full text, DOI:10.1007/s10534-011-9410-0

Kote-Jarai, Z.; Al Olama, A. Amin; Leongamornlert, D.; Tymrakiewicz, M.; Saunders, E.; Guy, M.; Giles, G. G.; Severi, G.; Southey, M.; Hopper, J. L.; Sit, K. C.; Harris, J. M.; Batra, J.; Spurdle, A. B.; Clements, J. A.; Hamdy, F.; Neal, D.; Donovan, J.; Muir, K.; Pharoah, P. D. P.; Chanock, S. J.; Brown, N.; Benlloch, S.; Castro, E.; Mahmud, N.; O'Brien, L.; Hall, A.; Sawyer, E.; Wilkinson, R.; Easton, D. F.; Eeles, R. A.
Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript
HUMAN GENETICS, 129:687-694, JUN 2011
abstract, full text, DOI:10.1007/s00439-011-0981-1

Yang, Ming-Jun; Zhang, Xin
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1774-1785, JUN 2011
abstract, full text, DOI:10.1002/prot.23000

Karthik, Suresh; Senapati, Sanjib
Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1830-1840, JUN 2011
abstract, full text, DOI:10.1002/prot.23008

Gutierrez, Pablo; Bastos-Aristizabal, Sara; Marin, Mauricio
STRUCTURAL MODELLING OF POTATO VIRUS A (PVA, POTYVIRUS) COAT PROTEIN
Actualidades Biologicas (Medellin), 33:93-102, JAN-JUN 2011
abstract, full text

Floquet, Nicolas; Hernandez, Jean-Francois; Boucher, Jean-Luc; Martinez, Jean
L-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors?
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1325-1335, JUN 2011
abstract, full text, DOI:10.1021/ci100422v

Yokota, Rio; Bardhan, Jaydeep P.; Knepley, Matthew G.; Barba, L. A.; Hamada, Tsuyoshi
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
COMPUTER PHYSICS COMMUNICATIONS, 182:1272-1283, JUN 2011
abstract, full text, DOI:10.1016/j.cpc.2011.02.013

Prates, Erica T.; Souza, Paulo C. T.; Pickholz, Monica; Skaf, Munir S.
CHARMM-Based Parameterization of Neutral Articaine-A Widely Used Local Anesthetic
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1339-1345, JUN-JUL 2011
abstract, full text, DOI:10.1002/qua.22701

Hansson, Anders; Souza, Paulo C. T.; Silveira, Rodrigo L.; Martinez, Leandro; Skaf, Munir S.
CHARMM Force Field Parameterization of Rosiglitazone
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1346-1354, JUN-JUL 2011
abstract, full text, DOI:10.1002/qua.22638

Poghosyan, Armen H.; Arsenyan, Levon H.; Gharabekyan, Hrant H.; Falkenhagen, Sandra; Koetz, Joachim; Shahinyan, Aram A.
Molecular dynamics simulations of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of poly(diallyldimethylammonium chloride) (PDADMAC)
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 358:175-181, JUN 1 2011
abstract, full text, DOI:10.1016/j.jcis.2011.01.091

Qu, Zheng-Wang; Zhu, Hui; May, Volkhard
Vibrational Spectral Signatures of Peptide Secondary Structures: N-methylation and Side chain Hydrogen Bond in Cyclosporin A
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1500-1518, JUN 2011
abstract, full text, DOI:10.1002/jcc.21728

Riihimaki, Tiina A.; Kukkurainen, Sampo; Varjonen, Suvi; Horha, Jarno; Nyholm, Thomas K. M.; Kulomaa, Markku S.; Hytonen, Vesa P.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
PLOS ONE, 6 Art. No. e20535, MAY 31 2011
abstract, full text, DOI:10.1371/journal.pone.0020535

Timko, Jeff; De Castro, Alexandra; Kuyucak, Serdar
Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 204510, MAY 28 2011
abstract, full text, DOI:10.1063/1.3595261

O'Connor, Joseph W.; Klauda, Jeffery B.
Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6455-6464, MAY 26 2011
abstract, full text, DOI:10.1021/jp108650u

Satpati, Priyadarshi; Clavaguera, Carine; Ohanessian, Gilles; Simonson, Thomas
Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6749-6763, MAY 26 2011
abstract, full text, DOI:10.1021/jp201934p

Huang, Yu-ming M.; Chang, Chia-en A.
Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics
BMC BIOPHYSICS, 4 Art. No. 12, MAY 25 2011
abstract, full text, DOI:10.1186/2046-1682-4-12

Sorensen, Jesper; Palmer, David S.; Qvist, Karsten Bruun; Schiott, Birgit
Initial Stage of Cheese Production: A Molecular Modeling Study of Bovine and Camel Chymosin Complexed with Peptides from the Chymosin-Sensitive Region of kappa-Casein
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 59:5636-5647, MAY 25 2011
abstract, full text, DOI:10.1021/jf104898w

Kaye, Martin D.; Schmalzl, Karin; Nibali, Valeria Conti; Tarek, Mounir; Rheinstaedter, Maikel C.
Ethanol enhances collective dynamics of lipid membranes
PHYSICAL REVIEW E, 83 Art. No. 050907, MAY 25 2011
abstract, full text, DOI:10.1103/PhysRevE.83.050907

Schreiner, Eduard; Trabuco, Leonardo G.; Freddolino, Peter L.; Schulten, Klaus
Stereochemical errors and their implications for molecular dynamics simulations
BMC BIOINFORMATICS, 12 Art. No. 190, MAY 23 2011
abstract, full text, TCBG publications, DOI:10.1186/1471-2105-12-190

Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D. J.; Ho, N. T.; Ho, C.; Fischetti, R. F.
WAXS Studies of the Structural Diversity of Hemoglobin in Solution
JOURNAL OF MOLECULAR BIOLOGY, 408:909-921, MAY 20 2011
abstract, full text, DOI:10.1016/j.jmb.2011.02.062

Stewart, Mikaela D.; Morgan, Brittany; Massi, Francesca; Igumenova, Tatyana I.
Probing the Determinants of Diacylglycerol Binding Affinity in the C1B Domain of Protein Kinase C alpha
JOURNAL OF MOLECULAR BIOLOGY, 408:949-970, MAY 20 2011
abstract, full text, DOI:10.1016/j.jmb.2011.03.020

Jiang, Jun; Mukamel, Shaul
Probing Amyloid Fibril Growth by Two-Dimensional Near-Ultraviolet Spectroscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6321-6328, MAY 19 2011
abstract, full text, DOI:10.1021/jp201164u

Bai, Qifeng; Shen, Yulin; Yao, Xiaojun; Wang, Fang; Du, Yuping; Wang, Qin; Jin, Nengzhi; Hai, Jun; Hu, Tiejun; Yang, Jinbo
Modeling a New Water Channel That Allows SET9 to Dimethylate p53
PLOS ONE, 6 Art. No. e19856, MAY 19 2011
abstract, full text, DOI:10.1371/journal.pone.0019856

Ramachandran, Abhijit; Guo, Qingjiang; Iqbal, Samir M.; Liu, Yaling
Coarse-Grained Molecular Dynamics Simulation of DNA Trans location in Chemically Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6138-6148, MAY 19 2011
abstract, full text, DOI:10.1021/jp101052x

Wilson, Michael A.; Wei, Chenyu; Bjelkmar, Paer; Wallace, B. A.; Pohorille, Andrew
Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance
BIOPHYSICAL JOURNAL, 100:2394-2402, MAY 18 2011
abstract, full text, DOI:10.1016/j.bpj.2011.03.054

Chen, Po-Chia; Kuyucak, Serdar
Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
BIOPHYSICAL JOURNAL, 100:2466-2474, MAY 18 2011
abstract, full text, DOI:10.1016/j.bpj.2011.03.052

Gumbart, James; Chipot, Christophe; Schulten, Klaus
Free Energy of Nascent-Chain Folding in the Translocon
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7602-7607, MAY 18 2011
abstract, full text, TCBG publications, DOI:10.1021/ja2019299

Verde, Ana Vila; Beltramo, Peter J.; Maranas, Janna K.
Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics
LANGMUIR, 27:5918-5926, MAY 17 2011
abstract, full text, DOI:10.1021/la104814z

Maekawa, Hiroaki; Ballano, Gema; Toniolo, Claudio; Ge, Nien-Hui
Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5168-5182, MAY 12 2011
abstract, full text, DOI:10.1021/jp105527n

Weng, Lindong; Chen, Cong; Zuo, Jianguo; Li, Weizhong
Molecular Dynamics Study of Effects of Temperature and Concentration on Hydrogen-Bond Abilities of Ethylene Glycol and Glycerol: Implications for Cryopreservation
JOURNAL OF PHYSICAL CHEMISTRY A, 115:4729-4737, MAY 12 2011
abstract, full text, DOI:10.1021/jp111162w

Ketko, MaryBeth H.; Kamath, Ganesh; Potoff, Jeffrey J.
Development of an Optimized Intermolecular Potential for Sulfur Dioxide
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4949-4954, MAY 5 2011
abstract, full text, DOI:10.1021/jp2010524

Berryman, Joshua T.; Radford, Sheena E.; Harris, Sarah A.
Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation
BIOPHYSICAL JOURNAL, 100:2234-2242, MAY 4 2011
abstract, full text, DOI:10.1016/j.bpj.2011.02.060

Gonidec, Mathieu; Biagi, Roberto; Corradini, Valdis; Moro, Fabrizio; De Renzi, Valentina; del Pennino, Umberto; Summa, Domenico; Muccioli, Luca; Zannoni, Claudio; Amabilino, David B.; Veciana, Jaume
Surface Supramolecular Organization of a Terbium(III) Double-Decker Complex on Graphite and its Single Molecule Magnet Behavior
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6603-6612, MAY 4 2011
abstract, full text, DOI:10.1021/ja109296c

Sonntag, Yonathan; Musgaard, Maria; Olesen, Claus; Schiott, Birgit; Moller, Jesper Vuust; Nissen, Poul; Thogersen, Lea
Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
NATURE COMMUNICATIONS, 2 Art. No. 304, MAY 2011
abstract, full text, DOI:10.1038/ncomms1307

Vemparala, Satyavani; Mehrotra, Sonali; Balaram, Hemalatha
Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: A molecular dynamics and normal mode analysis study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:630-637, MAY 2011
abstract, full text, DOI:10.1016/j.bbapap.2011.03.012

Aprikian, Pavel; Interlandi, Gianluca; Kidd, Brian A.; Le Trong, Isolde; Tchesnokova, Veronika; Yakovenko, Olga; Whitfield, Matt J.; Bullitt, Esther; Stenkamp, Ronald E.; Thomas, Wendy E.; Sokurenko, Evgeni V.
The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor
PLOS BIOLOGY, 9 Art. No. e1000617, MAY 2011
abstract, full text, DOI:10.1371/journal.pbio.1000617

Camargo, Hendricka; Nusspaumer, Gretel; Abia, David; Briceno, Veronica; Remacha, Miguel; Ballesta, Juan P. G.
The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2
NUCLEIC ACIDS RESEARCH, 39:3735-3743, MAY 2011
abstract, full text, DOI:10.1093/nar/gkq1356

Chew, Teong Han; Joyce-Tan, Kwee Hong; Akma, Farizuwana; Shamsir, Mohd Shahir
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics
BIOINFORMATICS, 27:1320-1321, MAY 1 2011
abstract, full text, DOI:10.1093/bioinformatics/btr109

Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie
Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils
BIOMACROMOLECULES, 12:1781-1794, MAY 2011
abstract, full text, DOI:10.1021/bm2001507

Postila, Pah A.; Ylilauri, Mildw; Pentikaien, Olli T.
Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1037-1047, MAY 2011
abstract, full text, DOI:10.1021/ci2000055

Lin, Ying-Wu; Ying, Tian-Lei; Liao, Li-Fu
Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b (5)
JOURNAL OF MOLECULAR MODELING, 17:971-978, MAY 2011
abstract, full text, DOI:10.1007/s00894-010-0795-4

Malkhed, Vasavi; Gudlur, Bargavi; Kondagari, Bhargavi; Dulapalli, Ramasree; Vuruputuri, Uma
Study of interactions between Mycobacterium tuberculosis proteins: SigK and anti-SigK
JOURNAL OF MOLECULAR MODELING, 17:1109-1119, MAY 2011
abstract, full text, DOI:10.1007/s00894-010-0792-7

Schlick, Tamar; Collepardo-Guevara, Rosana; Halvorsen, Leif Arthur; Jung, Segun; Xiao, Xia
Biomolecular modeling and simulation: a field coming of age
QUARTERLY REVIEWS OF BIOPHYSICS, 44:191-228, MAY 2011
abstract, full text, DOI:10.1017/S0033583510000284

Kutzner, Carsten; Czub, Jacek; Grubmueller, Helmut
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1381-1393, MAY 2011
abstract, full text, DOI:10.1021/ct100666v

Khrenova, Maria G.; Domratcheva, Tatiana; Schlichting, Ilme; Grigorenko, Bella L.; Nemukhin, Alexander V.
Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 87:564-573, MAY-JUN 2011
abstract, full text, DOI:10.1111/j.1751-1097.2010.00861.x

Darian, Eva; Guvench, Olgun; Yu, Bing; Qu, Cheng-Kui; MacKerell, Alexander D., Jr.
Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1573-1588, MAY 2011
abstract, full text, DOI:10.1002/prot.22984

Martinez, Leandro; Malliavin, Therese E.; Blondel, Arnaud
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1649-1661, MAY 2011
abstract, full text, DOI:10.1002/prot.22991

Fezoua-Boubegtiten, Zahia; Desbat, Bernard; Brisson, Alain; Gounou, Celine; Laguerre, Michel; Lecomte, Sophie
Effect of Mg2+ versus Ca2+ on the behavior of Annexin A5 in a membrane-bound state
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:641-649, MAY 2011
abstract, full text, DOI:10.1007/s00249-010-0665-0

Bellesia, Giovanni; Jewett, Andrew I.; Shea, Joan-Emma
Relative stability of de novo four-helix bundle proteins: Insights from coarse grained molecular simulations
PROTEIN SCIENCE, 20:818-826, MAY 2011
abstract, full text, DOI:10.1002/pro.605

Sapay, Nicolas; Tieleman, D. Peter
Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1400-1410, MAY 2011
abstract, full text, DOI:10.1002/jcc.21726

Koenig, Gerhard; Boresch, Stefan
Non-Boltzmann Sampling and Bennett's Acceptance Ratio Method: How to Profit from Bending the Rules
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1082-1090, APR 30 2011
abstract, full text, DOI:10.1002/jcc.21687

Lettieri, Steven; Mamonov, Artem B.; Zuckerman, Daniel M.
Extending Fragment-Based Free Energy Calculations with Library Monte Carlo Simulation: Annealing in Interaction Space
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1135-1143, APR 30 2011
abstract, full text, DOI:10.1002/jcc.21695

Busby, Ben; Oashi, Taiji; Willis, Chris D.; Ackermann, Maegen A.; Kontrogianni-Konstantopoulos, Aikaterini; MacKerell, Alexander D., Jr.; Bloch, Robert J.
Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies
JOURNAL OF MOLECULAR BIOLOGY, 408:321-334, APR 29 2011
abstract, full text, DOI:10.1016/j.jmb.2011.01.053

Conejo-Garcia, Ana; Pisani, Leonardo; del Carmen Nunez, Maria; Catto, Marco; Nicolotti, Orazio; Leonetti, Francesco; Campos, Joaquin M.; Gallo, Miguel A.; Espinosa, Antonio; Carotti, Angelo
Homodimeric Bis-Quaternary Heterocyclic Ammonium Salts as Potent Acetyl- and Butyrylcholinesterase Inhibitors: A Systematic Investigation of the Influence of Linker and Cationic Heads over Affinity and Selectivity
JOURNAL OF MEDICINAL CHEMISTRY, 54:2627-2645, APR 28 2011
abstract, full text, DOI:10.1021/jm101299d

Patra, Niladri; Kral, Petr
Controlled Self-Assembly of Filled Micelles on Nanotubes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6146-6149, APR 27 2011
abstract, full text, DOI:10.1021/ja2009778

Murphy, Drew L.; Jaeger, Joachim; Sweasy, Joann B.
A Triad Interaction in the Fingers Subdomain of DNA Polymerase Beta Controls Polymerase Activity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6279-6287, APR 27 2011
abstract, full text, DOI:10.1021/ja111099b

Swedberg, Joakim E.; de Veer, Simon J.; Sit, Kei C.; Reboul, Cyril F.; Buckle, Ashley M.; Harris, Jonathan M.
Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network
PLOS ONE, 6 Art. No. e19302, APR 27 2011
abstract, full text, DOI:10.1371/journal.pone.0019302

Walch, Stephen P.
Effect of Solvation on the Oxygen Reduction Reaction on Pt Catalyst
JOURNAL OF PHYSICAL CHEMISTRY C, 115:7377-7391, APR 21 2011
abstract, full text, DOI:10.1021/jp106497h

Agirrezabala, Xabier; Schreiner, Eduard; Trabuco, Leonardo G.; Lei, Jianlin; Ortiz-Meoz, Rodrigo F.; Schulten, Klaus; Green, Rachel; Frank, Joachim
Structural insights into cognate versus near-cognate discrimination during decoding
EMBO JOURNAL, 30:1497-1507, APR 20 2011
abstract, full text, TCBG publications, DOI:10.1038/emboj.2011.58

Reboul, Cyril F.; Andrews, Daniel A.; Nahar, Musammat F.; Buckle, Ashley M.; Roujeinikova, Anna
Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor
PLOS ONE, 6 Art. No. e18981, APR 20 2011
abstract, full text, DOI:10.1371/journal.pone.0018981

Sun, Gang; Lu, Kunquan; Kun, Ferenc
Percolation-induced conductor-insulator transition in a system of metal spheres in a dielectric fluid
PHYSICAL REVIEW E, 83 Art. No. 041405, APR 15 2011
abstract, full text, DOI:10.1103/PhysRevE.83.041405

Lian, Peng; Wei, Dong-Qing; Wang, Jing-Fang; Chou, Kuo-Chen
An Allosteric Mechanism Inferred from Molecular Dynamics Simulations on Phospholamban Pentamer in Lipid Membranes
PLOS ONE, 6 Art. No. e18587, APR 15 2011
abstract, full text, DOI:10.1371/journal.pone.0018587

Nurminen, Elisa M.; Pihlavisto, Marjo; Lazar, Laszlo; Pentikainen, Ulla; Fueloep, Ferenc; Pentikainen, Olli T.
Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 54:2143-2154, APR 14 2011
abstract, full text, DOI:10.1021/jm200059p

Zhao, Xiongce
Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 115:6181-6189, APR 14 2011
abstract, full text, DOI:10.1021/jp110013r

Delemotte, Lucie; Tarek, Mounir; Klein, Michael L.; Amaral, Cristiano; Treptow, Werner
Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:6109-6114, APR 12 2011
abstract, full text, DOI:10.1073/pnas.1102724108

Wei, Chenyu; Pohorile, Andrew
Permeation of Nucleosides through Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3681-3688, APR 7 2011
abstract, full text, DOI:10.1021/jp112104r

Suyetin, Mikhail V.; Vakhrushev, Alexander V.
Guided Carbon Nanocapsules for Hydrogen Storage
JOURNAL OF PHYSICAL CHEMISTRY C, 115:5485-5491, APR 7 2011
abstract, full text, DOI:10.1021/jp111415q

Narita, Akihiro; Oda, Toshiro; Maeda, Yuichiro
Structural basis for the slow dynamics of the actin filament pointed end
EMBO JOURNAL, 30:1230-1237, APR 6 2011
abstract, full text, DOI:10.1038/emboj.2011.48

Jang, Hyunbum; Arce, Fernando Teran; Mustata, Mirela; Ramachandran, Srinivasan; Capone, Ricardo; Nussinov, Ruth; Lal, Ratnesh
Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link
BIOPHYSICAL JOURNAL, 100:1775-1783, APR 6 2011
abstract, full text, DOI:10.1016/j.bpj.2011.01.072

Song, Sang-Hun; Freddolino, Peter L.; Nash, Abigail I.; Carroll, Elizabeth C.; Schulten, Klaus; Gardner, Kevin H.; Larsen, Delmar S.
Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site
BIOCHEMISTRY, 50:2411-2423, APR 5 2011
abstract, full text, TCBG publications, DOI:10.1021/bi200198x

Beckham, Gregg T.; Bomble, Yannick J.; Bayer, Edward A.; Himmel, Michael E.; Crowley, Michael F.
Applications of computational science for understanding enzymatic deconstruction of cellulose
CURRENT OPINION IN BIOTECHNOLOGY, 22:231-238, APR 2011
abstract, full text, DOI:10.1016/j.copbio.2010.11.005

Cardinali, Angela; Tursi, Nunzia; Ligorio, Angela; Giuffrida, Maria Gabriella; Napolitano, Lorenzo; Caliandro, Rocco; Sergio, Lucrezia; Di Venere, Donato; Lattanzio, Vincenzo; Sonnante, Gabriella
Purification, biochemical characterization and cloning of a new cationic peroxidase isoenzyme from artichoke
PLANT PHYSIOLOGY AND BIOCHEMISTRY, 49:395-403, APR 2011
abstract, full text, DOI:10.1016/j.plaphy.2011.01.028

Vorob'ev, Yu. N.
Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration
MOLECULAR BIOLOGY, 45:309-317, APR 2011
abstract, full text, DOI:10.1134/S0026893311020208

Bucher, Denis; Grant, Barry J.; Markwick, Phineus R.; McCammon, J. Andrew
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002034, APR 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002034

Wang, Jin; Wang, Yong; Chu, Xiakun; Hagen, Stephen J.; Han, Wei; Wang, Erkang
Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1001118, APR 2011
abstract, full text, DOI:10.1371/journal.pcbi.1001118

Xie, Li; Evangelidis, Thomas; Xie, Lei; Bourne, Philip E.
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002037, APR 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002037

Robinson, Mark W.; Corvo, Ileana; Jones, Peter M.; George, Anthony M.; Padula, Matthew P.; To, Joyce; Cancela, Martin; Rinaldi, Gabriel; Tort, Jose F.; Roche, Leda; Dalton, John P.
Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica
PLOS NEGLECTED TROPICAL DISEASES, 5 Art. No. e1012, APR 2011
abstract, full text, DOI:10.1371/journal.pntd.0001012

Chodera, John D.; Mobley, David L.; Shirts, Michael R.; Dixon, Richard W.; Branson, Kim; Pande, Vijay S.
Alchemical free energy methods for drug discovery: progress and challenges
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:150-160, APR 2011
abstract, full text, DOI:10.1016/j.sbi.2011.01.011

Lee, Jun Hyuck; Park, HaJeung; Park, Soo Jeong; Kim, Hak Jun; Eom, Soo Hyun
The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 407:207-212, APR 1 2011
abstract, full text, DOI:10.1016/j.bbrc.2011.02.141

Ghosh-Kumar, Manjira; Alam, Tanfis I.; Draper, Bonnie; Stack, John D.; Rao, Venigalla B.
Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4
NUCLEIC ACIDS RESEARCH, 39:2742-2755, APR 2011
abstract, full text, DOI:10.1093/nar/gkq1191

Buch, Idit; Tsai, Chung-Jung; Wolfson, Haim J.; Nussinov, Ruth
Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
PROTEIN AND PEPTIDE LETTERS, 18:362-372, APR 2011
abstract, full text, DOI:10.2174/092986611794653996

Liang Hao; Liu Tao; Chen FangJin; Liu ZhaoQing; Liu ShaoJun
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2)
SCIENCE CHINA-LIFE SCIENCES, 54:336-341, APR 2011
abstract, full text, DOI:10.1007/s11427-011-4156-z

Preat, Julien; Zanuy, David; Perpete, Eric A.; Aeman, Carlos
Binding of Cationic Conjugated Polymers to DNA: Atomistic Simulations of Adducts Involving the Dickerson's Dodecamer
BIOMACROMOLECULES, 12:1298-1304, APR 2011
abstract, full text, DOI:10.1021/bm200022n

Andronico, Alessio; Randall, Arlo; Benz, Ryan W.; Baldi, Pierre
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:760-776, APR 2011
abstract, full text, DOI:10.1021/ci100223t

Bahrami, M.; Kalantarinejad, R.; Aghaei, M. J.; Azadi, N.
Simulation of the Interaction of Carbon Nanotubes and External Flow
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:563-567, APR 2011
abstract, full text, DOI:10.1166/jctn.2011.1723

Roth, M. W.; Balasubramanya, M. K.; Bergmann, P.; Karl, M.; Connolly, M. J.; Gray, Paul A.
Predicted Anomalous Behavior of C-60 Fullerenes on Graphite at Low Temperature: A New Hindered Cooperative Rotational Transition
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:795-799, APR 2011
abstract, full text, DOI:10.1166/jctn.2011.1754

Staritzbichler, Rene; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gomez, Jose D.
GRIFFIN: A Versatile Methodology for Optimization of Protein-Lipid Interfaces for Membrane Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1167-1176, APR 2011
abstract, full text, DOI:10.1021/ct100576m

Firlej, Lucyna; Kuchta, Bogdan; Roth, Michael W.; Wexler, Carlos
Molecular simulations of intermediate and long alkanes adsorbed on graphite: Tuning of non-bond interactions
JOURNAL OF MOLECULAR MODELING, 17:811-816, APR 2011
abstract, full text, DOI:10.1007/s00894-010-0770-0

Vattulainen, Ilpo; Rog, Tomasz
Lipid Simulations: A Perspective on Lipids in Action
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 3 Art. No. a004655, APR 2011
abstract, full text, DOI:10.1101/cshperspect.a004655

Moss, Christopher L.; Chung, Thomas W.; Wyer, Jean A.; Nielsen, Steen Brondsted; Hvelplund, Preben; Turecek, Frantisek
Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:731-751, APR 2011
abstract, full text, DOI:10.1007/s13361-011-0083-2

Wada, Masahisa; Nishiyama, Yoshiharu; Bellesia, Giovanni; Forsyth, Trevor; Gnanakaran, S.; Langan, Paul
Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia
CELLULOSE, 18:191-206, APR 2011
abstract, full text, DOI:10.1007/s10570-010-9488-5

Olmez, Elif Ozkirimli; Alakent, Burak
Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:675-693, APR 2011
abstract, full text

Strzelecki, Janusz W.; Strzelecka, Joanna; Mikulska, Karolina; Tszydel, Mariusz; Balter, Aleksander; Nowak, Wieslaw
Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk
CENTRAL EUROPEAN JOURNAL OF PHYSICS, 9:482-491, APR 2011
abstract, full text, DOI:10.2478/s11534-010-0105-x

Kosevich, Marina V.; Zobnina, Valentina G.; Chagovets, Vitaliy V.; Boryak, Oleg A.
Observation of poly(ethylene glycol) clusters with the chlorine anion in the gas phase under electrospray conditions
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 25:713-718, MAR 30 2011
abstract, full text, DOI:10.1002/rcm.4919

Jones, Martin K.; Gu, Feifei; Catte, Andrea; Li, Ling; Segrest, Jere P.
"Sticky" and "Promiscuous", the Yin and Yang of Apolipoprotein A-I Termini in Discoidal High-Density Lipoproteins: A Combined Computational-Experimental Approach
BIOCHEMISTRY, 50:2249-2263, MAR 29 2011
abstract, full text, DOI:10.1021/bi101301g

Boettcher, John M.; Davis-Harrison, Rebecca L.; Clay, Mary C.; Nieuwkoop, Andrew J.; Ohkubo, Y. Zenmei; Tajkhorshid, Emad; Morrissey, James H.; Rienstra, Chad M.
Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers
BIOCHEMISTRY, 50:2264-2273, MAR 29 2011
abstract, full text, DOI:10.1021/bi1013694

Geppert, Tim; Hoy, Benjamin; Wessler, Silja; Schneider, Gisbert
Context-Based Identification of Protein-Protein Interfaces and "Hot-Spot" Residues
CHEMISTRY & BIOLOGY, 18:344-353, MAR 25 2011
abstract, full text, DOI:10.1016/j.chembiol.2011.01.005

Ozboyaci, Musa; Gursoy, Attila; Erman, Burak; Keskin, Ozlem
Molecular Recognition of H3/H4 Histone Tails by the Tudor Domains of JMJD2A: A Comparative Molecular Dynamics Simulations Study
PLOS ONE, 6 Art. No. e14765, MAR 25 2011
abstract, full text, DOI:10.1371/journal.pone.0014765

Shukla, Diwakar; Zamolo, Laura; Cavallotti, Carlo; Trout, Bernhardt L.
Understanding the Role of Arginine as an Eluent in Affinity Chromatography via Molecular Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2645-2654, MAR 24 2011
abstract, full text, DOI:10.1021/jp111156z

Dalosto, Sergio D.; Tinte, Silvia
Fluctuation Effects of the Electric Field Induced by Water on a Graphene Dot Band Gap
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4381-4386, MAR 24 2011
abstract, full text, DOI:10.1021/jp109297p

Zhao, Chunfeng; Noskov, Sergei Yu.
The Role of Local Hydration and Hydrogen-Bonding Dynamics in Ion and Solute Release from Ion-Coupled Secondary Transporters
BIOCHEMISTRY, 50:1848-1856, MAR 22 2011
abstract, full text, DOI:10.1021/bi101454f

Radadia, Adarsh D.; Stavis, Courtney J.; Carr, Rogan; Zeng, Hongjun; King, William P.; Carlisle, John A.; Aksimentiev, Aleksei; Hamers, Robert J.; Bashir, Rashid
Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces
ADVANCED FUNCTIONAL MATERIALS, 21:1040-1050, MAR 22 2011
abstract, full text, DOI:10.1002/adfm.201002251

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 115101, MAR 21 2011
abstract, full text, DOI:10.1063/1.3560442

Bhattacharya, Swati; Muzard, Julien; Payet, Linda; Mathe, Jerome; Bockelmann, Ulrich; Aksimentiev, Aleksei; Viasnoff, Virgile
Rectification of the Current in alpha-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4255-4264, MAR 17 2011
abstract, full text, DOI:10.1021/jp111441p

Mihailescu, Mihaela; Vaswani, Rishi G.; Jardon-Valadez, Eduardo; Castro-Roman, Francisco; Freites, J. Alfredo; Worcester, David L.; Chamberlin, A. Richard; Tobias, Douglas J.; White, Stephen H.
Acyl-Chain Methyl Distributions of Liquid-Ordered and -Disordered Membranes
BIOPHYSICAL JOURNAL, 100:1455-1462, MAR 16 2011
abstract, full text, DOI:10.1016/j.bpj.2011.01.035

Dixit, Purushottam D.; Asthagiri, D.
The Role of Bulk Protein in Local Models of Ion-Binding to Proteins: Comparative Study of KcsA, Its Semisynthetic Analog with a Locked-in Binding Site, and Valinomycin
BIOPHYSICAL JOURNAL, 100:1542-1549, MAR 16 2011
abstract, full text, DOI:10.1016/j.bpj.2011.01.044

Parthasarathy, Sudhakar; Long, Fei; Miller, Yifat; Xiao, Yiling; McElheny, Dan; Thurber, Kent; Ma, Buyong; Nussinov, Ruth; Ishii, Yoshitaka
Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's beta by Solid-State NMR Spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3390-3400, MAR 16 2011
abstract, full text, DOI:10.1021/ja1072178

McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.
DNA-Based Optomechanical Molecular Motor
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3452-3459, MAR 16 2011
abstract, full text, DOI:10.1021/ja109071a

Lee, One-Sun; Stupp, Samuel I.; Schatz, George C.
Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3677-3683, MAR 16 2011
abstract, full text, DOI:10.1021/ja110966y

Wedberg, Rasmus; O'Connell, John P.; Peters, Gunther H.; Abildskov, Jens
Total and direct correlation function integrals from molecular simulation of binary systems
FLUID PHASE EQUILIBRIA, 302:32-42, MAR 15 2011
abstract, full text, DOI:10.1016/j.fluid.2010.10.004

Haspel, Nurit; Zanuy, David; Nussinov, Ruth; Teesalu, Tambet; Ruoslahti, Erkki; Aleman, Carlos
Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach
BIOCHEMISTRY, 50:1755-1762, MAR 15 2011
abstract, full text, DOI:10.1021/bi101662j

Zhang, Qi Charles; Yeh, Tzu-lan; Leyva, Alfonso; Frank, Leslie G.; Miller, Jason; Kim, Yujin E.; Langen, Ralf; Finkbeiner, Steven; Amzel, Mario L.; Ross, Christopher A.; Poirier, Michelle A.
A Compact beta Model of huntingtin Toxicity
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:8188-8196, MAR 11 2011
abstract, full text, DOI:10.1074/jbc.M110.192013

Grafmueller, Andrea; Voth, Gregory A.
Intrinsic Bending of Microtubule Protofilaments
STRUCTURE, 19:409-417, MAR 9 2011
abstract, full text, DOI:10.1016/j.str.2010.12.020

Akgun, Ugur; Khademi, Shahram
Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3970-3975, MAR 8 2011
abstract, full text, DOI:10.1073/pnas.1007240108

Uhart, Marina; Iglesias, Alberto A.; Bustos, Diego M.
Structurally Constrained Residues Outside the Binding Motif Are Essential in the Interaction of 14-3-3 and Phosphorylated Partner
JOURNAL OF MOLECULAR BIOLOGY, 406:552-557, MAR 4 2011
abstract, full text, DOI:10.1016/j.jmb.2010.12.043

Ayuso-Tejedor, Sara; Garcia-Fandino, Rebeca; Orozco, Modesto; Sancho, Javier; Bernado, Pau
Structural Analysis of an Equilibrium Folding Intermediate in the Apoflavodoxin Native Ensemble by Small-Angle X-ray Scattering
JOURNAL OF MOLECULAR BIOLOGY, 406:604-619, MAR 4 2011
abstract, full text, DOI:10.1016/j.jmb.2010.12.027

Khan, Najat S.; Perez-Aguilar, Jose Manuel; Kaufmann, Tara; Hill, P. Aru; Taratula, Olena; Lee, One-Sun; Carroll, Patrick J.; Saven, Jeffery G.; Dmochowski, Ivan J.
Multiple Hindered Rotators in a Gyroscope-Inspired Tribenzylamine Hemicryptophane
JOURNAL OF ORGANIC CHEMISTRY, 76:1418-1424, MAR 4 2011
abstract, full text, DOI:10.1021/jo102480s

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
The Unique Alzheimer's beta-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:2742-2748, MAR 2 2011
abstract, full text, DOI:10.1021/ja1100273

Cui, Haosheng; Lyman, Edward; Voth, Gregory A.
Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
BIOPHYSICAL JOURNAL, 100:1271-1279, MAR 2 2011
abstract, full text, DOI:10.1016/j.bpj.2011.01.036

Wallrapp, Frank H.; Guallar, Victor
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:315-322, MAR-APR 2011
abstract, full text, DOI:10.1002/wcms.27

Prasad, Nirmal K.; Vindal, Vaibhav; Kumar, Vikash; Kabra, Ashish; Phogat, Navneet; Kumar, Manoj
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase
JOURNAL OF MOLECULAR MODELING, 17:533-541, MAR 2011
abstract, full text, DOI:10.1007/s00894-010-0744-2

Gonzalez, Angel; Murcia, Marta; Benhamu, Bellinda; Campillo, Mercedes; Lopez-Rodriguez, Maria L.; Pardo, Leonardo
The importance of solvation in the design of ligands targeting membrane proteins
MEDCHEMCOMM, 2:160-164, MAR 2011
abstract, full text, DOI:10.1039/c0md00258e

Cai, Wen Sheng; Wang, Teng; Liu, Ying Zhe; Liu, Peng; Chipot, Christophe; Shao, Xue Guang
Free Energy Calculations for Cyclodextrin Inclusion Complexes
CURRENT ORGANIC CHEMISTRY, 15:839-847, MAR 2011
abstract, full text

Mazars, Martial
Long ranged interactions in computer simulations and for quasi-2D systems
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 500:43-116, MAR 2011
abstract, full text, DOI:10.1016/j.physrep.2010.11.004

Heroux, Maxime S.; Mohan, Anne D.; Olsen, Kenneth W.
Ligand Migration in the Truncated Hemoglobin of Mycobacterium tuberculosis
IUBMB LIFE, 63:214-220, MAR 2011
abstract, full text, DOI:10.1002/iub.438

Patra, Niladri; Song, Yuanbo; Kral, Petr
Self-Assembly of Graphene Nanostructures on Nanotubes
ACS NANO, 5:1798-1804, MAR 2011
abstract, full text, DOI:10.1021/nn102531h

Janovec, Ladislav; Kozurkova, Maria; Sabolova, Danica; Ungvarsky, Jan; Paulikova, Helena; Plsikova, Jana; Vantova, Zuzana; Imrich, Jan
Cytotoxic 3,6-bis((imidazolidinone)imino)acridines: Synthesis, DNA binding and molecular modeling
BIOORGANIC & MEDICINAL CHEMISTRY, 19:1790-1801, MAR 1 2011
abstract, full text, DOI:10.1016/j.bmc.2011.01.012

Perez-Sanchez, Horacio; Wenzel, Wolfgang
Optimization Methods for Virtual Screening on Novel Computational Architectures
CURRENT COMPUTER-AIDED DRUG DESIGN, 7:44-52, MAR 2011
abstract, full text, DOI:10.2174/157340911793743565

Singh, L. R.; Poddar, N. K.; Dar, T. A.; Rahman, S.; Kumar, R.; Ahmad, F.
Forty Years of Research on Osmolyte-Induced Protein Folding and Stability
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:1-23, MAR 2011
abstract, full text

Lin, Ying-Wu
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:679-684, MAR 2011
abstract, full text, DOI:10.1002/prot.22928

Chennamsetty, Naresh; Voynov, Vladimir; Kayser, Veysel; Helk, Bernhard; Trout, Bernhardt L.
Prediction of protein binding regions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:888-897, MAR 2011
abstract, full text, DOI:10.1002/prot.22926

Fogolari, Federico; Corazza, Alessandra; Varini, Nicola; Rotter, Matteo; Gumral, Devrim; Codutti, Luca; Rennella, Enrico; Viglino, Paolo; Bellotti, Vittorio; Esposito, Gennaro
Molecular dynamics simulation of beta(2)-microglobulin in denaturing and stabilizing conditions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:986-1001, MAR 2011
abstract, full text, DOI:10.1002/prot.22940

Beretta, Giangiacomo; Artali, Roberto; Caneva, Enrico; Facino, Roberto Maffei
Conformation of the tridimensional structure of 1,2,3,4,6-pentagalloyl-beta-D-glucopyranose (PGG) by H-1 NMR, NOESY and theoretical study and membrane interaction in a simulated phospholipid bilayer: a first insight
MAGNETIC RESONANCE IN CHEMISTRY, 49:132-136, MAR 2011
abstract, full text, DOI:10.1002/mrc.2718

Qiu, Hu; Shen, Rong; Guo, Wanlin
Vibrating carbon nanotubes as water pumps
NANO RESEARCH, 4:284-289, MAR 2011
abstract, full text, DOI:10.1007/s12274-010-0080-y

Tsoulos, Ioannis G.; Stavrakoudis, Athanassios
Eucb: A C plus plus program for molecular dynamics trajectory analysis
COMPUTER PHYSICS COMMUNICATIONS, 182:834-841, MAR 2011
abstract, full text, DOI:10.1016/j.cpc.2010.11.032

Corry, Ben
Water and ion transport through functionalised carbon nanotubes: implications for desalination technology
ENERGY & ENVIRONMENTAL SCIENCE, 4:751-759, MAR 2011
abstract, full text, DOI:10.1039/c0ee00481b

Vanschouwen, Bryan M. B.; Oblinsky, Daniel G.; Gordon, Heather L.; Rothstein, Stuart M.
Structure Propensities in Mutated Polyglutamine Peptides
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 3:1-16, MAR 2011
abstract, full text, DOI:10.1007/s12539-011-0058-9

Iliopoulos, A. P.; Michopoulos, J. G.; Lambrakos, S. G.; Bernstein, N.
Performance of inverse atomistic scale fracture modeling on GPGPU architectures
JOURNAL OF COMPUTATIONAL SCIENCE, 2:39-46, MAR 2011
abstract, full text, DOI:10.1016/j.jocs.2010.12.005

Trabuco, Leonardo G.; Schreiner, Eduard; Gumbart, James; Hsin, Jen; Villa, Elizabeth; Schulten, Klaus
Applications of the molecular dynamics flexible fitting method
JOURNAL OF STRUCTURAL BIOLOGY, 173:420-427, MAR 2011
abstract, full text, TCBG publications, DOI:10.1016/j.jsb.2010.09.024

Wang, Xu; Lee, Hsiau-Wei; Liu, Yizhou; Prestegard, James H.
Structural NMR of protein oligomers using hybrid methods
JOURNAL OF STRUCTURAL BIOLOGY, 173:515-529, MAR 2011
abstract, full text, DOI:10.1016/j.jsb.2010.11.005

Min, Seung Kyu; Kim, Woo Youn; Cho, Yeonchoo; Kim, Kwang S.
Fast DNA sequencing with a graphene-based nanochannel device
NATURE NANOTECHNOLOGY, 6:162-165, MAR 2011
abstract, full text, DOI:10.1038/NNANO.2010.283

Silvestre-Ryan, Jordi; Lin, Yuchun; Chu, Jhih-Wei
"Fluctuograms'' Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002023, MAR 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002023

Gumbart, James; Chipot, Christophe; Schulten, Klaus
Free-energy cost for translocon-assisted insertion of membrane proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3596-3601, MAR 1 2011
abstract, full text, TCBG publications, DOI:10.1073/pnas.1012758108

Peplowski, Lukasz; Sikora, Mateusz; Nowak, Wieslaw; Cieplak, Marek
Molecular jamming-The cystine slipknot mechanical clamp in all-atom simulations
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 085102, FEB 28 2011
abstract, full text, DOI:10.1063/1.3553801

NategholEslam, Mostafa; Holland, Bryan W.; Gray, C. G.; Tomberli, Bruno
Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force
PHYSICAL REVIEW E, 83 Art. No. 021114, FEB 28 2011
abstract, full text, DOI:10.1103/PhysRevE.83.021114

Megow, Joerg; Roeder, Beate; Kulesza, Alexander; Bonacic-Koutecky, Vlasta; May, Volkhard
A Mixed Quantum-Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Forster Theory and beyond
CHEMPHYSCHEM, 12:645-656, FEB 25 2011
abstract, full text, DOI:10.1002/cphc.201000857

Su, Chih-Chia; Long, Feng; Zimmermann, Michael T.; Rajashankar, Kanagalaghatta R.; Jernigan, Robert L.; Yu, Edward W.
Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli
NATURE, 470:558-U153, FEB 24 2011
abstract, full text, DOI:10.1038/nature09743

Li, Xiaochuan (Edward); Tobacman, Larry S.; Mun, Ji Young; Craig, Roger; Fischer, Stefan; Lehman, William
Tropomyosin Position on F-Actin Revealed by EM Reconstruction and Computational Chemistry
BIOPHYSICAL JOURNAL, 100:1005-1013, FEB 16 2011
abstract, full text, DOI:10.1016/j.bpj.2010.12.3697

Spiriti, Justin; Binder, Jennifer K.; Levitus, Marcia; van der Vaart, Arjan
Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair
BIOPHYSICAL JOURNAL, 100:1049-1057, FEB 16 2011
abstract, full text, DOI:10.1016/j.bpj.2011.01.014

Hsin, Jen; Schulten, Klaus
Improved Resolution of Tertiary Structure Elasticity in Muscle Protein
BIOPHYSICAL JOURNAL, 100:L22-L24, FEB 16 2011
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2011.01.019

Santiso, Erik E.; Trout, Bernhardt L.
A general set of order parameters for molecular crystals
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 064109, FEB 14 2011
abstract, full text, DOI:10.1063/1.3548889

Liu, Yingzhe; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
JOURNAL OF PHYSICAL CHEMISTRY C, 115:1851-1856, FEB 10 2011
abstract, full text, DOI:10.1021/jp111981y

Su, Zhi-Yuan; Wang, Yeng-Tseng
Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:796-802, FEB 10 2011
abstract, full text, DOI:10.1021/jp107599v

Mroginski, Maria Andrea; Kaminski, Steve; von Stetten, David; Ringsdorf, Simone; Gaertner, Wolfgang; Essen, Lars-Oliver; Hildebrandt, Peter
Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1220-1231, FEB 10 2011
abstract, full text, DOI:10.1021/jp108265h

Zhou, Ruhong; Li, Jingyuan; Hua, Lan; Yang, Zaixing; Berne, B. J.
Comment on "Urea-Mediated Protein Denaturation: A Consensus View"
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1323-1326, FEB 10 2011
full text, DOI:10.1021/jp105160a

Oliveira, Augusto F.; Gemming, Sibylle; Seifert, Gotthard
Conformational Analysis of Aqueous BMP-2 Using Atomistic Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1122-1130, FEB 10 2011
abstract, full text, DOI:10.1021/jp106092d

Shukla, Diwakar; Trout, Bernhardt L.
Preferential Interaction Coefficients of Proteins in Aqueous Arginine Solutions and Their Molecular Origins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1243-1253, FEB 10 2011
abstract, full text, DOI:10.1021/jp108586b

Garate, J. -A.; English, Niall J.; MacElroy, J. M. D.
Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 055110, FEB 7 2011
abstract, full text, DOI:10.1063/1.3529428

Yeh, In-Chul; Wallqvist, Anders
On the proper calculation of electrostatic interactions in solid-supported bilayer systems
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 055109, FEB 7 2011
abstract, full text, DOI:10.1063/1.3548836

Martinez, Anna Victoria; DeSensi, Susan C.; Dominguez, Laura; Rivera, Eva; Straub, John E.
Protein folding in a reverse micelle environment: The role of confinement and dehydration
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 055107, FEB 7 2011
abstract, full text, DOI:10.1063/1.3545982

Sapir, Liel; Harries, Daniel
Linking Trehalose Self-Association with Binary Aqueous Solution Equation of State
JOURNAL OF PHYSICAL CHEMISTRY B, 115:624-634, FEB 3 2011
abstract, full text, DOI:10.1021/jp109780n

Olbrich, Carsten; Struempfer, Johan; Schulten, Klaus; Kleinekathoefer, Ulrich
Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:758-764, FEB 3 2011
abstract, full text, TCBG publications, DOI:10.1021/jp1099514

Bastug, Turgut; Kuyucak, Serdar
Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels
BIOPHYSICAL JOURNAL, 100:629-636, FEB 2 2011
abstract, full text, DOI:10.1016/j.bpj.2010.12.3718

Kokhan, Oleksandr; Shinkarev, Vladimir P.
All-Atom Molecular Dynamics Simulations Reveal Significant Differences in Interaction between Antimycin and Conserved Amino Acid Residues in Bovine and Bacterial bc(1) Complexes
BIOPHYSICAL JOURNAL, 100:720-728, FEB 2 2011
abstract, full text, DOI:10.1016/j.bpj.2010.12.3705

Skjevik, Age Aleksander; Haug, Bengt Erik; Lygre, Henning; Teigen, Knut
Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 154:18-25, FEB 2011
abstract, full text, DOI:10.1016/j.bpc.2010.12.002

Qu, Yuanyuan; Zhou, Hao; Li, Ang; Ma, Fang; Zhou, Jiti
Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA-4 by catalytic and structural properties analysis
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 89:655-663, FEB 2011
abstract, full text, DOI:10.1007/s00253-010-2874-y

Morales-Quintana, Luis; Fuentes, Lida; Gaete-Eastman, Carlos; Herrera, Raul; Alejandra Moya-Leon, Maria
Structural characterization and substrate specificity of VpAAT1 protein related to ester biosynthesis in mountain papaya fruit
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:635-642, FEB 2011
abstract, full text, DOI:10.1016/j.jmgm.2010.11.011

Falconi, Mattia; Oteri, Francesco; Di Palma, Francesco; Pandey, Saurabh; Battistoni, Andrea; Desideri, Alessandro
Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:181-194, FEB 2011
abstract, full text, DOI:10.1007/s10822-010-9409-6

Grasso, Giuseppe; Pietropaolo, Adriana; Spoto, Giuseppe; Pappalardo, Giuseppe; Tundo, Grazia Raffaella; Ciaccio, Chiara; Coletta, Massimo; Rizzarelli, Enrico
Copper(I) and Copper(II) Inhibit A beta Peptides Proteolysis by Insulin-Degrading Enzyme Differently: Implications for Metallostasis Alteration in Alzheimer's Disease
CHEMISTRY-A EUROPEAN JOURNAL, 17:2752-2762, FEB 2011
abstract, full text, DOI:10.1002/chem.201002809

Niazi, Umar H. K.; Bibby, Jaclyn; Sutcliffe, Michael J.
In-silico characterization of the effects of phosphorylated tyrosines 86 and 106 on structure and binding of MAL: insight into hyperinflammatory response to infection by the human malaria parasites
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:53-65, FEB 2011
abstract, full text, DOI:10.3109/10799893.2010.512014

Gossett, J. Jared; Harvey, Stephen C.
Computational Screening and Design of DNA-Linked Molecular Nanowires
NANO LETTERS, 11:604-608, FEB 2011
abstract, full text, DOI:10.1021/nl103665z

Kamisetty, Hetunandan; Ramanathan, Arvind; Bailey-Kellogg, Chris; Langmead, Christopher James
Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:444-462, FEB 2011
abstract, full text, DOI:10.1002/prot.22894

Novak, Brian R.; Moldovan, Dorel; Waldrop, Grover L.; de Queiroz, Marcio S.
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:622-632, FEB 2011
abstract, full text, DOI:10.1002/prot.22910

Kalikka, Janne; Akola, Jaakko
Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:181-194, FEB 2011
abstract, full text, DOI:10.1007/s00249-010-0638-3

Chakrabarti, Bornali; Bairagya, Hridoy R.; Mallik, Payel; Mukhopadhyay, Bishnu P.; Bera, Asim K.
An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2 ions in Matrix Metalloproteinase 13 of Human
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:503-516, FEB 2011
abstract, full text

Chen, Wei; Lou, Jizhong; Hsin, Jen; Schulten, Klaus; Harvey, Stephen C.; Zhu, Cheng
Molecular Dynamics Simulations of Forced Unbending of Integrin alpha(V)beta(3)
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1001086, FEB 2011
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1001086

Gushchin, Ivan Yu; Gordeliy, Valentin I.; Grudinin, Sergei
Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction
BIOCHEMISTRY, 50:574-580, FEB 1 2011
abstract, full text, DOI:10.1021/bi101032a

Calderon, Christopher P.
Estimation and Inference of Diffusion Coefficients in Complex Biomolecular Environments
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:280-290, FEB 2011
abstract, full text, DOI:10.1021/ct1004966

Kawatsu, Tsutomu; Lundberg, Marcus; Morokuma, Keiji
Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:390-401, FEB 2011
abstract, full text, DOI:10.1021/ct1005592

Mustata, Gabriela; Li, Mei; Zevola, Nicki; Bakan, Ahmet; Zhang, Lin; Epperly, Michael; Greenberger, Joel S.; Yu, Jian; Bahar, Ivet
Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:281-290, FEB 2011
abstract, full text, DOI:10.2174/156802611794072641

Yan, Qi; Murphy-Ullrich, Joanne E.; Song, Yuhua
Molecular and Structural Insight into the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1-Calreticulin Binding
BIOCHEMISTRY, 50:566-573, FEB 1 2011
abstract, full text, DOI:10.1021/bi101639y

Khurana, Ekta; DeVane, Russell H.; Dal Peraro, Matteo; Klein, Michael L.
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:530-537, FEB 2011
abstract, full text, DOI:10.1016/j.bbamem.2010.03.025

Kotsikorou, Eyangelia; Lynch, Diane L.; Abood, Mary E.; Reggio, Patricia H.
Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55
CHEMISTRY AND PHYSICS OF LIPIDS, 164:131-143, FEB 2011
abstract, full text, DOI:10.1016/j.chemphyslip.2010.12.003

Zhang, Ji-Long; Zheng, Qing-Chuan; Zhang, Hong-Xing
Theoretical improvement of the specific inhibitor of human carbonic anhydrase VII
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 35:50-56, FEB 2011
abstract, full text, DOI:10.1016/j.compbiolchem.2011.01.001

Bowman, Gregory R.; Voelz, Vincent A.; Pande, Vijay S.
Taming the complexity of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:4-11, FEB 2011
abstract, full text, DOI:10.1016/j.sbi.2010.10.006

Kim, Soo-Kyung; Li, Youyong; Abrol, Ravinder; Heo, Jiyoung; Goddard, William A., I.I.I.
Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:420-433, FEB 2011
abstract, full text, DOI:10.1021/ci100375b

Nowosieski, Marcin; Hoffmann, Marcin; Wyrwicz, Lucjan S.; Stepniak, Piotr; Plewczynski, Dariusz M.; Lazniewski, Michal; Ginalski, Krzysztof; Rychlewski, Leszek
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:455-462, FEB 2011
abstract, full text, DOI:10.1021/ci100403b

Arsawang, Uthumporn; Saengsawang, Oraphan; Rungrotmongkol, Thanyada; Sornmee, Purinchaya; Wittayanarakul, Kitiyaporn; Remsungnen, Tawun; Hannongbua, Supot
How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:591-596, FEB 2011
abstract, full text, DOI:10.1016/j.jmgm.2010.11.002

Yun, Sijung; Guy, H. Robert
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:663-675, FEB 2011
abstract, full text, DOI:10.1016/j.jmgm.2010.12.002

Olbrich, Carsten; Liebers, Joerg; Kleinekathoefer, Ulrich
Modeling of light-harvesting in purple bacteria using a time-dependent Hamiltonian approach
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 248:393-398, FEB 2011
abstract, full text, DOI:10.1002/pssb.201000651

Huang, Danzhi; Caflisch, Amedeo
The Free Energy Landscape of Small Molecule Unbinding
PLOS COMPUTATIONAL BIOLOGY, 7 Art. No. e1002002, FEB 2011
abstract, full text, DOI:10.1371/journal.pcbi.1002002

Henriques, Elsa S.; Brito, Rui M. M.; Soares, Hugo; Ventura, Sonia; de Oliveira, Vivian L.; Parkhouse, R. Michael E.
Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus
PROTEIN SCIENCE, 20:247-255, FEB 2011
abstract, full text, DOI:10.1002/pro.554

Emileh, Ali; Abrams, Cameron F.
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain alpha 1 helix in an engineered HIV-1 gp120
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:537-546, FEB 2011
abstract, full text, DOI:10.1002/prot.22901

Shim, Joong-Youn; Rudd, James; Ding, Tomas T.
Distinct second extracellular loop structures of the brain cannabinoid CB1 receptor: Implication in ligand binding and receptor function
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:581-597, FEB 2011
abstract, full text, DOI:10.1002/prot.22907

Cruz, Felipe A.; Knepley, Matthew G.; Barba, L. A.
PetFMM-A dynamically load-balancing parallel fast multipole library
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, 85:403-428, JAN 28 2011
abstract, full text, DOI:10.1002/nme.2972

Hilder, Tamsyn A.; Gordon, Dan; Chung, Shin-Ho
Synthetic cation-selective nanotube: Permeant cations chaperoned by anions
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 045103, JAN 28 2011
abstract, full text, DOI:10.1063/1.3524310

Karino, Yasuhito; Matubayasi, Nobuyuki
Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 041105, JAN 28 2011
abstract, full text, DOI:10.1063/1.3535560

Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.
Discovering Conformational Sub-States Relevant to Protein Function
PLOS ONE, 6 Art. No. e15827, JAN 28 2011
abstract, full text, DOI:10.1371/journal.pone.0015827

Panecka, Joanna; Mura, Cameron; Trylska, Joanna
Molecular Dynamics of Potential rRNA Binders: Single-Stranded Nucleic Acids and Some Analogues
JOURNAL OF PHYSICAL CHEMISTRY B, 115:532-546, JAN 27 2011
abstract, full text, DOI:10.1021/jp106404u

Shan, Jufang; Javitch, Jonathan A.; Shi, Lei; Weinstein, Harel
The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter
PLOS ONE, 6 Art. No. e16350, JAN 27 2011
abstract, full text, DOI:10.1371/journal.pone.0016350

Ko, Eunhwa; Liu, Jing; Perez, Lisa M.; Lu, Genliang; Schaefer, Amber; Burgess, Kevin
Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:462-477, JAN 26 2011
abstract, full text, DOI:10.1021/ja1071916

Zuniga, Leandro; Marquez, Valeria; Gonzalez-Nilo, Fernando D.; Chipot, Christophe; Pablo Cid, L.; Sepulveda, Francisco V.; Isabel Niemeyer, Maria
Gating of a pH-Sensitive K-2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
PLOS ONE, 6 Art. No. e16141, JAN 25 2011
abstract, full text, DOI:10.1371/journal.pone.0016141

Liu, Li; Fang, Ying; Huang, Qingsheng; Wu, Jianhua
A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic alpha-Helical Peptide HP(2-20) and Its Four Analogues
PLOS ONE, 6 Art. No. e16441, JAN 24 2011
abstract, full text, DOI:10.1371/journal.pone.0016441

Zerbetto, Mirco; Buck, Matthias; Meirovitch, Eva; Polimeno, Antonino
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain N-15-H-1 and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1
JOURNAL OF PHYSICAL CHEMISTRY B, 115:376-388, JAN 20 2011
abstract, full text, DOI:10.1021/jp108633v

Jiang, Wei; Hardy, David J.; Phillips, James C.; MacKerell, Alexander D., Jr.; Schulten, Klaus; Roux, Benoit
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:87-92, JAN 20 2011
abstract, full text, TCBG publications, DOI:10.1021/jz101461d

Nury, Hugues; Van Renterghem, Catherine; Weng, Yun; Tran, Alphonso; Baaden, Marc; Dufresne, Virginie; Changeux, Jean-Pierre; Sonner, James M.; Delarue, Marc; Corringer, Pierre-Jean
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
NATURE, 469:428-+, JAN 20 2011
abstract, full text, DOI:10.1038/nature09647

Fritsch, Sebastian; Ivanov, Ivaylo; Wang, Hailong; Cheng, Xiaolin
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel
BIOPHYSICAL JOURNAL, 100:390-398, JAN 19 2011
abstract, full text, DOI:10.1016/j.bpj.2010.11.077

Brubaker, William D.; Freites, J. Alfredo; Golchert, Kory J.; Shapiro, Rebecca A.; Morikis, Vasilios; Tobias, Douglas J.; Martin, Rachel W.
Separating Instability from Aggregation Propensity in gamma S-Crystallin Variants
BIOPHYSICAL JOURNAL, 100:498-506, JAN 19 2011
abstract, full text, DOI:10.1016/j.bpj.2010.12.3691

Dendzik, Z.; Gorny, K.; Gwizdala, W.; Gburski, Z.
Dipolar relaxation of propylene glycol molecular cluster confined in carbon nanotubes of different chiralities-computer simulation study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:575-579, JAN 15 2011
abstract, full text, DOI:10.1016/j.jnoncrysol.2010.06.068

Kieslich, Chris A.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:707-716, JAN 15 2011
abstract, full text, DOI:10.1016/j.jnoncrysol.2010.05.087

Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T. Y.; Zhang, Tong-Yi
Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:684-688, JAN 14 2011
abstract, full text, DOI:10.1016/j.bbrc.2010.12.042

Wang, Chunhua; Ye, Fengbin; Velardez, Gustavo F.; Peters, Gunther H.; Westh, Peter
Affinity of Four Polar Neurotransmitters for Lipid Bilayer Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:196-203, JAN 13 2011
abstract, full text, DOI:10.1021/jp108368w

Venkatramani, Ravindra; Davis, Kathryn L.; Wierzbinski, Emil; Bezer, Silvia; Balaeff, Alexander; Keinan, Shahar; Paul, Amit; Kocsis, Laura; Beratan, David N.; Achim, Catalina; Waldeck, David H.
Evidence for a Near-Resonant Charge Transfer Mechanism for Double-Stranded Peptide Nucleic Acid
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:62-72, JAN 12 2011
abstract, full text, DOI:10.1021/ja107622m

Hilder, Tamsyn A.; Chung, Shin-Ho
Carbon nanotube as a gramicidin analogue
CHEMICAL PHYSICS LETTERS, 501:423-426, JAN 7 2011
abstract, full text, DOI:10.1016/j.cplett.2010.11.034

Bossis, Fabrizio; Palese, Luigi L.
Molecular dynamics in cytochrome c oxidase Mossbauer spectra deconvolution
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:438-442, JAN 7 2011
abstract, full text, DOI:10.1016/j.bbrc.2010.11.140

Sakata, Tetsuya; Kawashima, Yukio; Nakano, Haruyuki
Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study
JOURNAL OF CHEMICAL PHYSICS, 134 Art. No. 014501, JAN 7 2011
abstract, full text, DOI:10.1063/1.3506616

Koeksal, Mustafa; Jin, Yinghua; Coates, Robert M.; Croteau, Rodney; Christianson, David W.
Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis
NATURE, 469:116-U138, JAN 6 2011
abstract, full text, DOI:10.1038/nature09628

Thomas, Michael; Jayatilaka, Dylan; Corry, Ben
Mapping the Importance of Four Factors in Creating Monovalent Ion Selectivity in Biological Molecules
BIOPHYSICAL JOURNAL, 100:60-69, JAN 5 2011
abstract, full text, DOI:10.1016/j.bpj.2010.11.022

Wang, Teng; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
LANGMUIR, 27:91-97, JAN 4 2011
abstract, full text, DOI:10.1021/la103288j

Merchant, Bonnie A.; Madura, Jeffry D.
A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 7, 7:67-87, 2011
abstract, full text, DOI:10.1016/B978-0-444-53835-2.00003-1

Mukherjee, Rajib; Bishop, Thomas C.
Nucleosomal DNA: Kinked, Not Kinked, or Self-Healing Material?
FRONTIERS IN NUCLEIC ACIDS, 1082:69-92, 2011
abstract, full text

Lindberg, Gerrick E.; Knight, Chris; Jorn, Ryan; Dama, James F.; Voth, Gregory A.
Multiscale Simulation of Hydroxide Solvation and Transport in Anion Exchange Membranes
POLYMER ELECTROLYTE FUEL CELLS 11, 41:1785-1793, 2011
abstract, full text, DOI:10.1149/1.3635710

Tiber, Pinar Mega; Orun, Oya; Nacar, Cevdet; Sezerman, Ugur Osman; Severcan, Feride; Severcan, Mete; Matagne, Andre; Kan, Beki
Structural characterization of recombinant bovine Go alpha by spectroscopy and homology modeling
SPECTROSCOPY-BIOMEDICAL APPLICATIONS, 26:213-229, 2011
abstract, full text, DOI:10.3233/SPE-2011-0543

Jolley, Craig C.; Lucon, Janice; Uchida, Masaki; Reichhardt, Courtney; Vaughn, Mary J.; Lafrance, Ben J.; Douglas, Trevor
Structure, dynamics, and solvation in a disordered metal-organic coordination polymer: a multiscale study
JOURNAL OF COORDINATION CHEMISTRY, 64:4301-4317, 2011
abstract, full text, DOI:10.1080/00958972.2011.637555

Kass, Itamar; Reboul, Cyril F.; Buckle, Ashley M.
COMPUTATIONAL METHODS FOR STUDYING SERPIN CONFORMATIONAL CHANGE AND STRUCTURAL PLASTICITY
METHODS IN ENZYMOLOGY, VOL 501: SERPIN STRUCTURE AND EVOLUTION, 501:295-323, 2011
abstract, full text, DOI:10.1016/B978-0-12-385950-1.00014-6

Abou Hamad, I.; Novotny, M. A.; Wipf, D. O.; Rikvold, P. A.
A New Charging Method for Li-ion Batteries: Dependence of the charging time on the Direction of an Additional Oscillating Field
BATTERY/ENERGY TECHNOLOGY (GENERAL) - 218TH ECS MEETING, 33:33-37, 2011
abstract, full text, DOI:10.1149/1.3589919

Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Zatreanu, Diana; Sandu, Oana; Dascalu, Traian; Mihailescu, Dan Florin
THz spectroscopy and molecular modeling of bovine serum albumin under various hydration conditions
PHOTONICS, DEVICES, AND SYSTEMS V, 8306 Art. No. 83060N, 2011
abstract, full text, DOI:10.1117/12.912460

Orozco, Modesto; Orellana, Laura; Hospital, Adam; Naganathan, Athi N.; Emperador, Agusti; Carrillo, Oliver; Gelpi, J. L.
COARSE-GRAINED REPRESENTATION OF PROTEIN FLEXIBILITY. FOUNDATIONS, SUCCESSES, AND SHORTCOMINGS
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 85: COMPUTATIONAL CHEMISTRY METHODS IN STRUCTURAL BIOLOGY, 85:183-215, 2011
abstract, full text, DOI:10.1016/B978-0-12-386485-7.00005-3

Chipot, Christophe; Lelievre, Tony
ENHANCED SAMPLING OF MULTIDIMENSIONAL FREE-ENERGY LANDSCAPES USING ADAPTIVE BIASING FORCES
SIAM JOURNAL ON APPLIED MATHEMATICS, 71:1673-1695, 2011
abstract, full text, DOI:10.1137/10080600X

Dong, Xiu-Li; Qi, Wang; Tao, Wu; Ma, Li-Ying; Fu, Cai-Xia
The dynamic behaviours of protein BMP-2 on hydroxyapatite nanoparticles
MOLECULAR SIMULATION, 37:1097-1104, 2011
abstract, full text, DOI:10.1080/08927022.2011.582108

Hughes, Meghan; Xu, Haixia; Frederix, Pim W. J. M.; Smith, Andrew M.; Hunt, Neil T.; Tuttle, Tell; Kinloch, Ian A.; Ulijn, Rein V.
Biocatalytic self-assembly of 2D peptide-based nanostructures
SOFT MATTER, 7:10032-10038, 2011
abstract, full text, DOI:10.1039/c1sm05981e

Khelashvili, George; Rappolt, Michael; Chiu, See-Wing; Pabst, Georg; Harries, Daniel
Impact of sterol tilt on membrane bending rigidity in cholesterol and 7DHC-containing DMPC membranes
SOFT MATTER, 7:10299-10312, 2011
abstract, full text, DOI:10.1039/c1sm05937h

Engelbrecht, Tanja; Hauss, Thomas; Suess, Kevin; Vogel, Alexander; Roark, Matthew; Feller, Scott E.; Neubert, Reinhard H. H.; Dobner, Bodo
Characterisation of a new ceramide EOS species: synthesis and investigation of the thermotropic phase behaviour and influence on the bilayer architecture of stratum corneum lipid model membranes
SOFT MATTER, 7:8998-9011, 2011
abstract, full text, DOI:10.1039/c1sm05134b

Asghar, Waseem; Billo, Joseph A.; Iqbal, Samir M.
Solid State Nanopores for Selective Sensing of DNA
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, 107-128, 2011
abstract, full text, DOI:10.1007/978-1-4419-8252-0_5

Gracheva, Maria E.; Leroux, Amandine; Destine, Jacques; Leburton, Jean-Pierre
Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, 151-175, 2011
abstract, full text, DOI:10.1007/978-1-4419-8252-0_7

Comer, Jeffrey; Aksimentiev, Aleksei
Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, 335-356, 2011
abstract, full text, DOI:10.1007/978-1-4419-8252-0_14

Patriche, Simona; Matsushita, Shinji; Banu, Mihaela; Epureanu, Bogdan I.; Adachi, Taiji
Atomistic Mechano-Chemical Modeling of Kinesins
BIOINSPIRATION, BIOMIMETICS, AND BIOREPLICATION, 7975 Art. No. 797519, 2011
abstract, full text, DOI:10.1117/12.886303

Zhao, Ya-Pu; Wang, Feng-Chao; Chi, Mei
Molecular Dynamics Simulation and Molecular Orbital Method
HANDBOOK OF ADHESION TECHNOLOGY, VOL 1 AND 2, 1351-1384, 2011
abstract, full text, DOI:10.1007/978-3-642-01169-6_52

Stavrakoudis, Athanassios
Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions
MOLECULAR SIMULATION, 37:837-845, 2011
abstract, full text, DOI:10.1080/08927022.2011.566607

Nishizawa, Kazuhisa
Atomistic Molecular Simulation of Gating Modifier Venom Peptides - Two Binding Modes and Effects of Lipid Structure
MECHANOSENSITIVITY AND MECHANOTRANSDUCTION, 4:167-190, 2011
abstract, full text

Wang, Feng; Akin-Ojo, Omololu; Pinnick, Eric; Song, Yang
Approaching post-Hartree-Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method
MOLECULAR SIMULATION, 37:591-605, 2011
abstract, full text, DOI:10.1080/08927022.2011.565759

Abroshan, Hadi; Akbarzadeh, Hamed; Taherkhani, Farid; Parsafar, Gholamabbas
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamics study
MOLECULAR PHYSICS, 109:709-724, 2011
abstract, full text, DOI:10.1080/00268976.2010.549846

Carr, Rogan; Comer, Jeffrey; Ginsberg, Mark D.; Aksimentiev, Aleksei
Modeling Pressure-Driven Transport of Proteins Through a Nanochannel
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 10:75-82, JAN 2011
abstract, full text, DOI:10.1109/TNANO.2010.2062530

Calero, Carles; Faraudo, Jordi; Aguilella-Arzo, Marcel
Molecular dynamics simulations of concentrated aqueous electrolyte solutions
MOLECULAR SIMULATION, 37:123-134, 2011
abstract, full text, DOI:10.1080/08927022.2010.525513

Cazade, P. -A.; Bordat, P.; Baraille, I.; Brown, R.; Smith, W.; Todorov, I. T.
DL_POLY_2 adaptations for solvation studies
MOLECULAR SIMULATION, 37:43-52, 2011
abstract, full text, DOI:10.1080/08927022.2010.517531

Fung, Wilson W. L.; Aamodt, Tor M.
Thread Block Compaction for Efficient SIMT Control Flow
2011 IEEE 17TH INTERNATIONAL SYMPOSIUM ON HIGH-PERFORMANCE COMPUTER ARCHITECTURE (HPCA), 25-36, 2011
abstract, full text

Meneses, Esteban; Kale, Laxmikant V.; Bronevetsky, Greg
Dynamic Load Balance for Optimized Message Logging in Fault Tolerant HPC Applications
2011 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 281-289, 2011
abstract, full text, DOI:10.1109/CLUSTER.2011.39

Yakubovich, Alexander V.; Surdutovich, Eugene; Solov'yov, Andrey V.
Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach
7TH INTERNATIONAL CONFERENCE ON ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS ICAMDATA-2010, 1344:230-238, 2011
abstract, full text, DOI:10.1063/1.3585822

Friddle, Raymond W.; Battle, Keith; Trubetskoy, Vasily; Tao, Jinhui; Salter, E. Alan; Moradian-Oldak, Janet; De Yoreo, James J.; Wierzbicki, Andrzej
Single-Molecule Determination of the Face-Specific Adsorption of Amelogenin's C-Terminus on Hydroxyapatite
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:7541-7545, 2011
full text, DOI:10.1002/anie.201100181

Hsin, Jen; Struempfer, Johan; Lee, Eric H.; Schulten, Klaus
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory
ANNUAL REVIEW OF BIOPHYSICS, VOL 40, 40:187-203, 2011
abstract, full text, TCBG publications, DOI:10.1146/annurev-biophys-072110-125325

Jamadagni, Sumanth N.; Godawat, Rahul; Garde, Shekhar
Hydrophobicity of Proteins and Interfaces: Insights from Density Fluctuations
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 2, 2:147-171, 2011
abstract, full text, DOI:10.1146/annurev-chembioeng-061010-114156

Kortagere, Sandhya; Cheng, Shu-Yuan; Antonio, Tamara; Zhen, Juan; Reith, Maarten E. A.; Dutta, Aloke K.
Interaction of novel hybrid compounds with the D3 dopamine receptor: Site-directed mutagenesis and homology modeling studies
BIOCHEMICAL PHARMACOLOGY, 81:157-163, JAN 1 2011
abstract, full text, DOI:10.1016/j.bcp.2010.08.026

Lim, Joseph B.; Klauda, Jeffery B.
Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:323-331, JAN 2011
abstract, full text, DOI:10.1016/j.bbamem.2010.07.036

Kaila, Ville R. I.; Sharma, Vivek; Wikstrom, Marten
The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:80-84, JAN 2011
abstract, full text, DOI:10.1016/j.bbabio.2010.08.014

Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie
Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions
BIOMACROMOLECULES, 12:210-220, JAN 2011
abstract, full text, DOI:10.1021/bm101159p

Lee, One-Sun; Schatz, George C.
Computational Simulations of the Interaction of Lipid Membranes with DNA-Functionalized Gold Nanoparticles
BIOMEDICAL NANOETECHNOLOGY: METHODS AND PROTOCOLS, 726:283-296, 2011
abstract, full text, DOI:10.1007/978-1-61779-052-2_18

Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Forrer, Kurt; Helk, Bernhard; Trout, Bernhardt L.
Glycosylation influences on the aggregation propensity of therapeutic monoclonal antibodies
BIOTECHNOLOGY JOURNAL, 6:38-44, JAN 2011
abstract, full text, DOI:10.1002/biot.201000091

Gburski, Zygmunt; Gorny, Krzysztof
Impact of the Carbon Allotropes on Cholesterol Domain: MD Simulation
CARBON NANOTUBES - GROWTH AND APPLICATIONS, 493-508, 2011
full text

English, Niall J.; Garate, Jose-Antonio; MacElroy, J. M. Don
Electric-Field and Friction Effects on Carbon Nanotube-Assisted Water Self-Diffusion Across Lipid Membranes
CARBON NANOTUBES - GROWTH AND APPLICATIONS, 509-528, 2011
full text

Zuo, Guanghong; Fang, Haiping; Zhou, Ruhong
Nanotoxicity: Exploring the Interactions Between Carbon Nanotubes and Proteins
CARBON NANOTUBES - GROWTH AND APPLICATIONS, 539-564, 2011
full text

Milac, Adina L.; Anishkin, Andriy; Fatakia, Sarosh N.; Chow, Carson C.; Sukharev, Sergei; Guy, H. Robert
Structural models of TREK channels and their gating mechanism
CHANNELS, 5:23-33, JAN-FEB 2011
abstract, full text, DOI:10.4161/chan.5.1.13905

Papadopoulos, Theodoros A.; Muccioli, Luca; Athanasopoulos, Stavros; Walker, Alison B.; Zannoni, Claudio; Beljonne, David
Does supramolecular ordering influence exciton transport in conjugated systems? Insight from atomistic simulations
CHEMICAL SCIENCE, 2:1025-1032, 2011
abstract, full text, DOI:10.1039/c0sc00467g

Moss, Christopher L.; Chung, Thomas W.; Cerovsky, Vaclav; Turecek, Frantisek
ELECTRON TRANSFER DISSOCIATION OF A MELECTIN PEPTIDE: CORRELATING THE PRECURSOR ION STRUCTURE WITH PEPTIDE BACKBONE DISSOCIATIONS
COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, 76:295-309, 2011
abstract, full text, DOI:10.1135/cccc2011025

Veglia, G.; Traaseth, N. J.; Shi, L.; Verardi, R.; Gopinath, T.; Gustavsson, M.
The Hybrid Solution/Solid-State NMR Method for Membrane Protein Structure Determination
COMPREHENSIVE BIOPHYSICS, VOL 1: BIOPHYSICAL TECHNIQUES FOR STRUCTURAL CHARACTERIZATION OF MACROMOLECULES, 182-198, 2011
full text, DOI:10.1016/B978-0-12-374920-8.00115-6

Oldziej, S.; Czaplewski, C.; Liwo, A.; Vila, J. A.; Scheraga, H. A.
Computation of Structure, Dynamics, and Thermodynamics of Proteins
COMPREHENSIVE BIOPHYSICS, VOL 1: BIOPHYSICAL TECHNIQUES FOR STRUCTURAL CHARACTERIZATION OF MACROMOLECULES, 494-513, 2011
full text, DOI:10.1016/B978-0-12-374920-8.00126-0

Elber, R.; Cardenas, A. E.
Coarse-Grained Methods: Theory
COMPREHENSIVE BIOPHYSICS, VOL 9: SIMULATION AND MODELLING, 2-26, 2011
full text, DOI:10.1016/B978-0-12-374920-8.00902-4

Chow, E.; Klepeis, J. L.; Rendleman, C. A.; Dror, R. O.; Shaw, D. E.
New Technologies for Molecular Dynamics Simulations
COMPREHENSIVE BIOPHYSICS, VOL 9: SIMULATION AND MODELLING, 86-104, 2011
full text, DOI:10.1016/B978-0-12-374920-8.00908-5

Rudy, Y.
From Genes and Molecules to Organs and Organisms: Heart
COMPREHENSIVE BIOPHYSICS, VOL 9: SIMULATION AND MODELLING, 268-327, 2011
full text, DOI:10.1016/B978-0-12-374920-8.00924-3

Cashman, D. J.; Mamonov, A. B.; Bhatt, D.; Zuckerman, D. M.
Thermal Motions of the E. coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:211-220, JAN 2011
abstract, full text

Comer, Jeffrey R.; Wells, David B.; Aksimentiev, Aleksei
Modeling Nanopores for Sequencing DNA
DNA NANOTECHNOLOGY: METHODS AND PROTOCOLS, 749:317-358, 2011
abstract, full text, DOI:10.1007/978-1-61779-142-0_22

Lombardo, A.; Licciardello, G.; Bertuccio, A.; Vistoli, G.; Pedretti, A.
Virtual Screening Approach for the Identification of Potential Citrus Tristeza Virus Inhibitors
II INTERNATIONAL SYMPOSIUM ON CITRUS BIOTECHNOLOGY, 892:257-264, 2011
abstract, full text

Aguilella, Vicente M.; Queralt-Martin, Maria; Aguilella-Arzo, Marcel; Alcaraz, Antonio
Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
INTEGRATIVE BIOLOGY, 3:159-172, 2011
abstract, full text, DOI:10.1039/c0ib00048e

Wagner, Carolin; Olbrich, Carsten; Brutzer, Hergen; Salomo, Mathias; Kleinekathoefer, Ulrich; Keyser, Ulrich F.; Kremer, Friedrich
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations
JOURNAL OF BIOLOGICAL PHYSICS, 37:117-131, JAN 2011
abstract, full text, DOI:10.1007/s10867-010-9203-7

Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Trout, Bernhardt L.
Tryptophan-Tryptophan Energy Transfer and Classification of Tryptophan Residues in Proteins Using a Therapeutic Monoclonal Antibody as a Model
JOURNAL OF FLUORESCENCE, 21:275-288, JAN 2011
abstract, full text, DOI:10.1007/s10895-010-0715-0

Pizzirusso, A.; Savini, M.; Muccioli, L.; Zannoni, C.
An atomistic simulation of the liquid-crystalline phases of sexithiophene
JOURNAL OF MATERIALS CHEMISTRY, 21:125-133, 2011
abstract, full text, DOI:10.1039/c0jm01284j

Schow, Eric V.; Freites, J. Alfredo; Cheng, Philip; Bernsel, Andreas; von Heijne, Gunnar; White, Stephen H.; Tobias, Douglas J.
Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments
JOURNAL OF MEMBRANE BIOLOGY, 239:35-48, JAN 2011
abstract, full text, DOI:10.1007/s00232-010-9330-x

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Bera, Asim K.
Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II
JOURNAL OF MOLECULAR RECOGNITION, 24:35-44, JAN-FEB 2011
abstract, full text, DOI:10.1002/jmr.1021

Gangupomu, Vamshi K.; Capaldi, Franco M.
Interactions of Carbon Nanotube with Lipid Bilayer Membranes
JOURNAL OF NANOMATERIALS, Art. No. 830436, 2011
abstract, full text, DOI:10.1155/2011/830436

Chung, Thomas W.; Moss, Christopher L.; Zimnicka, Magdalena; Johnson, Richard S.; Moritz, Robert L.; Turecek, Frantisek
Electron-Capture and -Transfer Dissociation of Peptides Tagged with Tunable Fixed-Charge Groups: Structures and Dissociation Energetics
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:13-30, JAN 2011
abstract, full text, DOI:10.1007/s13361-010-0012-9

Lynch, Rebecca M.; Rong, Rong; Boliar, Saikat; Sethi, Anurag; Li, Bing; Mulenga, Joseph; Allen, Susan; Robinson, James E.; Gnanakaran, S.; Derdeyn, Cynthia A.
The B Cell Response Is Redundant and Highly Focused on V1V2 during Early Subtype C Infection in a Zambian Seroconverter
JOURNAL OF VIROLOGY, 85:905-915, JAN 2011
abstract, full text, DOI:10.1128/JVI.02006-10

Carr, Rogan; Comer, Jeffrey; Ginsberg, Mark D.; Aksimentiev, Aleksei
Atoms-to-microns model for small solute transport through sticky nanochannels
LAB ON A CHIP, 11:3766-3773, 2011
abstract, full text, DOI:10.1039/c1lc20697d

Gill, J. P.; Shaw, K. M.; Rountree, B. L.; Kehl, C. E.; Chiel, H. J.
Simulating Kinetic Processes in Time and Space on a Lattice
MATHEMATICAL MODELLING OF NATURAL PHENOMENA, 6:159-197, 2011
abstract, full text, DOI:10.1051/mmnp/20116609

Suyetin, M. V.; Vakhrushev, A. V.
Temperature-sensitive nanocapsule for drug delivery
MICRO & NANO LETTERS, 6:39-42, JAN 2011
abstract, full text, DOI:10.1049/mnl.2010.0137

Guo, Hao-Bo; Parks, Jerry M.; Johs, Alexander; Smith, Jeremy C.
Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage
MODELING OF MOLECULAR PROPERTIES, 311-324, 2011
full text

Tsaousis, Anastasios D.; Gaston, Daniel; Stechmann, Alexandra; Walker, Peter B.; Lithgow, Trevor; Roger, Andrew J.
A Functional Tom70 in the Human Parasite Blastocystis sp.: Implications for the Evolution of the Mitochondrial Import Apparatus
MOLECULAR BIOLOGY AND EVOLUTION, 28:781-791, JAN 2011
abstract, full text, DOI:10.1093/molbev/msq252

Telesco, Shannon E.; Shih, Andrew J.; Jia, Fei; Radhakrishnan, Ravi
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
MOLECULAR BIOSYSTEMS, 7:2066-2080, 2011
abstract, full text, DOI:10.1039/c0mb00345j

Figueira, A. C. M.; Saidemberg, D. M.; Souza, P. C. T.; Martinez, L.; Scanlan, T. S.; Baxter, J. D.; Skaf, M. S.; Palma, M. S.; Webb, P.; Polikarpov, I.
Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange
MOLECULAR ENDOCRINOLOGY, 25:15-31, JAN 2011
abstract, full text, DOI:10.1210/me.2010-0202

Chan, Henry; Kral, Petr
Self-standing nanoparticle membranes and capsules
NANOSCALE, 3:1881-1886, 2011
abstract, full text, DOI:10.1039/c0nr00912a

Chakrapani, Sudha; Cordero-Morales, Julio F.; Jogini, Vishwanath; Pan, Albert C.; Cortes, D. Marien; Roux, Benoit; Perozo, Eduardo
On the structural basis of modal gating behavior in K+ channels
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 18:67-+, JAN 2011
abstract, full text, DOI:10.1038/nsmb.1968

Pazos, Elena; Perez, Miguel; Gutierrez-de-Teran, Hugo; Orzaez, Mar; Guevara, Tatiana; Mascarenas, Jose L.; Eugenio Vazquez, M.
Rational design of a cyclin A fluorescent peptide sensor
ORGANIC & BIOMOLECULAR CHEMISTRY, 9:7629-7632, 2011
abstract, full text, DOI:10.1039/c1ob06009k

Gubbins, Keith E.; Liu, Ying-Chun; Moore, Joshua D.; Palmer, Jeremy C.
The role of molecular modeling in confined systems: impact and prospects
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:58-85, 2011
abstract, full text, DOI:10.1039/c0cp01475c

Wang, Teng; Shao, Xueguang; Cai, Wensheng; Xue, Yonglai; Wang, Shuai; Feng, Xizeng
Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1140-1151, 2011
abstract, full text, DOI:10.1039/c0cp00678e

Jiang, Jun; Mukamel, Shaul
Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:2394-2400, 2011
abstract, full text, DOI:10.1039/c0cp02047h

Bernini, Caterina; Pogni, Rebecca; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Basosia, Riccardo; Sinicropi, Adalgisa
EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:5078-5098, 2011
abstract, full text, DOI:10.1039/c0cp02151b

Chen, L. Y.
Exploring the free-energy landscapes of biological systems with steered molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6176-6183, 2011
abstract, full text, DOI:10.1039/c0cp02799e

Guest, Will C.; Cashman, Neil R.; Plotkin, Steven S.
A theory for the anisotropic and inhomogeneous dielectric properties of proteins
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6286-6295, 2011
abstract, full text, DOI:10.1039/c0cp02061c

Venturini, Alessandro; Zerbetto, Francesco
Dynamics of a lipid bilayer induced by electric fields
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9216-9222, 2011
abstract, full text, DOI:10.1039/c1cp20322c

Suyetin, Mikhail V.; Vakhrushev, Alexander V.
Nanocapsule with pump for methane storage
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9863-9870, 2011
abstract, full text, DOI:10.1039/c0cp01072c

Revilla-Lopez, Guillem; Torras, Juan; Nussinov, Ruth; Aleman, Carlos; Zanuy, David
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9986-9994, 2011
abstract, full text, DOI:10.1039/c0cp02572k

Deplazes, Evelyne; Jayatilaka, Dylan; Corry, Ben
Testing the use of molecular dynamics to simulate fluorophore motions and FRET
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11045-11054, 2011
abstract, full text, DOI:10.1039/c1cp20447e

Kawashima, Yukio; Nakano, Haruyuki; Jung, Jaewoon; Ten-no, Seiichiro
A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11731-11738, 2011
abstract, full text, DOI:10.1039/c1cp20438f

Wang, Qiuming; Shah, Nilam; Zhao, Jun; Wang, Chengshan; Zhao, Chao; Liu, Lingyun; Li, Lingyan; Zhou, Feimeng; Zheng, Jie
Structural, morphological, and kinetic studies of beta-amyloid peptide aggregation on self-assembled monolayers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15200-15210, 2011
abstract, full text, DOI:10.1039/c1cp21156k

Yamamoto, Takenori; Ohnishi, Shuhei
Molecular dynamics study on helium nanobubbles in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:16142-16145, 2011
abstract, full text, DOI:10.1039/c1cp22018g

Reith, Daniel; Mirny, Leonid; Virnau, Peter
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT, Issue 191, 135-145, 2011
abstract, full text

Romo, Tod D.; Grossfield, Alan
Validating and improving elastic network models with molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:23-34, JAN 2011
abstract, full text, DOI:10.1002/prot.22855

Mustafa, Morad; Mirza, Amar; Kannan, Natarajan
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:99-114, JAN 2011
abstract, full text, DOI:10.1002/prot.22862

Banu, Mihaela; Patriche, Simona; Coman, Malina; Matsushita, S.; Tofan, Alice; Epureanu, A.
Investigation of ubiquitin deformation mechanism under induced stretch-compression loads
ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY, 52:449-454, 2011
abstract, full text

Lyubartsev, Alexander P.; Rabinovich, Alexander L.
Recent development in computer simulations of lipid bilayers
SOFT MATTER, 7:25-39, 2011
abstract, full text, DOI:10.1039/c0sm00457j

Sun, Sheng; Wong, Joseph T. Y.; Zhang, Tong-Yi
Molecular dynamics simulations of phase transition of lamellar lipid membrane in water under an electric field
SOFT MATTER, 7:147-152, 2011
abstract, full text, DOI:10.1039/c0sm00555j

Feng, Jie; Pandey, Ras B.; Berry, Rajiv J.; Farmer, Barry L.; Naik, Rajesh R.; Heinz, Hendrik
Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
SOFT MATTER, 7:2113-2120, 2011
abstract, full text, DOI:10.1039/c0sm01118e

Arce, Fernando Teran; Jang, Hyunbum; Ramachandran, Srinivasan; Landon, Preston B.; Nussinov, Ruth; Lal, Ratnesh
Polymorphism of amyloid beta peptide in different environments: implications for membrane insertion and pore formation
SOFT MATTER, 7:5267-5273, 2011
abstract, full text, DOI:10.1039/c1sm05162h

Shinoda, Wataru; DeVane, Russell; Klein, Michael L.
Coarse-grained force field for ionic surfactants
SOFT MATTER, 7:6178-6186, 2011
abstract, full text, DOI:10.1039/c1sm05173c

Teixeira-Dias, Bruno; Zanuy, David; Poater, Jordi; Sola, Miquel; Estrany, Francesc; del Valle, Luis J.; Aleman, Carlos
Binding of 6-mer single-stranded homo-nucleotides to poly(3,4-ethylenedioxythiophene): specific hydrogen bonds with guanine
SOFT MATTER, 7:9922-9932, 2011
abstract, full text, DOI:10.1039/c1sm05856h

Castelletto, V.; Moulton, C. M.; Cheng, G.; Hamley, I. W.; Hicks, Matthew R.; Rodger, Alison; Lopez-Perez, Daniel E.; Revilla-Lopez, Guillermo; Aleman, Carlos
Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif
SOFT MATTER, 7:11405-11415, 2011
abstract, full text, DOI:10.1039/c1sm06550e

Wang, Yong; Dewdney, Tamaria G.; Liu, Zhigang; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Kovari, Ladislau C.
X-RAY CRYSTAL STRUCTURE AND DYNAMICS REVEAL HIV-1 PROTEASE DRUG INTERACTIONS
STUDIA UNIVERSITATIS BABES-BOLYAI CHEMIA, 56:221-230, 2011
abstract, full text

Andriichenko, N.N.; Khrenova, M.G.; Nemukhin, A.V.; Grigorenko, B.L.
Modeling Mechanism of Hydrolysis Reactions of the Cyclic Guanosine Monophosphates in Aqueous Solution
Vestnik Moskovskogo universiteta. Seriya 2: Khimiya, 52:277-280, 2011
abstract, full text

Zhang, Minhua; Lue, Shouqin; Li, Guowei; Mao, Zhilei; Yu, Xin; Sun, Weining; Tang, Zhangcheng; Long, Mian; Su, Weiai
Identification of a Residue in Helix 2 of Rice Plasma Membrane Intrinsic Proteins That Influences Water Permeability
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:41982-41992, DEC 31 2010
abstract, full text, DOI:10.1074/jbc.M110.101790

Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip; Polonsky, Stas; Stolovitzky, Gustavo; Martyna, Glenn
Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:17172-17176, DEC 30 2010
abstract, full text, DOI:10.1021/jp108865q

Neumann, Anna; Baginski, Maciej; Czub, Jacek
How Do Sterols Determine the Antifungal Activity of Amphotericin B? Free Energy of Binding between the Drug and Its Membrane Targets
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:18266-18272, DEC 29 2010
abstract, full text, DOI:10.1021/ja1074344

Jia Xuebing; Zhang Jun; Sun Hongwei; Chen Lan; Shen Rongxin; Lai Chengming
Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception
ACTA CHIMICA SINICA, 68:2500-2508, DEC 28 2010
abstract, full text

Buch, Idit; Fishelovitch, Dan; London, Nir; Raveh, Barak; Wolfson, Haim J.; Nussinov, Ruth
Allosteric Regulation of Glycogen Synthase Kinase 3 beta: A Theoretical Study
BIOCHEMISTRY, 49:10890-10901, DEC 28 2010
abstract, full text, DOI:10.1021/bi100822q

Jones, Martin K.; Zhang, Lei; Catte, Andrea; Li, Ling; Oda, Michael N.; Ren, Gang; Segrest, Jere P.
Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:41161-41171, DEC 24 2010
abstract, full text, DOI:10.1074/jbc.M110.187799

Kaminski, Steve; Mroginski, Maria Andrea
Molecular Dynamics of Phycocyanobilin Binding Bacteriophytochromes: A Detailed Study of Structural and Dynamic Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16677-16686, DEC 23 2010
abstract, full text, DOI:10.1021/jp104903u

Patapati, Kalliopi K.; Glykos, Nicholas M.
Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
PLOS ONE, 5 Art. No. e15290, DEC 20 2010
abstract, full text, DOI:10.1371/journal.pone.0015290

Kim, Taekyung; Cooper, John A.; Sept, David
The Interaction of Capping Protein with the Barbed End of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 404:794-802, DEC 17 2010
abstract, full text, DOI:10.1016/j.jmb.2010.10.017

Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Capone, Ricardo; Lal, Ratnesh; Nussinov, Ruth
beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels
JOURNAL OF MOLECULAR BIOLOGY, 404:917-934, DEC 17 2010
abstract, full text, DOI:10.1016/j.jmb.2010.10.025

DeVane, Russell; Jusufi, Arben; Shinoda, Wataru; Chiu, Chi-cheng; Nielsen, Steven O.; Moore, Preston B.; Klein, Michael L.
Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16364-16372, DEC 16 2010
abstract, full text, DOI:10.1021/jp1070264

Du, Hongbo; Wickramasinghe, Ranil; Qian, Xianghong
Effects of Salt on the Lower Critical Solution Temperature of Poly (N-Isopropylacrylamide)
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16594-16604, DEC 16 2010
abstract, full text, DOI:10.1021/jp105652c

Watanabe, Akira; Choe, Seungho; Chaptal, Vincent; Rosenberg, John M.; Wright, Ernest M.; Grabe, Michael; Abramson, Jeff
The mechanism of sodium and substrate release from the binding pocket of vSGLT
NATURE, 468:988-U162, DEC 16 2010
abstract, full text, DOI:10.1038/nature09580

Turgut, Deniz; Atilgan, Ali Rana; Atilgan, Canan
Assortative Mixing in Close-Packed Spatial Networks
PLOS ONE, 5 Art. No. e15551, DEC 16 2010
abstract, full text, DOI:10.1371/journal.pone.0015551

Chen, Ke; Eargle, John; Sarkar, Krishnarjun; Gruebele, Martin; Luthey-Schulten, Zaida
Functional Role of Ribosomal Signatures
BIOPHYSICAL JOURNAL, 99:3930-3940, DEC 15 2010
abstract, full text, DOI:10.1016/j.bpj.2010.09.062

Kaila, Ville R. I.; Johansson, Mikael P.; Sundholm, Dage; Wikstroem, Marten
Interheme electron tunneling in cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:21470-21475, DEC 14 2010
abstract, full text, DOI:10.1073/pnas.1005889107

Mirza, Amar; Mustafa, Morad; Talevich, Eric; Kannan, Natarajan
Co-Conserved Features Associated with cis Regulation of ErbB Tyrosine Kinases
PLOS ONE, 5 Art. No. e14310, DEC 13 2010
abstract, full text, DOI:10.1371/journal.pone.0014310

Carnevale, Vincenzo; Fiorin, Giacomo; Levine, Benjamin G.; DeGrado, William F.; Klein, Michael L.
Multiple Proton Confinement in the M2 Channel from the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20856-20863, DEC 9 2010
abstract, full text, DOI:10.1021/jp107431g

Nonella, Marco; Seeger, Stefan
Monitoring peptide-surface interaction by means of molecular dynamics simulation
CHEMICAL PHYSICS, 378:73-81, DEC 9 2010
abstract, full text, DOI:10.1016/j.chemphys.2010.10.005

Davis, William B.; Bjorklund, Chad C.; Cho, Paul S.
Hole Transport Dynamics in Mixed Sequence DNA Can Vary with Salt Concentration: An Experimental and Theoretical Analysis
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20821-20833, DEC 9 2010
abstract, full text, DOI:10.1021/jp107191m

Lue, Shouqin; Zhang, Yan; Long, Mian
Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations
PLOS ONE, 5 Art. No. e15417, DEC 8 2010
abstract, full text, DOI:10.1371/journal.pone.0015417

Xiao, Fei; Weng, Jingwei; Fan, Kangnian; Wang, Wenning
Mechanism of Ser88 Phosphorylation-Induced Dimer Dissociation in Dynein Light Chain LC8
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15663-15672, DEC 2 2010
abstract, full text, DOI:10.1021/jp1048869

Gao, Meng; She, Zhen-Su; Zhou, Ruhong
Key Residues that Play a Critical Role in Urea-Induced Lysozyme Unfolding
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15687-15693, DEC 2 2010
abstract, full text, DOI:10.1021/jp1052453

Sawada, Toshihiko; Fedorov, Dmitri G.; Kitaura, Kazuo
Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15700-15705, DEC 2 2010
abstract, full text, DOI:10.1021/jp1068895

Papadopoulos, G.; Grigoroudis, A. I.; Kyriakidis, D. A.
Dimerization of the AtoC response regulator and modelling of its binding to DNA
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:565-572, DEC 2010
abstract, full text, DOI:10.1016/j.jmgm.2010.10.004

Tipmanee, Varomyalin; Oberhofer, Harald; Park, Mina; Kim, Kwang S.; Blumberger, Jochen
Prediction of Reorganization Free Energies for Biological Electron Transfer: A Comparative Study of Ru-Modified Cytochromes and a 4-Helix Bundle Protein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:17032-17040, DEC 1 2010
abstract, full text, DOI:10.1021/ja107876p

Menz, William J.; Penna, Matthew J.; Biggs, Mark J.
TNAMD: Implementation of TIGER2 in NAMD
COMPUTER PHYSICS COMMUNICATIONS, 181:2082-2085, DEC 2010
abstract, full text, DOI:10.1016/j.cpc.2010.09.011

Shaikh, Saher Afshan; Wen, Po-Chao; Enkavi, Giray; Huang, Zhijian; Tajkhorshid, Emad
Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2481-2500, DEC 2010
abstract, full text, DOI:10.1166/jctn.2010.1636

Lee, One-Sun; Schatz, George C.
Conformation of DNA Between Gold Surfaces
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2568-2573, DEC 2010
abstract, full text, DOI:10.1166/jctn.2010.1643

Hu, Guodong; Chen, L. Y.
In silico experiments of single-chain antibody fragment against drugs of abuse
BIOPHYSICAL CHEMISTRY, 153:97-103, DEC 2010
abstract, full text, DOI:10.1016/j.bpc.2010.10.008

Janosi, Lorant; Gorfe, Alemayehu A.
Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras
BIOPHYSICAL JOURNAL, 99:3666-3674, DEC 1 2010
abstract, full text, DOI:10.1016/j.bpj.2010.10.031

Wieden, Hans Joachim; Mercier, Evan; Gray, John; Steed, Brett; Yawney, Davis
A Combined Molecular Dynamics and Rapid Kinetics Approach to Identify Conserved Three-Dimensional Communication Networks in Elongation Factor Tu
BIOPHYSICAL JOURNAL, 99:3735-3743, DEC 1 2010
abstract, full text, DOI:10.1016/j.bpj.2010.10.013

Kaila, Ville R. I.; Verkhovsky, Michael I.; Wikstrom, Marten
Proton-Coupled Electron Transfer in Cytochrome Oxidase
CHEMICAL REVIEWS, 110:7062-7081, DEC 2010
full text, DOI:10.1021/cr1002003

Salsbury, Freddie R., Jr.
Molecular dynamics simulations of protein dynamics and their relevance to drug discovery
CURRENT OPINION IN PHARMACOLOGY, 10:738-744, DEC 2010
abstract, full text, DOI:10.1016/j.coph.2010.09.016

Matsushita, Shinji; Adachi, Taiji; Inoue, Yasuhiro; Hojo, Masaki; Sokabe, Masahiro
Evaluation of extensional and torsional stiffness of single actin filaments by molecular dynamics analysis
JOURNAL OF BIOMECHANICS, 43:3162-3167, DEC 1 2010
abstract, full text, DOI:10.1016/j.jbiomech.2010.07.022

Bhargavi, K.; Chaitanya, P. Kalyan; Ramasree, D.; Vasavi, M.; Murthy, D. K.; Uma, V.
Homology Modeling and Docking Studies of Human Bcl-2L10 Protein
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:379-391, DEC 2010
abstract, full text

Jimenez, Veronica A.
Quantum-Chemical Study on the Bioactive Conformation of Epothilones
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:2176-2190, DEC 2010
abstract, full text, DOI:10.1021/ci1003416

Illingworth, Christopher J. R.; Furini, Simone; Domene, Carmen
Computational Studies on Polarization Effects and Selectivity in K+ Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3780-3792, DEC 2010
abstract, full text, DOI:10.1021/ct100276c

Banas, Pavel; Hollas, Daniel; Zgarbova, Marie; Jurecka, Petr; Orozco, Modesto; Cheatham, Thomas E., I.I.I.; Sponer, Jiri; Otyepka, Michal
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3836-3849, DEC 2010
abstract, full text, DOI:10.1021/ct100481h

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang
vmdICE: A Plug-In for Rapid Evaluation of Molecular Dynamics Simulations using VMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2868-2873, DEC 2010
abstract, full text, DOI:10.1002/jcc.21581

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto
How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations
JOURNAL OF MOLECULAR MODELING, 16:1845-1851, DEC 2010
abstract, full text, DOI:10.1007/s00894-010-0687-7

Dominguez, M.; Rezende, M. Caroli
The Cationic Halochromism of Phenolate Betaines: Molecular Dynamics and Quantum Mechanics Studies
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 7:995-1003, DEC 2010
abstract, full text

Oliveira, A. F.; Gemming, S.; Seifert, G.
Molecular dynamics simulations of BMP-2 adsorption on a hydrophobic surface
MATERIALWISSENSCHAFT UND WERKSTOFFTECHNIK, 41:1048-1053, DEC 2010
abstract, full text, DOI:10.1002/mawe.201000707

Morcos, Faruck; Chatterjee, Santanu; McClendon, Christopher L.; Brenner, Paul R.; Lopez-Rendon, Roberto; Zintsmaster, John; Ercsey-Ravasz, Maria; Sweet, Christopher R.; Jacobson, Matthew P.; Peng, Jeffrey W.; Izaguirre, Jesus A.
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1001015, DEC 2010
abstract, full text, DOI:10.1371/journal.pcbi.1001015

Vogler, Christine; Huber, Claudia; Waldmann, Tanja; Ettig, Ramona; Braun, Lora; Izzo, Annalisa; Daujat, Sylvain; Chassignet, Isabelle; Joaquin Lopez-Contreras, Andres; Fernandez-Capetillo, Oscar; Dundr, Miroslav; Rippe, Karsten; Laengst, Gernot; Schneider, Robert
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
PLOS GENETICS, 6 Art. No. e1001234, DEC 2010
abstract, full text, DOI:10.1371/journal.pgen.1001234

Shafrir, Yinon; Durell, Stewart R.; Anishkin, Andriy; Guy, H. Robert
Beta-barrel models of soluble amyloid beta oligomers and annular protofibrils
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:3458-3472, DEC 2010
abstract, full text, DOI:10.1002/prot.22832

Tuukkanen, Anne; Huang, Bingding; Henschel, Andreas; Stewart, Francis; Schroeder, Michael
Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking
PROTEOMICS, 10:4186-4195, DEC 2010
abstract, full text, DOI:10.1002/pmic.201000283

Megow, Joerg; Kulesza, Alexander; Qu, Zheng-wang; Ronneberg, Thomas; Bonacic-Koutecky, Vlasta; May, Volkhard
A harmonic approximation of intramolecular vibrations in a mixed quantum-classical methodology: Linear absorbance of a dissolved Pheophorbid-a molecule as an example
CHEMICAL PHYSICS, 377:10-14, NOV 25 2010
abstract, full text, DOI:10.1016/j.chemphys.2010.08.008

Shi, Wei; Sorescu, Dan C.
Molecular Simulations of CO2 and H-2 Sorption into Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][Tf2N]) Confined in Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15029-15041, NOV 25 2010
abstract, full text, DOI:10.1021/jp106500p

Furlan, Sara; Hureau, Christelle; Faller, Peter; La Penna, Giovanni
Modeling the Cu+ Binding in the 1-16 Region of the Amyloid-beta Peptide Involved in Alzheimer's Disease
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15119-15133, NOV 25 2010
abstract, full text, DOI:10.1021/jp102928h

Li, Jinghua; Du, Likai; Wang, Lushan
Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15261-15268, NOV 25 2010
abstract, full text, DOI:10.1021/jp1064177

Wang, Wei; Castelan-Vega, Juan A.; Jimenez-Alberto, Alicia; Vassell, Russell; Ye, Zhiping; Weiss, Carol D.
A mutation in the receptor binding site enhances infectivity of 2009 H1N1 influenza hemagglutinin pseudotypes without changing antigenicity
VIROLOGY, 407:374-380, NOV 25 2010
abstract, full text, DOI:10.1016/j.virol.2010.08.027

McIntyre, Neil R.; Lowe, Edward W., Jr.; Belof, Jonathan L.; Ivkovic, Milena; Shafer, Jacob; Space, Brian; Merkler, David J.
Evidence for Substrate Preorganization in the Peptidylglycine alpha-Amidating Monooxygenase Reaction Describing the Contribution of Ground State Structure to Hydrogen Tunneling
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16393-16402, NOV 24 2010
abstract, full text, DOI:10.1021/ja1019194

Cheng, Mary Hongying; Coalson, Rob D.; Tang, Pei
Molecular Dynamics and Brownian Dynamics Investigation of Ion Permeation and Anesthetic Halothane Effects on a Proton-Gated Ion Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16442-16449, NOV 24 2010
abstract, full text, DOI:10.1021/ja105001a

Gnanasambandan, Kavitha; Magis, Andrew; Sayeski, Peter P.
The Constitutive Activation of Jak2-V617F Is Mediated by a pi Stacking Mechanism Involving Phenylalanines 595 and 617
BIOCHEMISTRY, 49:9972-9984, NOV 23 2010
abstract, full text, DOI:10.1021/bi1014858

Ma, Buyong; Nussinov, Ruth
Polymorphic C-terminal beta-Sheet Interactions Determine the Formation of Fibril or Amyloid beta-derived Diffusible Ligand-like Globulomer for the Alzheimer A beta 42 Dodecamer
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:37102-37110, NOV 19 2010
abstract, full text, DOI:10.1074/jbc.M110.133488

Kim, Youngchang; Zhou, Min; Moy, Shiu; Morales, Jennifer; Cunningham, Mark A.; Joachimiak, Andrzej
High-Resolution Structure of the Nitrile Reductase QueF Combined with Molecular Simulations Provide Insight into Enzyme Mechanism
JOURNAL OF MOLECULAR BIOLOGY, 404:127-137, NOV 19 2010
abstract, full text, DOI:10.1016/j.jmb.2010.09.042

Jin, Shengye; Snoeberger, Robert C., I.I.I.; Issac, Abey; Stockwell, David; Batista, Victor S.; Lian, Tianquan
Single-Molecule Interfacial Electron Transfer in Donor-Bridge-Nanoparticle Acceptor Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14309-14319, NOV 18 2010
abstract, full text, DOI:10.1021/jp911662g

da Silva, Robson; Rego, Luis G. C.; Freire, Jose A.; Rodriguez, Javier; Laria, Daniel; Batista, Victor S.
Study of Redox Species and Oxygen Vacancy Defects at TiO2-Electrolyte Interfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 114:19433-19442, NOV 18 2010
abstract, full text, DOI:10.1021/jp107385e

Law, Ruby H. P.; Lukoyanova, Natalya; Voskoboinik, Ilia; Caradoc-Davies, Tom T.; Baran, Katherine; Dunstone, Michelle A.; D'Angelo, Michael E.; Orlova, Elena V.; Coulibaly, Fasseli; Verschoor, Sandra; Browne, Kylie A.; Ciccone, Annette; Kuiper, Michael J.; Bird, Phillip I.; Trapani, Joseph A.; Saibil, Helen R.; Whisstock, James C.
The structural basis for membrane binding and pore formation by lymphocyte perforin
NATURE, 468:447-U277, NOV 18 2010
abstract, full text, DOI:10.1038/nature09518

Trylska, Joanna
Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome
JOURNAL OF PHYSICS-CONDENSED MATTER, 22 Art. No. 453101, NOV 17 2010
abstract, full text, DOI:10.1088/0953-8984/22/45/453101

Jolley, Craig C.; Douglas, Trevor
Ion Accumulation in a Protein Nanocage: Finding Noisy Temporal Sequences Using a Genetic Algorithm
BIOPHYSICAL JOURNAL, 99:3385-3393, NOV 17 2010
abstract, full text, DOI:10.1016/j.bpj.2010.09.001

Gangupomu, Vamshi K.; Abrams, Cameron F.
All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics
BIOPHYSICAL JOURNAL, 99:3438-3444, NOV 17 2010
abstract, full text, DOI:10.1016/j.bpj.2010.09.054

Weis, Felix; Bron, Patrick; Giudice, Emmanuel; Rolland, Jean-Paul; Thomas, Daniel; Felden, Brice; Gillet, Reynald
tmRNA-SmpB: a journey to the centre of the bacterial ribosome
EMBO JOURNAL, 29:3810-3818, NOV 17 2010
abstract, full text, DOI:10.1038/emboj.2010.252

Fu, Jie; Hashem, Yaser; Wower, Iwona; Lei, Jianlin; Liao, Hstau Y.; Zwieb, Christian; Wower, Jacek; Frank, Joachim
Visualizing the transfer-messenger RNA as the ribosome resumes translation
EMBO JOURNAL, 29:3819-3825, NOV 17 2010
abstract, full text, DOI:10.1038/emboj.2010.255

Anishkin, A.; Akitake, B.; Kamaraju, K.; Chiang, C.-.S.; Sukharev, S.
Hydration properties of mechanosensitive channel pores define the energetics of gating
JOURNAL OF PHYSICS-CONDENSED MATTER, 22 Art. No. 454120, NOV 17 2010
abstract, full text, DOI:10.1088/0953-8984/22/45/454120

Luan, Binquan; Aksimentiev, Aleksei
Control and reversal of the electrophoretic force on DNA in a charged nanopore
JOURNAL OF PHYSICS-CONDENSED MATTER, 22 Art. No. 454123, NOV 17 2010
abstract, full text, DOI:10.1088/0953-8984/22/45/454123

Zwolak, Michael; Wilson, James; Di Ventra, Massimiliano
Dehydration and ionic conductance quantization in nanopores
JOURNAL OF PHYSICS-CONDENSED MATTER, 22 Art. No. 454126, NOV 17 2010
abstract, full text, DOI:10.1088/0953-8984/22/45/454126

Demerdash, Omar N. A.; Buyan, Amanda; Mitchell, Julie C.
ReplicOpter: A replicate optimizer for flexible docking
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:3156-3165, NOV 15 2010
abstract, full text, DOI:10.1002/prot.22811

Llop-Tous, Immaculada; Madurga, Sergio; Giralt, Ernest; Marzabal, Pablo; Torrent, Margarita; Ludevid, M. Dolors
Relevant Elements of a Maize gamma-Zein Domain Involved in Protein Body Biogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:35633-35644, NOV 12 2010
abstract, full text, DOI:10.1074/jbc.M110.116285

Halder, Sukanya; Bhattacharyya, Dhananjay
Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14028-14040, NOV 11 2010
abstract, full text, DOI:10.1021/jp102835t

Meyer, Tim; D'Abramo, Marco; Hospital, Adam; Rueda, Manuel; Ferrer-Costa, Carles; Perez, Alberto; Carrillo, Oliver; Camps, Jordi; Fenollosa, Caries; Repchevsky, Dmitry; Lluis Gelpi, Josep; Orozco, Modesto
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
STRUCTURE, 18:1399-1409, NOV 10 2010
abstract, full text, DOI:10.1016/j.str.2010.07.013

Kim, HyeongJun; Hsin, Jen; Liu, Yanxin; Selvin, Paul R.; Schulten, Klaus
Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain
STRUCTURE, 18:1443-1449, NOV 10 2010
abstract, full text, TCBG publications, DOI:10.1016/j.str.2010.09.011

Kalantari-Nejad, R.; Bahrami, M.; Rafii-Tabar, H.; Rungger, I.; Sanvito, S.
Computational modeling of a carbon nanotube-based DNA nanosensor
NANOTECHNOLOGY, 21 Art. No. 445501, NOV 5 2010
abstract, full text, DOI:10.1088/0957-4484/21/44/445501

Lupieri, Paola; Ippoliti, Emiliano; Altoe, Piero; Garavelli, Marco; Mwalaba, M.; Carloni, Paolo
Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car-Parrinello and TDDFT/CASPT2 Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3403-3409, NOV 2010
abstract, full text, DOI:10.1021/ct100384f

Shu, Dan; Zhang, Hui; Petrenko, Roman; Meller, Jarek; Guo, Peixuan
Dual-Channel Single-Molecule Fluorescence Resonance Energy Transfer to Establish Distance Parameters for RNA Nanoparticles
ACS NANO, 4:6843-6853, NOV 2010
abstract, full text, DOI:10.1021/nn1014853

Kuhn, Misty L.; Figueroa, Carlos M.; Aleanzi, Mabel; Olsen, Kenneth W.; Iglesias, Alberto A.; Ballicora, Miguel A.
Bi-National and Interdisciplinary Course in Enzyme Engineering
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 38:370-379, NOV-DEC 2010
abstract, full text, DOI:10.1002/bmb.20438

Karachevtsev, V. A.; Plokhotnichenko, A. M.; Karachevtsev, M. V.; Leontiev, V. S.
Decrease of carbon nanotube UV light absorption induced by pi-pi-stacking interaction with nucleotide bases
CARBON, 48:3682-3691, NOV 2010
abstract, full text, DOI:10.1016/j.carbon.2010.06.009

Urreizti, R.; Moya-Garcia, A. A.; Pino-Angeles, A.; Cozar, M.; Langkilde, A.; Fanhoe, U.; Esteves, C.; Arribas, J.; Vilaseca, M. A.; Perez-Duenas, B.; Pineda, M.; Gonzalez, V.; Artuch, R.; Baldellou, A.; Vilarinho, L.; Fowler, B.; Ribes, A.; Sanchez-Jimenez, F.; Grinberg, D.; Balcells, S.
Molecular characterization of five patients with homocystinuria due to severe methylenetetrahydrofolate reductase deficiency
CLINICAL GENETICS, 78:441-448, NOV 2010
abstract, full text, DOI:10.1111/j.1399-0004.2010.01391.x

Rosales-Hernandez, Martha C.; Mendieta-Wejebe, Jessica E.; Trujillo-Ferrara, Jose G.; Correa-Basurto, Jose
Homology modeling and molecular dynamics of CYP1A1 and CYP2B1 to explore the metabolism of aryl derivatives by docking and experimental assays
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:4845-4855, NOV 2010
abstract, full text, DOI:10.1016/j.ejmech.2010.07.055

Bhatele, Abhinav; Wesolowski, Lukasz; Bohm, Eric; Solomonik, Edgar; Kale, Laxmikant V.
Understanding Application Performance via Micro-benchmarks on Three Large Supercomputers: Intrepid, Ranger and Jaguar
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 24:411-427, NOV 2010
abstract, full text, DOI:10.1177/1094342010370603

Wang, Qi; Mach, Robert H.; Luedtke, Robert R.; Reichert, David E.
Subtype Selectivity of Dopamine Receptor Ligands: Insights from Structure and Ligand-Based Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1970-1985, NOV 2010
abstract, full text, DOI:10.1021/ci1002747

Wereszczynski, Jeff; McCammon, J. Andrew
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3285-3292, NOV 2010
abstract, full text, DOI:10.1021/ct100322t

Musiani, Francesco; Bertosa, Branimir; Magistrato, Alessandra; Zambelli, Barbara; Turano, Paola; Losasso, Valeria; Micheletti, Cristian; Ciurli, Stefano; Carloni, Paolo
Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3503-3515, NOV 2010
abstract, full text, DOI:10.1021/ct900635z

Lugli, Francesca; Toschi, Francesca; Biscarini, Fabio; Zerbetto, Francesco
Electric Field Effects on Short Fibrils of A beta Amyloid Peptides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3516-3526, NOV 2010
abstract, full text, DOI:10.1021/ct1001335

Arcisio-Miranda, Manoel; Muroi, Yukiko; Chowdhury, Sandipan; Chanda, Baron
Molecular mechanism of allosteric modification of voltage-dependent sodium channels by local anesthetics
JOURNAL OF GENERAL PHYSIOLOGY, 136:541-554, NOV 2010
abstract, full text, DOI:10.1085/jgp.201010438

Hsu, Cheng-Kuo; Park, Sheldon
Computational and mutagenesis studies of the streptavidin native dimer interface
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:295-308, NOV 2010
abstract, full text, DOI:10.1016/j.jmgm.2010.09.009

Imai, Yosuke; Liu, Xinli; Yamagishi, Junya; Mori, Kenichi; Neya, Saburo; Hoshino, Tyuji
Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:461-469, NOV 2010
abstract, full text, DOI:10.1016/j.jmgm.2010.09.002

Duddela, Srikanth; Sekhar, P. Nataraj; Padmavati, G. V.; Banerjee, Amit Kumar; Murty, U. S. N.
Probing the structure of human glucose transporter 2 and analysis of protein ligand interactions
MEDICINAL CHEMISTRY RESEARCH, 19:836-853, NOV 2010
abstract, full text, DOI:10.1007/s00044-009-9234-4

Bauer, Amy L.; Hlavacek, William S.; Unkefer, Pat J.; Mu, Fangping
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1001007, NOV 2010
abstract, full text, DOI:10.1371/journal.pcbi.1001007

Fatmi, M. Qaiser; Chang, Chia-en A.
The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000994, NOV 2010
abstract, full text, DOI:10.1371/journal.pcbi.1000994

Fu, Yi; Ding, Yanrui; Chen, Zhiguo; Sun, Jun; Fang, Wei; Xu, Wenbo
Study on the Relationship Between Cyclodextrin Glycosyltransferase Thermostability and Salt Bridge Formation by Molecular Dynamics Simulation
PROTEIN AND PEPTIDE LETTERS, 17:1403-1411, NOV 2010
abstract, full text

Kashif Sadiq, S.; De Fabritiis, Gianni
Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2873-2885, NOV 1 2010
abstract, full text, DOI:10.1002/prot.22806

Zhmurov, A.; Dima, R. I.; Kholodov, Y.; Barsegov, V.
SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2984-2999, NOV 1 2010
abstract, full text, DOI:10.1002/prot.22824

Shukla, Diwakar; Trout, Bernhardt L.
Interaction of Arginine with Proteins and the Mechanism by Which It Inhibits Aggregation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13426-13438, OCT 28 2010
abstract, full text, DOI:10.1021/jp108399g

Xia, Zhen; Gardner, David Paul; Gutell, Robin R.; Ren, Pengyu
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13497-13506, OCT 28 2010
abstract, full text, DOI:10.1021/jp104926t

Rogaski, Brent; Lim, Joseph B.; Klauda, Jeffery B.
Sterol Binding and Membrane Lipid Attachment to the Osh4 Protein of Yeast
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13562-13573, OCT 28 2010
abstract, full text, DOI:10.1021/jp106890e

Dolores Elola, M.; Rodriguez, Javier; Laria, Daniel
Structure and dynamics of liquid methanol confined within functionalized silica nanopores
JOURNAL OF CHEMICAL PHYSICS, 133 Art. No. 154707, OCT 21 2010
abstract, full text, DOI:10.1063/1.3503886

Issa, Zeena K.; Manke, Charles W.; Jena, Bhanu P.; Potoff, Jeffrey J.
Ca2+ Bridging of Apposed Phospholipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13249-13254, OCT 21 2010
abstract, full text, DOI:10.1021/jp105781z

Dalhaimer, Paul; Pollard, Thomas D.
Molecular Dynamics Simulations of Arp2/3 Complex Activation
BIOPHYSICAL JOURNAL, 99:2568-2576, OCT 20 2010
abstract, full text, DOI:10.1016/j.bpj.2010.08.027

Feig, Michael; Burton, Zachary F.
RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation
BIOPHYSICAL JOURNAL, 99:2577-2586, OCT 20 2010
abstract, full text, DOI:10.1016/j.bpj.2010.08.010

Teif, Vladimir B.; Ettig, Ramona; Rippe, Karsten
A Lattice Model for Transcription Factor Access to Nucleosomal DNA
BIOPHYSICAL JOURNAL, 99:2597-2607, OCT 20 2010
abstract, full text, DOI:10.1016/j.bpj.2010.08.019

Kokhan, Oleksandr; Wraight, Colin A.; Tajkhorshid, Emad
The Binding Interface of Cytochrome c and Cytochrome c(1) in the bc(1) Complex: Rationalizing the Role of Key Residues
BIOPHYSICAL JOURNAL, 99:2647-2656, OCT 20 2010
abstract, full text, DOI:10.1016/j.bpj.2010.08.042

Elli, Stefano; Eusebio, Lidia; Gronchi, Paolo; Ganazzoli, Fabio; Goisis, Marco
Modeling the Adsorption Behavior of Linear End-Functionalized Poly(ethylene glycol) on an Ionic Substrate by a Coarse-Grained Monte Carlo Approach
LANGMUIR, 26:15814-15823, OCT 19 2010
abstract, full text, DOI:10.1021/1a102962z

Kubiak-Ossowska, Karina; Mulheran, Paul A.
Mechanism of Hen Egg White Lysozyme Adsorption on a Charged Solid Surface
LANGMUIR, 26:15954-15965, OCT 19 2010
abstract, full text, DOI:10.1021/la102960m

Iturrioz, Xavier; Gerbier, Romain; Leroux, Vincent; Alvear-Perez, Rodrigo; Maigret, Bernard; Llorens-Cortes, Catherine
By Interacting with the C-terminal Phe of Apelin, Phe(255) and Trp(259) in Helix VI of the Apelin Receptor Are Critical for Internalization
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:32627-32637, OCT 15 2010
abstract, full text, DOI:10.1074/jbc.M110.127167

Calandrini, Vania; Abergel, Daniel; Kneller, Gerald R.
Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment
JOURNAL OF CHEMICAL PHYSICS, 133 Art. No. 145101, OCT 14 2010
abstract, full text, DOI:10.1063/1.3486195

Cerutti, David S.; Freddolino, Peter L.; Duke, Robert E., Jr.; Case, David A.
Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12811-12824, OCT 14 2010
abstract, full text, DOI:10.1021/jp105813j

Bonomi, Massimiliano; Barducci, Alessandro; Gervasio, Francesco L.; Parrinello, Michele
Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer
PLOS ONE, 5 Art. No. e13208, OCT 13 2010
abstract, full text, DOI:10.1371/journal.pone.0013208

Saharay, Moumita; Guo, Hong; Smith, Jeremy C.
Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS
PLOS ONE, 5 Art. No. e12947, OCT 12 2010
abstract, full text, DOI:10.1371/journal.pone.0012947

Guo, Qinglan; Weng, Jingwei; Xu, Xiaogang; Wang, Minghua; Wang, Xiaoying; Ye, Xinyu; Wang, Wenning; Wang, Minggui
A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis
BMC STRUCTURAL BIOLOGY, 10 Art. No. 33, OCT 8 2010
abstract, full text, DOI:10.1186/1472-6807-10-33

Montserret, Roland; Saint, Nathalie; Vanbelle, Christophe; Salvay, Andres Gerardo; Simorre, Jean-Pierre; Ebel, Christine; Sapay, Nicolas; Renisio, Jean-Guillaume; Boeckmann, Anja; Steinmann, Eike; Pietschmann, Thomas; Dubuisson, Jean; Chipot, Christophe; Penin, Francois
NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:31446-31461, OCT 8 2010
abstract, full text, DOI:10.1074/jbc.M110.122895

Karachevtsev, Victor A.; Zarudnev, Evgen S.; Stepanian, Stepan G.; Glamazda, Alexander Yu.; Karachevtsev, Maksym V.; Adamowicz, Ludwik
Raman Spectroscopy and Theoretical Characterization of Nanohybrids of Porphyrins with Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 114:16215-16222, OCT 7 2010
abstract, full text, DOI:10.1021/jp104093q

Dang, Shangyu; Sun, Linfeng; Huang, Yongjian; Lu, Feiran; Liu, Yufeng; Gong, Haipeng; Wang, Jiawei; Yan, Nieng
Structure of a fucose transporter in an outward-open conformation
NATURE, 467:734-U130, OCT 7 2010
abstract, full text, DOI:10.1038/nature09406

Faraudo, Jordi; Calero, Caries; Aguilella-Arzo, Marcel
Ionic Partition and Transport in Multi-Ionic Channels: A Molecular Dynamics Simulation Study of the OmpF Bacterial Porin
BIOPHYSICAL JOURNAL, 99:2107-2115, OCT 6 2010
abstract, full text, DOI:10.1016/j.bpj.2010.07.058

Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 99:2200-2207, OCT 6 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.067

Ho, Ming-Hsun; De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.
Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13702-13712, OCT 6 2010
abstract, full text, DOI:10.1021/ja102933y

Yang, Yuling; Li, Xiaoyi; Jiang, Jinliang; Du, Huailiang; Zhao, Lina; Zhao, Yuliang
Control Performance and Biomembrane Disturbance of Carbon Nanotube Artificial Water Channels by Nitrogen-Doping
ACS NANO, 4:5755-5762, OCT 2010
abstract, full text, DOI:10.1021/nn1014825

Chen, L. Y.
Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations
BIOPHYSICAL CHEMISTRY, 151:178-180, OCT 2010
abstract, full text, DOI:10.1016/j.bpc.2010.05.014

de Araujo, Alexandre Suman; Martinez, Leandro; Nicoluci, Ricardo de Paula; Skaf, Munir S.; Polikarpov, Igor
Structural modeling of high-affinity thyroid receptor-ligand complexes
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:1523-1536, OCT 2010
abstract, full text, DOI:10.1007/s00249-010-0610-2

Surdutovich, E.; Yakubovich, A. V.; Solov'yov, A. V.
Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes
EUROPEAN PHYSICAL JOURNAL D, 60:101-108, OCT 2010
abstract, full text, DOI:10.1140/epjd/e2010-00232-3

Revilla-Lopez, Guillermo; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Aleman, Carlos; Zanuy, David
Conformational Profile of a Proline-Arginine Hybrid
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1781-1789, OCT 2010
abstract, full text, DOI:10.1021/ci100135f

Ozer, Gungor; Valeev, Edward F.; Quirk, Stephen; Hernandez, Rigoberto
Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3026-3038, OCT 2010
abstract, full text, DOI:10.1021/ct100320g

Janosi, Lorant; Gorfe, Alemayehu A.
Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3267-3273, OCT 2010
abstract, full text, DOI:10.1021/ct100381g

Umeda, Hiroaki; Inadomi, Yuichi; Watanabe, Toshio; Yagi, Toru; Ishimoto, Takayoshi; Ikegami, Tsutomu; Tadano, Hiroto; Sakurai, Tetsuya; Nagashima, Umpei
Parallel Fock Matrix Construction with Distributed Shared Memory Model for the FMO-MO Method
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2381-2388, OCT 2010
abstract, full text, DOI:10.1002/jcc.21531

Corry, Ben; Hurst, Annette C.; Pal, Prithwish; Nomura, Takeshi; Rigby, Paul; Martinac, Boris
An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation
JOURNAL OF GENERAL PHYSIOLOGY, 136:483-494, OCT 2010
abstract, full text, DOI:10.1085/jgp.200910376

Trabuco, Leonardo G.; Schreiner, Eduard; Eargle, John; Cornish, Peter; Ha, Taekjip; Luthey-Schulten, Zaida; Schulten, Klaus
The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle
JOURNAL OF MOLECULAR BIOLOGY, 402:741-760, OCT 1 2010
abstract, full text, TCBG publications, DOI:10.1016/j.jmb.2010.07.056

Messner, Simon; Altmeyer, Matthias; Zhao, Hongtao; Pozivil, Andrea; Roschitzki, Bernd; Gehrig, Peter; Rutishauser, Dorothea; Huang, Danzhi; Caflisch, Amedeo; Hottiger, Michael O.
PARP1 ADP-ribosylates lysine residues of the core histone tails
NUCLEIC ACIDS RESEARCH, 38:6350-6362, OCT 2010
abstract, full text, DOI:10.1093/nar/gkq463

Xu, Jiancong; Smith, Jeremy C.
Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants
PROTEIN ENGINEERING DESIGN & SELECTION, 23:759-768, OCT 2010
abstract, full text, DOI:10.1093/protein/gzq049

Liu, Jian; Fan, Jianfen; Tang, Min; Cen, Min; Yan, Jianfeng; Liu, Zhao; Zhou, Weigun
Water Diffusion Behaviors and Transportation Properties in Transmembrane Cyclic Hexa-, Octa- and Decapeptide Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12183-12192, SEP 30 2010
abstract, full text, DOI:10.1021/jp1039207

Chebil, Latifa; Chipot, Christophe; Archambault, Fabien; Humeau, Catherine; Engasser, Jean Marc; Ghoul, Mohamed; Dehez, Francois
Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12308-12313, SEP 30 2010
abstract, full text, DOI:10.1021/jp104569k

Olbrich, Carsten; Kleinekathoefer, Ulrich
Time-Dependent Atomistic View on the Electronic Relaxation in Light-Harvesting System II
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12427-12437, SEP 30 2010
abstract, full text, DOI:10.1021/jp106542v

Foley, Meredith C.; Padow, Victoria A.; Schlick, Tamar
DNA Pol lambda's Extraordinary Ability To Stabilize Misaligned DNA
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13403-13416, SEP 29 2010
abstract, full text, DOI:10.1021/ja1049687

Lee, Tai-Sung; York, Darrin M.
Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13505-13518, SEP 29 2010
abstract, full text, DOI:10.1021/ja105956u

Veluraja, Kasinadar; Selvin, Jeyasigamani F. A.; Venkateshwari, Selvakumar; Priyadarzini, Thanu R. K.
3DSDSCAR-a three dimensional structural database for sialic acid-containing through molecular dynamics simulation
CARBOHYDRATE RESEARCH, 345:2030-2037, SEP 23 2010
abstract, full text, DOI:10.1016/j.carres.2010.06.021

Priet, Stephane; Zlatev, Ivan; Barvik, Ivan, Jr.; Geerts, Katrien; Leyssen, Pieter; Neyts, Johan; Dutartre, Helene; Canard, Bruno; Vasseur, Jean-Jacques; Morvan, Francois; Alvarez, Karine
3 '-Deoxy Phosphoramidate Dinucleosides as Improved Inhibitors of Hepatitis C Virus Subgenomic Replicon and NS5B Polymerase Activity
JOURNAL OF MEDICINAL CHEMISTRY, 53:6608-6617, SEP 23 2010
abstract, full text, DOI:10.1021/jm100102v

Khelashvili, George; Mondal, Sayan; Andersen, Olaf S.; Weinstein, Harel
Cholesterol Modulates the Membrane Effects and Spatial Organization of Membrane-Penetrating Ligands for G-Protein Coupled Receptors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12046-12057, SEP 23 2010
abstract, full text, DOI:10.1021/jp106373r

Jiang, Jun; Abramavicius, Darius; Falvo, Cyril; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul
Simulation of Two-Dimensional Ultraviolet Spectroscopy of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12150-12156, SEP 23 2010
abstract, full text, DOI:10.1021/jp1046968

Long, Feng; Su, Chih-Chia; Zimmermann, Michael T.; Boyken, Scott E.; Rajashankar, Kanagalaghatta R.; Jernigan, Robert L.; Yu, Edward W.
Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport
NATURE, 467:484-U140, SEP 23 2010
abstract, full text, DOI:10.1038/nature09395

Hilder, Tamsyn A.; Gordon, Dan; Chung, Shin-Ho
Synthetic Chloride-Selective Carbon Nanotubes Examined by Using Molecular and Stochastic Dynamics
BIOPHYSICAL JOURNAL, 99:1734-1742, SEP 22 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.034

Lyman, Edward; Cui, Haosheng; Voth, Gregory A.
Water under the BAR
BIOPHYSICAL JOURNAL, 99:1783-1790, SEP 22 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.074

Chen, Qiang; Cheng, Mary Hongying; Xu, Yan; Tang, Pei
Anesthetic Binding in a Pentameric Ligand-Gated Ion Channel: GLIC
BIOPHYSICAL JOURNAL, 99:1801-1809, SEP 22 2010
abstract, full text, DOI:10.1016/j.bpj.2010.07.023

Faustino, Ignacio; Perez, Alberto; Orozco, Modesto
Toward a Consensus View of Duplex RNA Flexibility
BIOPHYSICAL JOURNAL, 99:1876-1885, SEP 22 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.061

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi
Hydration property of globular proteins: An analysis of solvation free energy by energy representation method
CHEMICAL PHYSICS LETTERS, 497:218-222, SEP 20 2010
abstract, full text, DOI:10.1016/j.cplett.2010.08.008

Garcia-Mata, Carlos; Wang, Jianwen; Gajdanowicz, Pawel; Gonzalez, Wendy; Hills, Adrian; Donald, Naomi; Riedelsberger, Janin; Amtmann, Anna; Dreyer, Ingo; Blatt, Michael R.
A Minimal Cysteine Motif Required to Activate the SKOR K+ Channel of Arabidopsis by the Reactive Oxygen Species H2O2
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:29286-29294, SEP 17 2010
abstract, full text, DOI:10.1074/jbc.M110.141176

Lai, Chun-Liang; Landgraf, Kyle E.; Voth, Gregory A.; Falke, Joseph J.
Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKC alpha C2 Domain: A Combined Molecular Dynamics and Experimental Study
JOURNAL OF MOLECULAR BIOLOGY, 402:301-310, SEP 17 2010
abstract, full text, DOI:10.1016/j.jmb.2010.07.037

Aliaga, Carolina; Briones, Luis; Caroli Rezende, Marcos; Tirapegui, Cristian
The thermochromism of the E-T(30) betaine in a micro-heterogeneous medium: A spectral and dynamics simulation study
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 349:565-570, SEP 15 2010
abstract, full text, DOI:10.1016/j.jcis.2010.05.088

Semenyuk, A.; Darian, E.; Liu, J.; Majumdar, A.; Cuenoud, B.; Miller, P. S.; MacKerell, A. D., Jr.; Seidman, M. M.
Targeting of an Interrupted Polypurine:Polypyrimidine Sequence in Mammalian Cells by a Triplex-Forming Oligonucleotide Containing a Novel Base Analogue
BIOCHEMISTRY, 49:7867-7878, SEP 14 2010
abstract, full text, DOI:10.1021/bi100797z

Pemmaraju, C. D.; Rungger, I.; Chen, X.; Rocha, A. R.; Sanvito, S.
Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands
PHYSICAL REVIEW B, 82 Art. No. 125426, SEP 14 2010
abstract, full text, DOI:10.1103/PhysRevB.82.125426

Nurminen, Elisa M.; Pihlavisto, Marjo; Lazar, Laszlo; Szakonyi, Zsolt; Pentikainen, Ulla; Fulop, Ferenc; Pentikainen, Olli T.
Synthesis, in Vitro Activity, and Three-Dimensional Quantitative Structure-Activity Relationship of Novel Hydrazine Inhibitors of Human Vascular Adhesion Protein-1
JOURNAL OF MEDICINAL CHEMISTRY, 53:6301-6315, SEP 9 2010
abstract, full text, DOI:10.1021/jm100337z

Tsai, C.h.i.n.g.-.W.; Liu, C.h.i.h.-.I.; Chan, Y.i.n.g.-.C.; Tsai, Hui-H G.; Ruaan, R.u.o.h.-.C.
Study of Conformation Effects on the Retention of Small Peptides in Reversed-Phase Chromatography by Thermodynamic Analysis and Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11620-11627, SEP 9 2010
abstract, full text, DOI:10.1021/jp101846n

Virtanen, Jouko J.; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.
Modeling the Hydration Layer around Proteins: HyPred
BIOPHYSICAL JOURNAL, 99:1611-1619, SEP 8 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.027

Wang, Zun-Jing; Deserno, Markus
Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field
NEW JOURNAL OF PHYSICS, 12 Art. No. 095004, SEP 8 2010
abstract, full text, DOI:10.1088/1367-2630/12/9/095004

Chen, Qu; Moore, Joshua D.; Liu, Ying-Chun; Roussel, Thomas J.; Wang, Qi; Wu, Tao; Gubbins, Keith E.
Transition from single-file to Fickian diffusion for binary mixtures in single-walled carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 133 Art. No. 094501, SEP 7 2010
abstract, full text, DOI:10.1063/1.3469811

Kim, Soo-Kyung; Li, Youyong; Park, Changmoon; Abrol, Ravinder; Goddard, William A., I.I.I.
Prediction of the Three-Dimensional Structure for the Rat Urotensin II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic Simulations
CHEMMEDCHEM, 5:1594-1608, SEP 3 2010
abstract, full text, DOI:10.1002/cmdc.201000175

Pisani, Leonardo; Catto, Marco; Giangreco, Ilenia; Leonetti, Francesco; Nicolotti, Orazio; Stefanachi, Angela; Cellamare, Saverio; Carotti, Angelo
Design, Synthesis, and Biological Evaluation of Coumarin Derivatives Tethered to an Edrophonium-like Fragment as Highly Potent and Selective Dual Binding Site Acetylcholinesterase Inhibitors
CHEMMEDCHEM, 5:1616-1630, SEP 3 2010
abstract, full text, DOI:10.1002/cmdc.201000210

Ziemys, A.; Grattoni, A.; Fine, D.; Hussain, F.; Ferrari, M.
Confinement Effects on Monosaccharide Transport in Nanochannels
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11117-11126, SEP 2 2010
abstract, full text, DOI:10.1021/jp103519d

Wang, Zun-Jing; Deserno, Markus
A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11207-11220, SEP 2 2010
abstract, full text, DOI:10.1021/jp102543j

Elenewski, Justin E.; Hackett, John C.
Free Energy Landscape of the Retinol/Serum Retinol Binding Protein Complex: A Biological Host-Guest System
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11315-11322, SEP 2 2010
abstract, full text, DOI:10.1021/jp104103f

Hameroff, Stuart R.; Craddock, Travis J. A.; Tuszynski, J. A.
"MEMORY BYTES" - MOLECULAR MATCH FOR CaMKII PHOSPHORYLATION ENCODING OF MICROTUBULE LATTICES
JOURNAL OF INTEGRATIVE NEUROSCIENCE, 9:253-267, SEP 2010
abstract, full text, DOI:10.1142/S0219635210002482

Barucha-Kraszewska, Justyna; Kraszewski, Sebastian; Jurkiewicz, Piotr; Ramseyer, Christophe; Hof, Martin
Numerical studies of the membrane fluorescent dyes dynamics in ground and excited states
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1724-1734, SEP 2010
abstract, full text, DOI:10.1016/j.bbamem.2010.05.020

Yancey, Jeremy A.; Vellore, Nadeem A.; Collier, Galen; Stuart, Steven J.; Latour, Robert A.
Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms
BIOINTERPHASES, 5:85-95, SEP 2010
abstract, full text, DOI:10.1116/1.3493470

Stavrakoudis, Athanassios
Conformational Flexibility in Designing Peptides for Immunology: The Molecular Dynamics Approach
CURRENT COMPUTER-AIDED DRUG DESIGN, 6:207-222, SEP 2010
abstract, full text

Arora, Neelima; Banerjee, Amit Kumar; Murty, U. S. N.
In silico Characterization of Shikimate Kinase of Shigella flexneri: A Potential Drug Target
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 2:280-290, SEP 2010
abstract, full text, DOI:10.1007/s12539-010-0012-2

Vivcharuk, Victor; Kaznessis, Yiannis N.
Dimerization of Protegrin-1 in Different Environments
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 11:3177-3194, SEP 2010
abstract, full text, DOI:10.3390/ijms11093177

Bucher, Denis; Gray-Weale, Angus; Kuyucak, Serdar
Ab Initio Study of Water Polarization in the Hydration Shell of Aqueous Hydroxide: Comparison between Polarizable and Nonpolarizable Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2888-2895, SEP 2010
abstract, full text, DOI:10.1021/ct1003719

Sit, Patrick H-L.; Migliore, Agostino; Ho, Ming-Hsun; Klein, Michael L.
Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron-Dioxygen Intermediates and Proton Transfer in Superoxide Reductase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2896-2909, SEP 2010
abstract, full text, DOI:10.1021/ct900599q

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Testa, Bernard
Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 24:771-787, SEP 2010
abstract, full text, DOI:10.1007/s10822-010-9373-1

Stone, John E.; Hardy, David J.; Ufimtsev, Ivan S.; Schulten, Klaus
GPU-accelerated molecular modeling coming of age
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:116-125, SEP 2010
abstract, full text, TCBG publications, DOI:10.1016/j.jmgm.2010.06.010

Abroshan, Hadi; Akbarzadeh, Hamed; Parsafar, Golam Abbas
Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 23:866-877, SEP 2010
abstract, full text, DOI:10.1002/poc.1679

Anitescu, Mihai; Park, Sanghyun
A linear assignment approach for the least-squares protein morphing problem
MATHEMATICAL PROGRAMMING, 125:195-203, SEP 2010
abstract, full text, DOI:10.1007/s10107-009-0269-6

Zhuravlev, Pavel I.; Wu, Sangwook; Potoyan, Davit A.; Rubinstein, Michael; Papoian, Garegin A.
Computing free energies of protein conformations from explicit solvent simulations
METHODS, 52:115-121, SEP 2010
abstract, full text, DOI:10.1016/j.ymeth.2010.05.003

Maffeo, Christopher; Aksimentiev, Aleksei
Single molecule force measurements: Insights from molecular simulations Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al.
PHYSICS OF LIFE REVIEWS, 7:353-354, SEP 2010
full text, DOI:10.1016/j.plrev.2010.07.004

Le, Ly; Lee, Eric H.; Hardy, David J.; Truong, Thanh N.; Schulten, Klaus
Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000939, SEP 2010
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1000939

Lee, Hsiau-Wei; Wylie, Greg; Bansal, Sonal; Wang, Xu; Barb, Adam W.; Macnaughtan, Megan A.; Ertekin, Asli; Montelione, Gaetano T.; Prestegard, James H.
Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping
PROTEIN SCIENCE, 19:1673-1685, SEP 2010
abstract, full text, DOI:10.1002/pro.447

Stabenfeldt, Sarah E.; Gossett, J. Jared; Barker, Thomas H.
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes
BLOOD, 116:1352-1359, AUG 26 2010
abstract, full text, DOI:10.1182/blood-2009-11-251801

Acharya, Rudresh; Carnevale, Vincenzo; Fiorin, Giacomo; Levine, Benjamin G.; Polishchuk, Alexei L.; Balannik, Victoria; Samish, Ilan; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.; Klein, Michael L.
Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:15075-15080, AUG 24 2010
abstract, full text, DOI:10.1073/pnas.1007071107

Zahran, Mai; Daidone, Isabella; Smith, Jeremy C.; Imhof, Petra
Mechanism of DNA Recognition by the Restriction Enzyme EcoRV
JOURNAL OF MOLECULAR BIOLOGY, 401:415-432, AUG 20 2010
abstract, full text, DOI:10.1016/j.jmb.2010.06.026

Cardone, A.; Hassan, S. A.; Albers, R. W.; Sriram, R. D.; Pant, H. C.
Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP
JOURNAL OF MOLECULAR BIOLOGY, 401:478-492, AUG 20 2010
abstract, full text, DOI:10.1016/j.jmb.2010.06.040

Casanovas, Jordi; Rodriguez-Ropero, Francisco; Zanuy, David; Aleman, Carlos
Microscopic details of the sensing ability of 15-crown-5-ether functionalized poly(bithiophene)
POLYMER, 51:4267-4272, AUG 19 2010
abstract, full text, DOI:10.1016/j.polymer.2010.06.062

Roos, W. H.; Gibbons, M. M.; Arkhipov, A.; Uetrecht, C.; Watts, N. R.; Wingfield, P. T.; Steven, A. C.; Heck, A. J. R.; Schulten, K.; Klug, W. S.; Wuite, G. J. L.
Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale
BIOPHYSICAL JOURNAL, 99:1175-1181, AUG 18 2010
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2010.05.033

Zou, Xueqing; Liu, Yanxin; Chen, Zhongzhou; Ines Cardenas-Jiron, Gloria; Schulten, Klaus
Flow-Induced beta-Hairpin Folding of the Glycoprotein Ib alpha beta-Switch
BIOPHYSICAL JOURNAL, 99:1182-1191, AUG 18 2010
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2010.05.035

Kurkcuoglu, Ozge; Bates, Paul A.
Mechanism of Cohesin Loading onto Chromosomes: A Conformational Dynamics Study
BIOPHYSICAL JOURNAL, 99:1212-1220, AUG 18 2010
abstract, full text, DOI:10.1016/j.bpj.2010.06.006

Piton, Jeremie; Petrella, Stephanie; Delarue, Marc; Andre-Leroux, Gwenaelle; Jarlier, Vincent; Aubry, Alexandra; Mayer, Claudine
Structural Insights into the Quinolone Resistance Mechanism of Mycobacterium tuberculosis DNA Gyrase
PLOS ONE, 5 Art. No. e12245, AUG 18 2010
abstract, full text, DOI:10.1371/journal.pone.0012245

Illingworth, Christopher J. R.; Loenarz, Christoph; Schofield, Christopher J.; Domene, Carmen
Chemical Basis for the Selectivity of the von Hippel Lindau Tumor Suppressor pVHL for Prolyl-Hydroxylated HIF-1 alpha
BIOCHEMISTRY, 49:6936-6944, AUG 17 2010
abstract, full text, DOI:10.1021/bi100358t

Sayyed-Ahmad, Abdallah; Lichtenberger, Lenard M.; Gorfe, Alemayehu A.
Structure and Dynamics of Cholic Acid and Dodecylphosphocholine-Cholic Acid Aggregates
LANGMUIR, 26:13407-13414, AUG 17 2010
abstract, full text, DOI:10.1021/la102106t

Raabe, Gabriele; Maginn, Edward J.
A Force Field for 3,3,3-Fluoro-1-propenes, Including HFO-1234yf
JOURNAL OF PHYSICAL CHEMISTRY B, 114:10133-10142, AUG 12 2010
abstract, full text, DOI:10.1021/jp102534z

Roxbury, Daniel; Manohar, Suresh; Jagota, Anand
Molecular Simulation of DNA beta-Sheet and beta-Barrel Structures on Graphite and Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 114:13267-13276, AUG 12 2010
abstract, full text, DOI:10.1021/jp1051497

Turecek, Frantisek; Chung, Thomas W.; Moss, Christopher L.; Wyer, Jean A.; Ehlerding, Anneli; Holm, Anne I. S.; Zettergren, Henning; Nielsen, Steen Brondsted; Hvelplund, Preben; Chamot-Rooke, Julia; Bythell, Benjamin; Paizs, Bela
The Histidine Effect. Electron Transfer and Capture Cause Different Dissociations and Rearrangements of Histidine Peptide Cation-Radicals
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:10728-10740, AUG 11 2010
abstract, full text, DOI:10.1021/ja907808h

Brannigan, Grace; LeBard, David N.; Henin, Jerome; Eckenhoff, Roderic G.; Klein, Michael L.
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:14122-14127, AUG 10 2010
abstract, full text, DOI:10.1073/pnas.1008534107

Miller, Yifat; Ma, Buyong; Tsai, Chung-Jung; Nussinov, Ruth
Hollow core of Alzheimer's A beta(42) amyloid observed by cryoEM is relevant at physiological pH
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:14128-14133, AUG 10 2010
abstract, full text, DOI:10.1073/pnas.1004704107

Saam, Jan; Rosini, Elena; Molla, Gianluca; Schulten, Klaus; Pollegioni, Loredano; Ghisla, Sandro
O-2 Reactivity of Flavoproteins DYNAMIC ACCESS OF DIOXYGEN TO THE ACTIVE SITE AND ROLE OF A H+ RELAY SYSTEM IN D-AMINO ACID OXIDASE
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:24439-24446, AUG 6 2010
abstract, full text, TCBG publications, DOI:10.1074/jbc.M110.131193

He, Xibing; Guvench, Olgun; MacKerell, Alexander D., Jr.; Klein, Michael L.
Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at the Water/Air Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9787-9794, AUG 5 2010
abstract, full text, DOI:10.1021/jp101860v

Priyakumar, U. Deva
Atomistic Details of the Ligand Discrimination Mechanism of S-MK/SAM-III Riboswitch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9920-9925, AUG 5 2010
abstract, full text, DOI:10.1021/jp1042427

Liu, Jin; Nussinov, Ruth
Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation
BIOPHYSICAL JOURNAL, 99:736-744, AUG 4 2010
abstract, full text, DOI:10.1016/j.bpj.2010.05.021

Broemstrup, Torben; Reuter, Nathalie
Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic Phospholipid Bilayers
BIOPHYSICAL JOURNAL, 99:825-833, AUG 4 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.064

Wereszczynski, Jeff; Andricioaei, Ioan
Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition
BIOPHYSICAL JOURNAL, 99:869-878, AUG 4 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.077

Sen, Kakali; Hackett, John C.
Peroxo-Iron Mediated Deformylation in Sterol 14 alpha-Demethylase Catalysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:10293-10305, AUG 4 2010
abstract, full text, DOI:10.1021/ja906192b

Kurland, Michael D.; Newcomer, Michael B.; Peterlin, Zita; Ryan, Kevin; Firestein, Stuart; Batista, Victor S.
Discrimination of Saturated Aldehydes by the Rat I7 Olfactory Receptor
BIOCHEMISTRY, 49:6302-6304, AUG 3 2010
abstract, full text, DOI:10.1021/bi100976w

Wang, Qiuming; Zhao, Jun; Yu, Xiang; Zhao, Chao; Li, Lingyan; Zheng, Jie
Alzheimer A beta(1-42) Monomer Adsorbed on the Self-Assembled Monolayers
LANGMUIR, 26:12722-12732, AUG 3 2010
abstract, full text, DOI:10.1021/la1017906

Cruz-Chu, Eduardo R.; Schulten, Klaus
Computational Microscopy of the Role of Protonable Surface Residues in Nanoprecipitation Oscillations
ACS NANO, 4:4463-4474, AUG 2010
abstract, full text, TCBG publications, DOI:10.1021/nn100399f

Shen, Rong; Guo, Wanlin; Zhong, Wenyu
Hydration valve controlled non-selective conduction of Na+ and K+ in the NaK channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1474-1479, AUG 2010
abstract, full text, DOI:10.1016/j.bbamem.2010.04.002

Mihajlovic, Maja; Lazaridis, Themis
Antimicrobial peptides in toroidal and cylindrical pores
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1485-1493, AUG 2010
abstract, full text, DOI:10.1016/j.bbamem.2010.04.004

Sharma, Vivek; Wikstrom, Marten; Kaila, Ville R. I.
Redox-coupled proton transfer in the active site of cytochrome cbb(3)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1797:1512-1520, AUG 2010
abstract, full text, DOI:10.1016/j.bbabio.2010.03.004

Seibold, Steve A.; Singh, Badri Nath; Zhang, Chunfen; Kireeva, Maria; Domecq, Celine; Bouchard, Annie; Nazione, Anthony M.; Feig, Michael; Cukier, Robert I.; Coulombe, Benoit; Kashlev, Mikhail; Hampsey, Michael; Burton, Zachary F.
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1799:575-587, AUG 2010
abstract, full text, DOI:10.1016/j.bbagrm.2010.05.002

Kunji, Edmund R. S.; Robinson, Alan J.
Coupling of proton and substrate translocation in the transport cycle of mitochondrial carriers
CURRENT OPINION IN STRUCTURAL BIOLOGY, 20:440-447, AUG 2010
abstract, full text, DOI:10.1016/j.sbi.2010.06.004

Banerjee, Avik; Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Nandi, Tapas K.; Bera, Asim K.
Structural insight to mutated Y116S transthyretin by molecular dynamics simulation
INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS, 47:197-202, AUG 2010
abstract, full text

Yuan, Ye; Knaggs, Michael H.; Poole, Leslie B.; Fetrow, Jacquelyn S.; Salsbury, Freddie R., Jr.
Conformational and Oligomeric Effects on the Cysteine pK(a) of Tryparedoxin Peroxidase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:51-70, AUG 2010
abstract, full text

Khrenova, M. G.; Nemukhin, A. V.; Grigorenko, B. L.; Krylov, A. I.; Domratcheva, T. M.
Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2293-2302, AUG 2010
abstract, full text, DOI:10.1021/ct100179p

Zhao, Ruijun; Shen, Juanfang; Skeel, Robert D.
Maximum Flux Transition Paths of Conformational Change
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2411-2423, AUG 2010
abstract, full text, DOI:10.1021/ct900689m

Phogat, Navneet; Vindal, Vaibhav; Kumar, Vikash; Inampudi, Krishna K.; Prasad, Nirmal K.
Sequence analysis, in silico modeling and docking studies of Caffeoyl CoA-O-methyltransferase of Populus trichopora
JOURNAL OF MOLECULAR MODELING, 16:1461-1471, AUG 2010
abstract, full text, DOI:10.1007/s00894-010-0656-1

Popov, A. V.; Vorob'ev, Yu. N.
GUI-BioPASED: A program for molecular dynamics simulations of biopolymers with a graphical user interface
MOLECULAR BIOLOGY, 44:648-654, AUG 2010
abstract, full text, DOI:10.1134/S0026893310040217

Wong-ekkabut, Jirasak; Miettinen, Markus S.; Dias, Cristiano; Karttunen, Mikko
Static charges cannot drive a continuous flow of water molecules through a carbon nanotube
NATURE NANOTECHNOLOGY, 5:555-557, AUG 2010
full text

Chirkova, Anna; Erlacher, Matthias D.; Clementi, Nina; Zywicki, Marek; Aigner, Michaela; Polacek, Norbert
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center
NUCLEIC ACIDS RESEARCH, 38:4844-4855, AUG 2010
abstract, full text, DOI:10.1093/nar/gkq213

Novak, Michael; Jaeger, Christof M.; Rumpel, Armin; Kropp, Henning; Peukert, Wolfgang; Clark, Timothy; Halik, Marcus
The morphology of integrated self-assembled monolayers and their impact on devices - A computational and experimental approach
ORGANIC ELECTRONICS, 11:1476-1482, AUG 2010
abstract, full text, DOI:10.1016/j.orgel.2010.05.009

Mura, Cameron; McCrimmon, Colin M.; Vertrees, Jason; Sawaya, Michael R.
An Introduction to Biomolecular Graphics
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000918, AUG 2010
full text, DOI:10.1371/journal.pcbi.1000918

Pan, Yongping; Nussinov, Ruth
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000878, AUG 2010
abstract, full text, DOI:10.1371/journal.pcbi.1000878

Shaikh, Saher Afshan; Tajkhorshid, Emad
Modeling and Dynamics of the Inward-Facing State of a Na+/Cl- Dependent Neurotransmitter Transporter Homologue
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000905, AUG 2010
abstract, full text, DOI:10.1371/journal.pcbi.1000905

Durrant, Jacob D.; Hall, Laurence; Swift, Robert V.; Landon, Melissa; Schnaufer, Achim; Amaro, Rommie E.
Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
PLOS NEGLECTED TROPICAL DISEASES, 4 Art. No. e803, AUG 2010
abstract, full text, DOI:10.1371/journal.pntd.0000803

Herrera, Alvaro I.; Al-Rawi, Ahlam; Cook, Gabriel A.; Gao, Jian; Iwamoto, Takeo; Prakash, Om; Tomich, John M.; Chen, Jianhan
Structural characterization of two pore-forming peptides: Consequences of introducing a C-terminal tryptophan
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2238-2250, AUG 1 2010
abstract, full text, DOI:10.1002/prot.22736

Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Capone, Ricardo; Lal, Ratnesh; Nussinov, Ruth
Structural Convergence Among Diverse, Toxic beta-Sheet Ion Channels
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9445-9451, JUL 29 2010
abstract, full text, DOI:10.1021/jp104073k

Fidelak, Jeremy; Juraszek, Jarek; Branduardi, Davide; Bianciotto, Marc; Luigi Gervasio, Francesco
Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9516-9524, JUL 29 2010
abstract, full text, DOI:10.1021/jp911689r

He, Yuhui; Shao, Lubing; Scheicher, Ralph H.; Grigoriev, Anton; Ahuja, Rajeev; Long, Shibing; Ji, Zhuoyu; Yu, Zhaoan; Liu, Ming
Differential conductance as a promising approach for rapid DNA sequencing with nanopore-embedded electrodes
APPLIED PHYSICS LETTERS, 97 Art. No. 043701, JUL 26 2010
abstract, full text, DOI:10.1063/1.3467194

Wang, Xiao-Qing; Yu, Tao; Sang, Jian-Ping; Zou, Xian-Wu; Chen, Tsung-Yu; Bolser, Diana; Zou, Xiaoqin
A Three-State Multi-Ion Kinetic Model for Conduction Properties of ClC-0 Chloride Channel
BIOPHYSICAL JOURNAL, 99:464-471, JUL 21 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.047

Balaraman, Gouthaman S.; Bhattacharya, Supriyo; Vaidehi, Nagarajan
Structural Insights into Conformational Stability of Wild-Type and Mutant beta(1)-Adrenergic Receptor
BIOPHYSICAL JOURNAL, 99:568-577, JUL 21 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.075

Prakash, Meher K.; Barducci, Alessandro; Parrinello, Michele
Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations
BIOPHYSICAL JOURNAL, 99:588-594, JUL 21 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.024

Wells, David B.; Aksimentiev, Aleksei
Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 99:629-637, JUL 21 2010
abstract, full text, DOI:10.1016/j.bpj.2010.04.038

Kokhan, Oleksandr; Shinkarev, Vladimir P.; Wraight, Colin A.
Binding of Imidazole to the Heme of Cytochrome c(1) and Inhibition of the bc(1) Complex from Rhodobacter sphaeroides I. EQUILIBRIUM AND MODELING STUDIES
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:22513-22521, JUL 16 2010
abstract, full text, DOI:10.1074/jbc.M110.128058

Vashisth, Harish; Abrams, Cameron F.
All-Atom Structural Models for Complexes of Insulin-Like Growth Factors IGF1 and IGF2 with Their Cognate Receptor
JOURNAL OF MOLECULAR BIOLOGY, 400:645-658, JUL 16 2010
abstract, full text, DOI:10.1016/j.jmb.2010.05.025

Shah, Jindal K.; Maginn, Edward J.
Molecular dynamics investigation of biomimetic ionic liquids
FLUID PHASE EQUILIBRIA, 294:197-205, JUL 15 2010
abstract, full text, DOI:10.1016/j.fluid.2010.03.036

Kumar, Ravinesh A.; Pilz, Daniela T.; Babatz, Timothy D.; Cushion, Thomas D.; Harvey, Kirsten; Topf, Maya; Yates, Laura; Robb, Stephanie; Uyanik, Goekhan; Mancini, Gracia M. S.; Rees, Mark I.; Harvey, Robert J.; Dobyns, William B.
TUBA1A mutations cause wide spectrum lissencephaly (smooth brain) and suggest that multiple neuronal migration pathways converge on alpha tubulins
HUMAN MOLECULAR GENETICS, 19:2817-2827, JUL 15 2010
abstract, full text, DOI:10.1093/hmg/ddq182

Liu, Lu Tian; Xu, Yan; Tang, Pei
Mechanistic Insights into Xenon Inhibition of NMDA Receptors from MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9010-9016, JUL 15 2010
abstract, full text, DOI:10.1021/jp101687j

Utesch, Tillmann; Mroginski, Maria Andrea
Three-Dimensional Structural Model of Chicken Liver Sulfite Oxidase in its Activated Form
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:2159-2164, JUL 15 2010
abstract, full text, DOI:10.1021/jz1005847

Melloni, Alfonso; Paccani, Riccardo Rossi; Donati, Donato; Zanirato, Vinicio; Sinicropi, Adalgisa; Parisi, Maria Laura; Martin, Elena; Ryazantsev, Mikhail; Ding, Wan Jian; Manuel Frutos, Luis; Basosi, Riccardo; Fusi, Stefania; Latterini, Loredana; Ferre, Nicolas; Olivucci, Massimo
Modeling, Preparation, and Characterization of a Dipole Moment Switch Driven by Z/E Photoisomerization
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:9310-9319, JUL 14 2010
abstract, full text, DOI:10.1021/ja906733q

Bondar, Ana-Nicoleta; del Val, Coral; Freites, J. Alfredo; Tobias, Douglas J.; White, Stephen H.
Dynamics of SecY Translocons with Translocation-Defective Mutations
STRUCTURE, 18:847-857, JUL 14 2010
abstract, full text, DOI:10.1016/j.str.2010.04.010

Ng, Yuen-Wai; Raghunathan, Devanathan; Chan, Perry M.; Baskaran, Yohendran; Smith, Derek J.; Lee, Chung-Hung; Verma, Chandra; Manser, Ed
Why an A-Loop Phospho-Mimetic Fails to Activate PAK1: Understanding an Inaccessible Kinase State by Molecular Dynamics Simulations
STRUCTURE, 18:879-890, JUL 14 2010
abstract, full text, DOI:10.1016/j.str.2010.04.011

Durrant, Jacob D.; Urbaniak, Michael D.; Ferguson, Michael A. J.; McCammon, J. Andrew
Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4 '-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness
JOURNAL OF MEDICINAL CHEMISTRY, 53:5025-5032, JUL 8 2010
abstract, full text, DOI:10.1021/jm100456a

Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien; Pan, Albert C.; Gagnon, Dominique G.; Dalmas, Olivier; Cordero-Morales, Julio F.; Chakrapani, Sudha; Roux, Benoit; Perozo, Eduardo
Structural basis for the coupling between activation and inactivation gates in K+ channels
NATURE, 466:272-U154, JUL 8 2010
abstract, full text, DOI:10.1038/nature09136

Jiao, Wanting; McDonald, Quentin; Coxon, James M.; Parker, Emily J.
Molecular Modeling Studies of Peptide Inhibitors Highlight the Importance of Conformational Prearrangement for Inhibition of Calpain
BIOCHEMISTRY, 49:5533-5539, JUL 6 2010
abstract, full text, DOI:10.1021/bi100048y

de Serrano, V. S.; Davis, M. F.; Gaff, J. F.; Zhang, Qi; Chen, Z.; D'Antonio, E. L.; Bowden, E. F.; Rose, R.; Franzen, S.
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 66:770-782, JUL 2010
abstract, full text, DOI:10.1107/S0907444910014605

Kraszewski, Sebastian; Tarek, Mounir; Treptow, Werner; Ramseyer, Christophe
Affinity of C-60 Neat Fullerenes with Membrane Proteins: A Computational Study on Potassium Channels
ACS NANO, 4:4158-4164, JUL 2010
abstract, full text, DOI:10.1021/nn100723r

Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.
A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 38:216-223, JUL-AUG 2010
abstract, full text, DOI:10.1002/bmb.20396

Schafer, Nick; Negrut, Dan
A Quantitative Assessment of the Potential of Implicit Integration Methods for Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS, 5 Art. No. 031012, JUL 2010
abstract, full text, DOI:10.1115/1.4001392

Dubey, Devendra K.; Tomar, Vikas
Tensile and Compressive Loading Effects on Texture Dependent Nanoscale Mechanical Behavior of Model Tropocollagen-Hydroxyapatite Biomaterials
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:1306-1316, JUL 2010
abstract, full text, DOI:10.1166/jctn.2010.1485

Castelan-Vega, Juan A.; Jimenez-Alberto, Alicia; Ribas-Aparicio, Rosa M.
Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA
JOURNAL OF MOLECULAR MODELING, 16:1213-1222, JUL 2010
abstract, full text, DOI:10.1007/s00894-009-0632-9

Lambry, Jean-Christophe; Beaumont, Edward; Tarus, Bogdan; Blanchard-Desce, Mireille; Slama-Schwok, Anny
Selective probing of a NADPH site controlled light-induced enzymatic catalysis
JOURNAL OF MOLECULAR RECOGNITION, 23:379-388, JUL-AUG 2010
abstract, full text, DOI:10.1002/jmr.1009

Kaszuba, Karol; Rog, Tomasz; Bryl, Krzysztof; Vattulainen, Ilpo; Karttunen, Mikko
Molecular Dynamics Simulations Reveal Fundamental Role of Water As Factor Determining Affinity of Binding of beta-Blocker Nebivolol to beta(2)-Adrenergic Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 114:8374-8386, JUL 1 2010
abstract, full text, DOI:10.1021/jp909971f

Krems, Matt; Pershin, Yuriy V.; Di Ventra, Massimiliano
Ionic Memcapacitive Effects in Nanopores
NANO LETTERS, 10:2674-2678, JUL 2010
abstract, full text, DOI:10.1021/nl1014734

Russell, John; Kral, Petr
Configuration-sensitive molecular sensing on doped graphene sheets
NANO RESEARCH, 3:472-480, JUL 2010
abstract, full text, DOI:10.1007/s12274-010-0007-7

Claxton, Derek P.; Quick, Matthias; Shi, Lei; de Carvalho, Fernanda Delmondes; Weinstein, Harel; Javitch, Jonathan A.; Mchaourab, Hassane S.
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter: sodium symporters
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17:822-U68, JUL 2010
abstract, full text, DOI:10.1038/nsmb.1854

Berjanskii, Mark; Liang, Yongjie; Zhou, Jianjun; Tang, Peter; Stothard, Paul; Zhou, You; Cruz, Joseph; MacDonell, Cam; Lin, Guohui; Lu, Paul; Wishart, David S.
PROSESS: a protein structure evaluation suite and server
NUCLEIC ACIDS RESEARCH, 38:W633-W640, JUL 2010
abstract, full text, DOI:10.1093/nar/gkq375

Porollo, Aleksey; Meller, Jaroslaw
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
NUCLEIC ACIDS RESEARCH, 38:W662-W666, JUL 2010
abstract, full text, DOI:10.1093/nar/gkq445

Palpant, Nathan J.; Houang, Evelyne M.; Delport, Wayne; Hastings, Kenneth E. M.; Onufriev, Alexey V.; Sham, Yuk Y.; Metzger, Joseph M.
Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations
PHYSIOLOGICAL GENOMICS, 42:287-299, JUL 2010
abstract, full text, DOI:10.1152/physiolgenomics.00033.2010

Brun, Sonia; Chaloin, Laurent; Gay, Bernard; Bernard, Eric; Devaux, Christian; Lionne, Corinne; Chazal, Nathalie; Briant, Laurence
Electrostatic repulsion between HIV-1 capsid proteins modulates hexamer plasticity and in vitro assembly
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2144-2156, JUL 2010
abstract, full text, DOI:10.1002/prot.22729

Jiang, Jun; Abramavicius, Darius; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul
Ultraviolet Spectroscopy of Protein Backbone Transitions in Aqueous Solution: Combined QM and MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:8270-8277, JUN 24 2010
abstract, full text, DOI:10.1021/jp101980a

Neelov, Alexey; Holm, Christian
Interlaced P3M algorithm with analytical and ik-differentiation
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 234103, JUN 21 2010
abstract, full text, DOI:10.1063/1.3430521

Nygaard, Rie; Valentin-Hansen, Louise; Mokrosinski, Jacek; Frimurer, Thomas M.; Schwartz, Thue W.
Conserved Water-mediated Hydrogen Bond Network between TM-I, -II, -VI, and -VII in 7TM Receptor Activation
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:19625-19636, JUN 18 2010
abstract, full text, DOI:10.1074/jbc.M110.106021

Katti, Dinesh R.; Pradhan, Shashindra M.; Katti, Kalpana S.
Directional dependence of hydroxyapatite-collagen interactions on mechanics of collagen
JOURNAL OF BIOMECHANICS, 43:1723-1730, JUN 18 2010
abstract, full text, DOI:10.1016/j.jbiomech.2010.02.027

Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo; O'Connor, Joseph W.; Tobias, Douglas J.; Mondragon-Ramirez, Carlos; Vorobyov, Igor; MacKerell, Alexander D., Jr.; Pastor, Richard W.
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7830-7843, JUN 17 2010
abstract, full text, DOI:10.1021/jp101759q

Liu, Peng; Cai, Wensheng; Chipot, Christophe; Shao, Xueguang
Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:1776-1780, JUN 17 2010
abstract, full text, DOI:10.1021/jz100414j

Schow, Eric V.; Freites, J. Alfredo; Gogna, Karun; White, Stephen H.; Tobias, Douglas J.
Down-State Model of the Voltage-Sensing Domain of a Potassium Channel
BIOPHYSICAL JOURNAL, 98:2857-2866, JUN 16 2010
abstract, full text, DOI:10.1016/j.bpj.2010.03.031

Adelman, Joshua L.; Chodera, John D.; Kuo, I-Feng W.; Miller, Thomas F., I.I.I.; Barsky, Daniel
The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp
BIOPHYSICAL JOURNAL, 98:3062-3069, JUN 16 2010
abstract, full text, DOI:10.1016/j.bpj.2010.03.056

Treptow, Werner; Klein, Michael L.
The Membrane-Bound State of K-2P Potassium Channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:8145-8151, JUN 16 2010
abstract, full text, DOI:10.1021/ja102191s

Feig, Michael; Gebreyohannes, Kahsay G.; McGuffin, Victoria L.
Conformational sampling of S- and R-warfarin in polar solvents: Implications for stereoselective complex formation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 949:41-51, JUN 15 2010
abstract, full text, DOI:10.1016/j.theochem.2010.03.001

Ko, Jeong-Ahn; Choi, Ho-Jin; Ha, Man-Yeong; Hong, Seung-Do; Yoon, Hyun-Sik
A Study on the Behavior of Water Droplet Confined between an Atomic Force Microscope Tip and Rough Surfaces
LANGMUIR, 26:9728-9735, JUN 15 2010
abstract, full text, DOI:10.1021/la100452m

Henkel, Michael; Mitzner, David; Henklein, Peter; Meyer-Almes, Franz-Josef; Moroni, Anna; DiFrancesco, Mattia L.; Henkes, Leonhard M.; Kreim, Michael; Kast, Stefan M.; Schubert, Ulrich; Thiel, Gerhard
The Proapoptotic Influenza A Virus Protein PB1-F2 Forms a Nonselective Ion Channel
PLOS ONE, 5 Art. No. e11112, JUN 15 2010
abstract, full text, DOI:10.1371/journal.pone.0011112

Mowrey, David; Haddadian, Esmael J.; Liu, Lu Tian; Willenbring, Dan; Xu, Yan; Tang, Pei
Unresponsive Correlated Motion in alpha 7 nAChR to Halothane Binding Explains Its Functional Insensitivity to Volatile Anesthetics
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7649-7655, JUN 10 2010
abstract, full text, DOI:10.1021/jp1009675

Luan, Binquan; Peng, Hongbo; Polonsky, Stas; Rossnagel, Steve; Stolovitzky, Gustavo; Martyna, Glenn
Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore
PHYSICAL REVIEW LETTERS, 104 Art. No. 238103, JUN 10 2010
abstract, full text, DOI:10.1103/PhysRevLett.104.238103

Abramavicius, Darius; Jiang, Jun; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul
Simulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7769-7775, JUN 9 2010
abstract, full text, DOI:10.1021/ja101968g

Giussani, Lara; Fois, Ettore; Gianotti, Enrica; Tabacchi, Gloria; Gamba, Aldo; Coluccia, Salvatore
On the Compatibility Criteria for Protein Encapsulation inside Mesoporous Materials
CHEMPHYSCHEM, 11:1757-1762, JUN 7 2010
abstract, full text, DOI:10.1002/cphc.200901038

Rungger, I.; Chen, X.; Schwingenschloegl, U.; Sanvito, S.
Finite-bias electronic transport of molecules in a water solution
PHYSICAL REVIEW B, 81 Art. No. 235407, JUN 4 2010
abstract, full text, DOI:10.1103/PhysRevB.81.235407

Zhang, Jilong; Zheng, Qingchuan; Zhang, Hongxing
Insight into the Dynamic Interaction of Different Carbohydrates with Human Surfactant Protein D: Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7383-7390, JUN 3 2010
abstract, full text, DOI:10.1021/jp9113078

Revilla-Lopez, Guillem; Torras, Juan; Curco, David; Casanovas, Jordi; Isabel Calaza, M.; Zanuy, David; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Grodzinski, Piotr; Aleman, Carlos
NCAD, a Database Integrating the Intrinsic Conformational Preferences of Non-Coded Amino Acids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7413-7422, JUN 3 2010
abstract, full text, DOI:10.1021/jp102092m

Capone, Ricardo; Mustata, Mirela; Jang, Hyunbum; Arce, Fernando Teran; Nussinov, Ruth; Lal, Ratnesh
Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies
BIOPHYSICAL JOURNAL, 98:2644-2652, JUN 2 2010
abstract, full text, DOI:10.1016/j.bpj.2010.02.024

Colizzi, Francesco; Perozzo, Remo; Scapozza, Leonardo; Recanatini, Maurizio; Cavalli, Andrea
Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7361-7371, JUN 2 2010
abstract, full text, DOI:10.1021/ja100259r

Tainer, John A.; McCammon, J. Andrew; Ivanov, Ivaylo
Recognition of the Ring-Opened State of Proliferating Cell Nuclear Antigen by Replication Factor C Promotes Eukaryotic Clamp-Loading
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7372-7378, JUN 2 2010
abstract, full text, DOI:10.1021/ja100365x

Dubey, Devendra K.; Tomar, Vikas
Role of Molecular Level Interfacial Forces in Hard Biomaterial Mechanics: A Review
ANNALS OF BIOMEDICAL ENGINEERING, 38:2040-2055, JUN 2010
abstract, full text, DOI:10.1007/s10439-010-9988-3

Krah, Alexander; Pogoryelov, Denys; Langer, Julian D.; Bond, Peter J.; Meier, Thomas; Faraldo-Gomez, Jose D.
Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase F-o rotors
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1797:763-772, JUN-JUL 2010
abstract, full text, DOI:10.1016/j.bbabio.2010.04.014

Guallar, Victor; Wallrapp, Frank H.
QM/MM methods: Looking inside heme proteins biochemisty
BIOPHYSICAL CHEMISTRY, 149:1-11, JUN 2010
abstract, full text, DOI:10.1016/j.bpc.2010.03.010

Chen, Wei; Lou, Jizhong; Zhu, Cheng
Simulated Thermal Unfolding of the von Willebrand Factor A Domains
CELLULAR AND MOLECULAR BIOENGINEERING, 3:117-127, JUN 2010
abstract, full text, DOI:10.1007/s12195-010-0117-z

Hertel, Brigitte; Tayefeh, Sascha; Kloss, Thomas; Hewing, Jennifer; Gebhardt, Manuela; Baumeister, Dirk; Moroni, Anna; Thiel, Gerhard; Kast, Stefan M.
Salt bridges in the miniature viral channel Kcv are important for function
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:1057-1068, JUN 2010
abstract, full text, DOI:10.1007/s00249-009-0451-z

Sereda, Yuriy V.; Bishop, Thomas C.
Evaluation of Elastic Rod Models with Long Range Interactions for Predicting Nucleosome Stability
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:867-887, JUN 2010
abstract, full text

Choudhury, Swarup Roy; Singh, Sanjay Kumar; Roy, Sujit; Sengupta, Dibyendu N.
An insight into the sequential, structural and phylogenetic properties of banana 1-aminocyclopropane-1-carboxylate synthase 1 and study of its interaction with pyridoxal-5 '-phosphate and aminoethoxyvinylglycine
JOURNAL OF BIOSCIENCES, 35:281-294, JUN 2010
abstract, full text, DOI:10.1007/s12038-010-0032-4

Virtanen, Salla I.; Pentikainen, Olli T.
Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1005-1011, JUN 2010
abstract, full text, DOI:10.1021/ci100121c

Morrone, Joseph A.; Zhou, Ruhong; Berne, B. J.
Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1798-1804, JUN 2010
abstract, full text, DOI:10.1021/ct100054k

Juneja, Alok; Numata, Jorge; Nilsson, Lennart; Knapp, Ernst Walter
Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1871-1883, JUN 2010
abstract, full text, DOI:10.1021/ct100075m

Morgan, Brittany R.; Massi, Francesca
Accurate Estimates of Free Energy Changes in Charge Mutations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1884-1893, JUN 2010
abstract, full text, DOI:10.1021/ct900565e

Preat, Julien; Rodriguez-Ropero, Francisco; Torras, Juan; Bertran, Oscar; Zanuy, David; Aleman, Carlos
Parameterization of the Torsional Potential for Calix[4]arene-Substituted Poly(thiophene)s
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1741-1751, JUN 2010
abstract, full text, DOI:10.1002/jcc.21463

Zhang, Yuebin; Lu, Ming; Cheng, Yingkun; Li, Zhengqiang
H-NOX domains display different tunnel systems for ligand migration
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:814-819, JUN 2010
abstract, full text, DOI:10.1016/j.jmgm.2010.02.007

Mathew, Damien C.; Luthey-Schulten, Zaida
Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study
ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 40:303-317, JUN 2010
abstract, full text, DOI:10.1007/s11084-010-9207-0

Schulz, Robert; Vargiu, Attilio V.; Collu, Francesca; Kleinekathoefer, Ulrich; Ruggerone, Paolo
Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000806, JUN 2010
abstract, full text, DOI:10.1371/journal.pcbi.1000806

Lin Yingwu
Expanding Protein Functionalities by Rational Design of Artificial Metal-Binding Sites
PROGRESS IN CHEMISTRY, 22:1203-1211, JUN 2010
abstract, full text

Salsbury, Freddie R., Jr.
Effects of Cisplatin Binding to DNA on the Dynamics of the E. coli MutS Dimer
PROTEIN AND PEPTIDE LETTERS, 17:744-750, JUN 2010
abstract, full text

Kovacic, Lidija; Novinec, Marko; Petan, Toni; Krizaj, Igor
Structural basis of the significant calmodulin-induced increase in the enzymatic activity of secreted phospholipases A(2)
PROTEIN ENGINEERING DESIGN & SELECTION, 23:479-487, JUN 2010
abstract, full text, DOI:10.1093/protein/gzq019

Morgan, Brittany R.; Massi, Francesca
A computational study of RNA binding and specificity in the tandem zinc finger domain of TIS11d
PROTEIN SCIENCE, 19:1222-1234, JUN 2010
abstract, full text, DOI:10.1002/pro.401

Weber, Valery; Merchant, Safir; Dixit, Purushottam D.; Asthagiri, D.
Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 204509, MAY 28 2010
abstract, full text, DOI:10.1063/1.3437061

Shinoda, Wataru; DeVane, Russell; Klein, Michael L.
Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6836-6849, MAY 27 2010
abstract, full text, DOI:10.1021/jp9107206

Sun, Tingting; Shao, Xueguang; Cai, Wensheng
Self-assembly behavior of beta-cyclodextrin and imipramine. A Free energy perturbation study
CHEMICAL PHYSICS, 371:84-90, MAY 25 2010
abstract, full text, DOI:10.1016/j.chemphys.2010.04.007

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Zinc ions promote Alzheimer A beta aggregation via population shift of polymorphic states
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:9490-9495, MAY 25 2010
abstract, full text, DOI:10.1073/pnas.0913114107

Unal, Hamiyet; Jagannathan, Rajaganapathi; Bhat, Manjunatha B.; Karnik, Sadashiva S.
Ligand-specific Conformation of Extracellular Loop-2 in the Angiotensin II Type 1 Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:16341-16350, MAY 21 2010
abstract, full text, DOI:10.1074/jbc.M109.094870

Forbes, Jeffrey G.; Flaherty, Denise B.; Ma, Kan; Qadota, Hiroshi; Benian, Guy M.; Wang, Kuan
Extensive and Modular Intrinsically Disordered Segments in C. elegans TTN-1 and Implications in Filament Binding, Elasticity and Oblique Striation
JOURNAL OF MOLECULAR BIOLOGY, 398:672-689, MAY 21 2010
abstract, full text, DOI:10.1016/j.jmb.2010.03.032

DeVane, Russell; Klein, Michael L.; Chiu, Chi-cheng; Nielsen, Steven O.; Shinoda, Wataru; Moore, Preston B.
Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6386-6393, MAY 20 2010
abstract, full text, DOI:10.1021/jp9117369

Chiu, Chi-cheng; DeVane, Russell; Klein, Michael L.; Shinoda, Wataru; Moore, Preston B.; Nielsen, Steven O.
Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6394-6400, MAY 20 2010
abstract, full text, DOI:10.1021/jp9117375

Shi, Wei; Sorescu, Dan C.; Luebke, David R.; Keller, Murphy J.; Wickramanayake, Shan
Molecular Simulations and Experimental Studies of Solubility and Diffusivity for Pure and Mixed Gases of H-2, CO2, and Ar Absorbed in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(Trifluoromethylsulfonyl)amide ([hmim][Tf2N])
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6531-6541, MAY 20 2010
abstract, full text, DOI:10.1021/jp101897b

Chennamsetty, Naresh; Voynov, Vladimir; Kayser, Veysel; Helk, Bernhard; Trout, Bernhardt L.
Prediction of Aggregation Prone Regions of Therapeutic Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6614-6624, MAY 20 2010
abstract, full text, DOI:10.1021/jp911706q

Ko, Youn Jo; Jo, Won Ho
Secondary Water Pore Formation for Proton Transport in a CIC Exchanger Revealed by an Atomistic Molecular-Dynamics Simulation
BIOPHYSICAL JOURNAL, 98:2163-2169, MAY 19 2010
abstract, full text, DOI:10.1016/j.bpj.2010.01.043

Khalili-Araghi, Fatemeh; Jogini, Vishwanath; Yarov-Yarovoy, Vladimir; Tajkhorshid, Emad; Roux, Benoit; Schulten, Klaus
Calculation of the Gating Charge for the Kv1.2 Voltage-Activated Potassium Channel
BIOPHYSICAL JOURNAL, 98:2189-2198, MAY 19 2010
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2010.02.056

Raghunathan, Devanathan; Gayen, Shovanlal; Grueber, Gerhard; Verma, Chandra S.
Crosstalk along the Stalk: Dynamics of the Interaction of Subunits B and F in the A(1)A(O) ATP Synthase of Methanosarcina mazei Gol
BIOCHEMISTRY, 49:4181-4190, MAY 18 2010
abstract, full text, DOI:10.1021/bi9021236

Jana, Gonzalo; Jimenez, Veronica; Villa-Freixa, Jordi; Prat-Resina, Xavier; Delgado, Eduardo; Alderete, Joel
Computational study on the carboligation reaction of acetohidroxyacid synthase: New approach on the role of the HEThDP- intermediate
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1774-1788, MAY 15 2010
abstract, full text, DOI:10.1002/prot.22693

Guo, Hao-Bo; Johs, Alexander; Parks, Jerry M.; Olliff, Lyn; Miller, Susan M.; Summers, Anne O.; Liang, Liyuan; Smith, Jeremy C.
Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II)
JOURNAL OF MOLECULAR BIOLOGY, 398:555-568, MAY 14 2010
abstract, full text, DOI:10.1016/j.jmb.2010.03.020

Pedersen, Palle J.; Adolph, Sidsel K.; Subramanian, Arun K.; Arouri, Ahmad; Andresen, Thomas L.; Mouritsen, Ole G.; Madsen, Robert; Madsen, Mogens W.; Peters, Gunther H.; Clausen, Mads H.
Liposomal Formulation of Retinoids Designed for Enzyme Triggered Release
JOURNAL OF MEDICINAL CHEMISTRY, 53:3782-3792, MAY 13 2010
abstract, full text, DOI:10.1021/jm100190c

Trabuco, Leonardo G.; Harrison, Christopher B.; Schreiner, Eduard; Schulten, Klaus
Recognition of the Regulatory Nascent Chain TnaC by the Ribosome
STRUCTURE, 18:627-637, MAY 12 2010
abstract, full text, TCBG publications, DOI:10.1016/j.str.2010.02.011

Zhang Yue-Bin; Cheng Ying-Kun; Lue Ming; Zhang Hua-Li; Li Zheng-Qiang
Function of the Hydrogen-bonding Network Between the Y-S-R Motif and the Heme Propionate Groups in sGC-HNOX Domain
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 31:1039-1044, MAY 10 2010
abstract, full text

Liu, Yingzhe; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Solubilizing Carbon Nanotubes through Noncovalent Functionalization. Insight from the Reversible Wrapping of Alginic Acid around a Single-Walled Carbon Nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5783-5789, MAY 6 2010
abstract, full text, DOI:10.1021/jp9110772

Fishelovitch, Dan; Shaik, Sason; Wolfson, Haim J.; Nussinov, Ruth
How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel?
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5964-5970, MAY 6 2010
abstract, full text, DOI:10.1021/jp101894k

Biro, Istvan; Pezeshki, Soroosh; Weingart, Helge; Winterhalter, Mathias; Kleinekathoefer, Ulrich
Comparing the Temperature-Dependent Conductance of the Two Structurally Similar E. coli Porins OmpC and OmpF
BIOPHYSICAL JOURNAL, 98:1830-1839, MAY 5 2010
abstract, full text, DOI:10.1016/j.bpj.2010.01.026

Nyce, Heather L.; Stober, Spencer T.; Abrams, Cameron F.; White, Michael M.
Mapping Spatial Relationships between Residues in the Ligand-Binding Domain of the 5-Ht(3) Receptor Using a Molecular Ruler
BIOPHYSICAL JOURNAL, 98:1847-1855, MAY 5 2010
abstract, full text, DOI:10.1016/j.bpj.2010.01.034

McGillick, Brian E.; Balius, Trent E.; Mukherjee, Sudipto; Rizzo, Robert C.
Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20
BIOCHEMISTRY, 49:3575-3592, MAY 4 2010
abstract, full text, DOI:10.1021/bi901915g

Goley, Erin D.; Rammohan, Aravind; Znameroski, Elizabeth A.; Firat-Karalar, Elif Nur; Sept, David; Welch, Matthew D.
An actin-filament-binding interface on the Arp2/3 complex is critical for nucleation and branch stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:8159-8164, MAY 4 2010
abstract, full text, DOI:10.1073/pnas.0911668107

Kast, David; Espinoza-Fonseca, L. Michel; Yi, Christina; Thomas, David D.
Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:8207-8212, MAY 4 2010
abstract, full text, DOI:10.1073/pnas.1001941107

Chiu, Chi-cheng; Maher, Marie C.; Dieckmann, Gregg R.; Nielsen, Steven O.
Molecular Dynamics Study of a Carbon Nanotube Binding Reversible Cyclic Peptide
ACS NANO, 4:2539-2546, MAY 2010
abstract, full text, DOI:10.1021/nn901484w

Collins, Louise; Parker, Alan L.; Gehman, John D.; Eckley, Lorna; Perugini, Matthew A.; Separovic, Frances; Fabre, John W.
Self-Assembly of Peptides into Spherical Nanoparticles for Delivery of Hydrophilic Moieties to the Cytosol
ACS NANO, 4:2856-2864, MAY 2010
abstract, full text, DOI:10.1021/nn901414q

Godsie, M. G.; Tolstova, A. P.; Oferkin, I. V.
Application of Molecular Dynamics Simulation to the Interpretation of Atomic Force Microscopy Data
Biofizika, 55:415-423, MAY-JUN 2010
abstract, full text

Sadiq, S. Kashif; Wright, David W.; Kenway, Owain A.; Coveney, Peter V.
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:890-905, MAY 2010
abstract, full text, DOI:10.1021/ci100007w

Cardone, Antonio; Albers, R. Wayne; Sriram, Ram D.; Pant, Harish C.
Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP
JOURNAL OF COMPUTATIONAL BIOLOGY, 17:707-721, MAY 2010
abstract, full text, DOI:10.1089/cmb.2009.0202

Cickovski, Trevor; Chatterjee, Santanu; Wenger, Jacob; Sweet, Christopher R.; Izaguirre, Jesus A.
MDLab: A Molecular Dynamics Simulation Prototyping Environment
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1345-1356, MAY 2010
abstract, full text, DOI:10.1002/jcc.21418

Mascayano, Carolina; Nunez, Gabriel; Acevedo, Waldo; Caroli Rezende, Marcos
Binding of arachidonic acid and two flavonoid inhibitors to human 12-and 15-lipoxygenases: a steered molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 16:1039-1045, MAY 2010
abstract, full text, DOI:10.1007/s00894-009-0616-9

Ohkubo, Y. Z.; Morrissey, J. H.; Tajkhorshid, E.
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 8:1044-1053, MAY 2010
abstract, full text, DOI:10.1111/j.1538-7836.2010.03826.x

Tsukada, M.; Watanabe, N.; Harada, M.; Tagami, K.
Theoretical simulation of noncontact atomic force microscopy in liquids
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B, 28, MAY 2010
abstract, full text, DOI:10.1116/1.3430541

Yang, Xiao-Dong; Tajkhorshid, Emad; Chen, Lin-Feng
Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-kappa B
MOLECULAR AND CELLULAR BIOLOGY, 30:2170-2180, MAY 1 2010
abstract, full text, DOI:10.1128/MCB.01343-09

Durrant, Jacob D.; Keranen, Henrik; Wilson, Benjamin A.; McCammon, J. Andrew
Computational Identification of Uncharacterized Cruzain Binding Sites
PLOS NEGLECTED TROPICAL DISEASES, 4 Art. No. e676, MAY 2010
abstract, full text, DOI:10.1371/journal.pntd.0000676

Vashisth, Harish; Abrams, Cameron F.
Docking of insulin to a structurally equilibrated insulin receptor ectodomain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1531-1543, MAY 1 2010
abstract, full text, DOI:10.1002/prot.22670

Aleksandrov, Alexey; Simonson, Thomas
Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:13807-13815, APR 30 2010
abstract, full text, DOI:10.1074/jbc.M110.109660

Eastman, Peter; Pande, Vijay S.
Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1268-1272, APR 30 2010
abstract, full text, DOI:10.1002/jcc.21413

Hsin, Jen; Chandler, Danielle E.; Gumbart, James; Harrison, Christopher B.; Sener, Melih; Strumpfer, Johan; Schulten, Klaus
Self-Assembly of Photosynthetic Membranes
CHEMPHYSCHEM, 11:1154-1159, APR 26 2010
abstract, full text, TCBG publications, DOI:10.1002/cphc.200900911

Mroginski, Maria A.; Kaminski, Steve; Hildebrandt, Peter
Raman Spectra of the Phycoviolobilin Cofactor in Phycoerythrocyanin Calculated by QM/MM Methods
CHEMPHYSCHEM, 11:1265-1274, APR 26 2010
abstract, full text, DOI:10.1002/cphc.200900895

Sgourakis, Nikolaos G.; Garcia, Angel E.
The Membrane Complex between Transducin and Dark-State Rhodopsin Exhibits Large-Amplitude Interface Dynamics on the Sub-Microsecond Timescale: Insights from All-Atom MD Simulations
JOURNAL OF MOLECULAR BIOLOGY, 398:161-173, APR 23 2010
abstract, full text, DOI:10.1016/j.jmb.2010.02.032

Carrascal, Noel; Green, David F.
Energetic Decomposition with the Generalized-Born and Poisson-Boltzmann Solvent Models: Lessons from Association of G-Protein Components
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5096-5116, APR 22 2010
abstract, full text, DOI:10.1021/jp910540z

Vidossich, Pietro; Florin, Giacomo; Alfonso-Prieto, Mercedes; Derat, Etienne; Shaik, Sason; Rovira, Carme
On the Role of Water in Peroxidase Catalysis: A Theoretical Investigation of HRP Compound I Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5161-5169, APR 22 2010
abstract, full text, DOI:10.1021/jp911170b

Chen, Xuebo; Gao, Lianghui; Fang, Weihai; Phillips, David Lee
Theoretical Insight into the Photodegradation of a Disulfide Bridged Cyclic Tetrapeptide in Solution and Subsequent Fast Unfolding-Refolding Events
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5206-5214, APR 22 2010
abstract, full text, DOI:10.1021/jp1003616

McCullagh, Martin; Hariharan, Mahesh; Lewis, Frederick D.; Markovitsi, Dimitra; Douki, Thierry; Schatz, George C.
Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5215-5221, APR 22 2010
abstract, full text, DOI:10.1021/jp100983t

Miao, Lingling; Schulten, Klaus
Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics
BIOPHYSICAL JOURNAL, 98:1658-1667, APR 21 2010
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.12.4305

Utiramerur, S.; Paulaitis, M. E.
Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 155102, APR 21 2010
abstract, full text, DOI:10.1063/1.3367977

Pfaendtner, Jim; De La Cruz, Enrique M.; Voth, Gregory A.
Actin filament remodeling by actin depolymerization factor/cofilin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:7299-7304, APR 20 2010
abstract, full text, DOI:10.1073/pnas.0911675107

Nesmelova, Irina V.; Ermakova, Elena; Daragan, Vladimir A.; Pang, Mabel; Menendez, Margarita; Lagartera, Laura; Solis, Dolores; Baum, Linda G.; Mayo, Kevin H.
Lactose Binding to Galectin-1 Modulates Structural Dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity
JOURNAL OF MOLECULAR BIOLOGY, 397:1209-1230, APR 16 2010
abstract, full text, DOI:10.1016/j.jmb.2010.02.033

Pyrkosz, Alexis Black; Eargle, John; Sethi, Anurag; Luthey-Schulten, Zaida
Exit Strategies for Charged tRNA from GluRS
JOURNAL OF MOLECULAR BIOLOGY, 397:1350-1371, APR 16 2010
abstract, full text, DOI:10.1016/j.jmb.2010.02.003

Sotomayor, Marcos; Weihofen, Wilhelm A.; Gaudet, Rachelle; Corey, David P.
Structural Determinants of Cadherin-23 Function in Hearing and Deafness
NEURON, 66:85-100, APR 15 2010
abstract, full text, DOI:10.1016/j.neuron.2010.03.028

Watanabe, Hidekazu; Yamaguchi, Shoichi; Sen, Sobhan; Morita, Akihiro; Tahara, Tahei
"Half-hydration" at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 144701, APR 14 2010
abstract, full text, DOI:10.1063/1.3372620

Steijl, R.; Barakos, George N.
Coupled Navier-Stokes-Molecular dynamics simulations using a multi-physics flow simulation framework
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 62:1081-1106, APR 10 2010
abstract, full text, DOI:10.1002/fld.2053

Lian, Peng; Liu, Limin Angela; Shi, Yongxiang; Bu, Yuxiang; Wei, Dongqing
Tethered-Hopping Model for Protein-DNA Binding and Unbinding Based on Sox2-Oct1-Hoxb1 Ternary Complex Simulations
BIOPHYSICAL JOURNAL, 98:1285-1293, APR 7 2010
abstract, full text, DOI:10.1016/j.bpj.2009.12.4274

Gubbins, Keith E.; Moore, Joshua D.
Molecular Modeling of Matter: Impact and Prospects in Engineering
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 49:3026-3046, APR 7 2010
full text, DOI:10.1021/ie901909c

Maginn, E. J.; Elliott, J. R.
Historical Perspective and Current Outlook for Molecular Dynamics As a Chemical Engineering Tool
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 49:3059-3078, APR 7 2010
full text, DOI:10.1021/ie901898k

Ishii, Seiji; Yano, Takato; Ebihara, Akio; Okamoto, Akihiro; Manzoku, Miho; Hayashi, Hideyuki
Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:10777-10785, APR 2 2010
abstract, full text, DOI:10.1074/jbc.M109.093781

Minoukadeh, K.; Chipot, C.; Lelievre, T.
Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1008-1017, APR 2010
abstract, full text, DOI:10.1021/ct900524t

Bellucci, Luca; Laino, Teodoro; Tafi, Andrea; Botta, Maurizio
Metadynamics Simulations of Enantioselective Acylation Give Insights into the Catalytic Mechanism of Burkholderia cepacia Lipase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1145-1156, APR 2010
abstract, full text, DOI:10.1021/ct900636w

Glass, Dennis C.; Krishnan, Marimuthu; Nutt, David R.; Smith, Jeremy C.
Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1390-1400, APR 2010
abstract, full text, DOI:10.1021/ct9006508

Lundberg, Marcus; Sasakura, Yoko; Zheng, Guishan; Morokuma, Keiji
Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1413-1427, APR 2010
abstract, full text, DOI:10.1021/ct100029p

Fratev, Filip; Jonsdottir, Svava Osk
The phosphorylation specificity of B-RAF(WT), B-RAF(D594V), B-RAF(V600E) and B-RAF(K601E) kinases: An in silico study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:598-603, APR 2010
abstract, full text, DOI:10.1016/j.jmgm.2009.12.005

Hilder, T. A.; Yang, R.; Ganesh, V.; Gordon, D.; Bliznyuk, A.; Rendell, A. P.; Chung, S. -H.
Validity of current force fields for simulations on boron nitride nanotubes
MICRO & NANO LETTERS, 5:150-156, APR 2010
abstract, full text, DOI:10.1049/mnl.2009.0112

Tchesnokova, Veronika; McVeigh, Annette L.; Kidd, Brian; Yakovenko, Olga; Thomas, Wendy E.; Sokurenko, Evgeni V.; Savarino, Stephen J.
Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli
MOLECULAR MICROBIOLOGY, 76:489-502, APR 2010
abstract, full text, DOI:10.1111/j.1365-2958.2010.07116.x

Belyy, Vladislav; Anishkin, Andriy; Kamaraju, Kishore; Liu, Naili; Sukharev, Sergei
The tension-transmitting 'clutch' in the mechanosensitive channel MscS
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17:451-U92, APR 2010
abstract, full text, DOI:10.1038/nsmb.1775

Chinappi, M.; Casciola, C. M.
Intrinsic slip on hydrophobic self-assembled monolayer coatings
PHYSICS OF FLUIDS, 22 Art. No. 042003, APR 2010
abstract, full text, DOI:10.1063/1.3394120

Mazorra-Manzano, Miguel A.; Tanaka, Takuji; Dee, Derek R.; Yada, Rickey Y.
Structure-function characterization of the recombinant aspartic proteinase A1 from Arabidopsis thaliana
PHYTOCHEMISTRY, 71:515-523, APR 2010
abstract, full text, DOI:10.1016/j.phytochem.2009.12.005

Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong
MUFOLD: A new solution for protein 3D structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1137-1152, APR 2010
abstract, full text, DOI:10.1002/prot.22634

Luan, Binquan; Carr, Rogan; Caffrey, Martin; Aksimentiev, Aleksei
The effect of calcium on the conformation of cobalamin transporter BtuB
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1153-1162, APR 2010
abstract, full text, DOI:10.1002/prot.22635

Giambasxu, George M.; Lee, Tai-Sung; Sosa, Carlos P.; Robertson, Michael P.; Scott, William G.; York, Darrin M.
Identification of dynamical hinge points of the L1 ligase molecular switch
RNA-A PUBLICATION OF THE RNA SOCIETY, 16:769-780, APR 2010
abstract, full text, DOI:10.1261/rna.1897810

Schwander, P.; Fung, R.; Phillips, G. N., Jr.; Ourmazd, A.
Mapping the conformations of biological assemblies
NEW JOURNAL OF PHYSICS, 12 Art. No. 035007, MAR 31 2010
abstract, full text, DOI:10.1088/1367-2630/12/3/035007

Van Schouwen, Bryan M. B.; Nakano, Miki; Watanabe, Hirofumi; Tanaka, Shigenori; Gordon, Heather L.; Rothstein, Stuart M.
Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 944:12-20, MAR 30 2010
abstract, full text, DOI:10.1016/j.theochem.2009.12.019

Yamtich, Jen; Starcevic, Daniela; Lauper, Julia; Smith, Elenoe; Shi, Idina; Rangarajan, Sneha; Jaeger, Joachim; Sweasy, Joann B.
Hinge Residue I174 Is Critical for Proper dNTP Selection by DNA Polymerase beta
BIOCHEMISTRY, 49:2326-2334, MAR 23 2010
abstract, full text, DOI:10.1021/bi901735a

Palmer, David S.; Christensen, Anders U.; Sorensen, Jesper; Celik, Leyla; Qvist, Karsten Bruun; Schiott, Birgit
Bovine Chymosin: A Computational Study of Recognition and Binding of Bovine kappa-Casein
BIOCHEMISTRY, 49:2563-2573, MAR 23 2010
abstract, full text, DOI:10.1021/bi902193u

Limongelli, Vittorio; Bonomi, Massimiliano; Marinelli, Luciana; Luigi Gervasio, Francesco; Cavalli, Andrea; Novellino, Ettore; Parrinello, Michele
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:5411-5416, MAR 23 2010
full text, DOI:10.1073/pnas.0913377107

Timko, Jeff; Bucher, Denis; Kuyucak, Serdar
Dissociation of NaCl in water from ab initio molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 114510, MAR 21 2010
abstract, full text, DOI:10.1063/1.3360310

Volkmann, Gerrit; Murphy, Peter W.; Rowland, Elden E.; Cronan, John E., Jr.; Liu, Xiang-Qin; Blouin, Christian; Byers, David M.
Intein-mediated Cyclization of Bacterial Acyl Carrier Protein Stabilizes Its Folded Conformation but Does Not Abolish Function
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:8605-8614, MAR 19 2010
abstract, full text, DOI:10.1074/jbc.M109.060863

Diaz, Jennifer A. Carvajal; Cagin, Tahir
Thermo-mechanical stability and strength of peptide nanostructures from molecular dynamics: self-assembled cyclic peptide nanotubes
NANOTECHNOLOGY, 21 Art. No. 115703, MAR 19 2010
abstract, full text, DOI:10.1088/0957-4484/21/11/115703

Lee, Eric H.; Hsin, Jen; von Castelmur, Eleonore; Mayans, Olga; Schulten, Klaus
Tertiary and Secondary Structure Elasticity of a Six-Ig Titin Chain
BIOPHYSICAL JOURNAL, 98:1085-1095, MAR 17 2010
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.12.4192

Wijesinha-Bettoni, Ramani; Alexeev, Yuri; Johnson, Phil; Marsh, Justin; Sancho, Ana I.; Abdullah, Syed U.; Mackie, Alan R.; Shewry, Peter R.; Smith, Lorna J.; Mills, E. N. Clare
The Structural Characteristics of Nonspecific Lipid Transfer Proteins Explain Their Resistance to Gastroduodenal Proteolysis
BIOCHEMISTRY, 49:2130-2139, MAR 16 2010
abstract, full text, DOI:10.1021/bi901939z

Abrams, Cameron F.; Vanden-Eijnden, Eric
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:4961-4966, MAR 16 2010
abstract, full text, DOI:10.1073/pnas.0914540107

Westrich, Ligia; Gil-Mast, Sara; Kortagere, Sandhya; Kuzhikandathil, Eldo V.
Development of tolerance in D3 dopamine receptor signaling is accompanied by distinct changes in receptor conformation
BIOCHEMICAL PHARMACOLOGY, 79:897-907, MAR 15 2010
abstract, full text, DOI:10.1016/j.bcp.2009.10.016

Rykunov, Dmitry; Fiser, Andras
New statistical potential for quality assessment of protein models and a survey of energy functions
BMC BIOINFORMATICS, 11 Art. No. 128, MAR 12 2010
abstract, full text, DOI:10.1186/1471-2105-11-128

Priyakumar, U. Deva; MacKerell, Alexander D., Jr.
Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch
JOURNAL OF MOLECULAR BIOLOGY, 396:1422-1438, MAR 12 2010
abstract, full text, DOI:10.1016/j.jmb.2009.12.024

Liu, Jin; Nussinov, Ruth
Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases
JOURNAL OF MOLECULAR BIOLOGY, 396:1508-1523, MAR 12 2010
abstract, full text, DOI:10.1016/j.jmb.2010.01.022

Knox, Craig K.; Voth, Gregory A.
Probing Selected Morphological Models of Hydrated Nation Using Large-Scale Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:3205-3218, MAR 11 2010
abstract, full text, DOI:10.1021/jp9112409

Vassiliev, Serguei; Comte, Pascal; Mahboob, Abdullah; Bruce, Doug
Tracking the Flow of Water through Photosystem II Using Molecular Dynamics and Streamline Tracing
BIOCHEMISTRY, 49:1873-1881, MAR 9 2010
abstract, full text, DOI:10.1021/bi901900s

Antipova, Olga; Orgel, Joseph P. R. O.
In Situ D-periodic Molecular Structure of Type II Collagen
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:7087-7096, MAR 5 2010
abstract, full text, DOI:10.1074/jbc.M109.060400

Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu; Pande, Vijay S.; Chodera, John D.; Schnieders, Michael J.; Haque, Imran; Mobley, David L.; Lambrecht, Daniel S.; DiStasio, Robert A., Jr.; Head-Gordon, Martin; Clark, Gary N. I.; Johnson, Margaret E.; Head-Gordon, Teresa
Current Status of the AMOEBA Polarizable Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2549-2564, MAR 4 2010
abstract, full text, DOI:10.1021/jp910674d

Khalfa, Adil; Tarek, Mounir
On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2676-2684, MAR 4 2010
abstract, full text, DOI:10.1021/jp9064196

Vivcharuk, Victor; Kaznessis, Yiannis
Free Energy Profile of the Interaction between a Monomer or a Dimer of Protegrin-1 in a Specific Binding Orientation and a Model Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2790-2797, MAR 4 2010
abstract, full text, DOI:10.1021/jp909640g

Kang, Yu; Wang, Qi; Liu, Ying-Chun; Shen, Jia-Wei; Wu, Tao
Diameter Selectivity of Protein Encapsulation in Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2869-2875, MAR 4 2010
abstract, full text, DOI:10.1021/jp905995s

Vorobyev, Dmitriy Yu.; Kuo, Chun-Hung; Kuroda, Daniel G.; Scott, J. Nathan; Vanderkooi, Jane M.; Hochstrasser, Robin M.
Water-Induced Relaxation of a Degenerate Vibration of Guanidium Using 2D IR Echo Spectroscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2944-2953, MAR 4 2010
abstract, full text, DOI:10.1021/jp909531s

Wang, Qiuming; Zhao, Chao; Zhao, Jun; Wang, Jingdai; Yang, Jui-Chen; Yu, Xiang; Zhen, Jie
Comparative Molecular Dynamics Study of A beta Adsorption on the Self-Assembled Monolayers
LANGMUIR, 26:3308-3316, MAR 2 2010
abstract, full text, DOI:10.1021/la903070y

Feng, Jianhua; Lucchinetti, Eliana; Enkavi, Giray; Wang, Yi; Gehrig, Peter; Roschitzki, Bernd; Schaub, Marcus C.; Tajkhorshid, Emad; Zaugg, Kathrin; Zaugg, Michael
Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY, 298:C740-C748, MAR 2010
abstract, full text, DOI:10.1152/ajpcell.00310.2009

Yamaguchi, Takami; Ishikawa, Takuji; Imai, Y.; Matsuki, N.; Xenos, Mikhail; Deng, Yuefan; Bluestein, Danny
Particle-Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices: Challenges and Future Directions
ANNALS OF BIOMEDICAL ENGINEERING, 38:1225-1235, MAR 2010
abstract, full text, DOI:10.1007/s10439-010-9904-x

Qiu, Hu; Ma, Shaojie; Shen, Rong; Guo, Wanlin
Dynamic and energetic mechanisms for the distinct permeation rate in AQP1 and AQP0
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:318-326, MAR 2010
abstract, full text, DOI:10.1016/j.bbamem.2009.11.015

Wang, Yeng-Tseng; Chan, Chen-hsiung; Su, Zhi-Yuan; Chen, Cheng-Lung
Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A(H1N1) influenza neuraminidase
BIOPHYSICAL CHEMISTRY, 147:74-80, MAR 2010
abstract, full text, DOI:10.1016/j.bpc.2009.12.002

Varin, Thibault; Gutierrez-de-Teran, Hugo; Castro, Marian; Brea, Jose; Fabis, Frederic; Dauphin, Francois; Aqvist, Johan; Lepailleur, Alban; Perez, Pilar; Burgueno, Javier; Miguel Vela, Jose; Isabel Loza, Maria; Rodrigo, Jordi
Phe369(7.38) at human 5-HT7 receptors confers interspecies selectivity to antagonists and partial agonists
BRITISH JOURNAL OF PHARMACOLOGY, 159:1069-1081, MAR 2010
abstract, full text, DOI:10.1111/j.1476-5381.2009.00481.x

Branschaedel, Marcus; Aird, Andrew; Zappe, Andrea; Tietz, Carsten; Krippner-Heidenreich, Anja; Scheurich, Peter
Dual function of cysteine rich domain (CRD) 1 of TNF receptor type 1: Conformational stabilization of CRD2 and control of receptor responsiveness
CELLULAR SIGNALLING, 22:404-414, MAR 2010
abstract, full text, DOI:10.1016/j.cellsig.2009.10.011

Bahar, Ivet; Lezon, Timothy R.; Bakan, Ahmet; Shrivastava, Indira H.
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
CHEMICAL REVIEWS, 110:1463-1497, MAR 2010
full text, DOI:10.1021/cr900095e

Tan, Jian J.; Cong, Xiao J.; Hu, Li M.; Wang, Cun X.; Jia, Lee; Liang, Xing-Jie
Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection
DRUG DISCOVERY TODAY, 15:186-197, MAR 2010
abstract, full text, DOI:10.1016/j.drudis.2010.01.004

Swain, Martin; Silva, Candida G.; Loureiro-Ferreira, Nuno; Ostropytskyy, Vitaliy; Brito, Joao; Riche, Olivier; Stahl, Frederick; Dubitzky, Werner; Brito, Rui M. M.
P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data mining
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING-THEORY METHODS AND APPLICATIONS, 26:424-433, MAR 2010
abstract, full text, DOI:10.1016/j.future.2009.08.008

Buch, I.; Harvey, M. J.; Giorgino, T.; Anderson, D. P.; De Fabritiis, G.
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:397-403, MAR 2010
abstract, full text, DOI:10.1021/ci900455r

Liwo, Adam; Oldziej, Stanislaw; Czaplewski, Cezary; Kleinerman, Dana S.; Blood, Philip; Scheraga, Harold A.
Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:890-909, MAR 2010
abstract, full text, DOI:10.1021/ct9004068

Ramanathan, Arvind; Agarwal, Pratul K.; Kurnikova, Maria; Langmead, Christopher J.
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL BIOLOGY, 17:309-324, MAR 2010
abstract, full text, DOI:10.1089/cmb.2009.0167

Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D., Jr.
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:671-690, MAR 2010
abstract, full text, DOI:10.1002/jcc.21367

Soriano-Ursua, Marvin A.; Trujillo-Ferrara, Jose G.; Alvarez-Cedillo, Jusus; Correa-Basurto, Jose
Docking studies on a refined human beta(2) adrenoceptor model yield theoretical affinity values in function with experimental values for R-ligands, but not for S-antagonists
JOURNAL OF MOLECULAR MODELING, 16:401-409, MAR 2010
abstract, full text, DOI:10.1007/s00894-009-0563-5

Isea, Raul; Luis Ramirez, Jose; Hoebeke, Johan
Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics
MEMORIAS DO INSTITUTO OSWALDO CRUZ, 105:123-126, MAR 2010
abstract, full text, DOI:10.1590/S0074-02762010000200002

Cilurzo, Francesco; Gennari, Chiara G. M.; Selmin, Francesca; Vistoli, Giulio
Effects of Metal Ions on Entero-Soluble Poly(methacrylic acid-methyl methacrylate) Coating: A Combined Analysis by ATR-FTIR Spectroscopy and Computational Approaches
MOLECULAR PHARMACEUTICS, 7:421-430, MAR-APR 2010
abstract, full text, DOI:10.1021/mp900199a

Lash-Van Wyhe, L. Leanne; Postila, Pekka A.; Tsubone, Koichi; Sasaki, Makoto; Pentikainen, Olli T.; Sakai, Ryuichi; Swanson, Geoffrey T.
Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine
NEUROPHARMACOLOGY, 58:640-649, MAR 2010
abstract, full text, DOI:10.1016/j.neuropharm.2009.11.013

Hicks, Stephen D.; Henley, C. L.
Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations
PHYSICAL REVIEW E, 81 Art. No. 030903, MAR 2010
abstract, full text, DOI:10.1103/PhysRevE.81.030903

Gedeon, Patrick C.; Indarte, Martin; Surratt, Christopher K.; Madura, Jeffry D.
Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:797-811, MAR 2010
abstract, full text, DOI:10.1002/prot.22601

Anishkin, Andriy; Milac, Adina L.; Guy, H. Robert
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:932-949, MAR 2010
abstract, full text, DOI:10.1002/prot.22618

Havel, Nurit; Geisbrecht, Brian V.; Lambris, John; Kavraki, Lydia
Multi-scale characterization of the energy landscape of proteins with application to the C3d/Efb-C complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1004-1014, MAR 2010
abstract, full text, DOI:10.1002/prot.22624

Dendzik, Z.; Gorny, K.; Kosmider, M.; Zurek, S.
CONFINEMENT SIZE EFFECT IN DIPOLAR RELAXATION OF GLYCEROL MOLECULES CLUSTER ENCAPSULATED INSIDE CARBON NANOTUBES - COMPUTER SIMULATION STUDY
REVIEWS ON ADVANCED MATERIALS SCIENCE, 23:42-51, MAR 2010
abstract, full text

Gburski, Zygmunt; Gorny, Krzysztof; Raczynski, Przemyslaw
The impact of a carbon nanotube on the cholesterol domain localized on a protein surface
SOLID STATE COMMUNICATIONS, 150:415-418, MAR 2010
abstract, full text, DOI:10.1016/j.ssc.2009.12.005

Diao, Jiankuai; Maniotis, Andrew J.; Folberg, Robert; Tajkhorshid, Emad
Interplay of mechanical and binding properties of Fibronectin type I
THEORETICAL CHEMISTRY ACCOUNTS, 125:397-405, MAR 2010
abstract, full text, DOI:10.1007/s00214-009-0677-y

Artavanis-Tsakonas, Katerina; Weihofen, Wilhelm A.; Antos, John M.; Coleman, Bradley I.; Comeaux, Christy A.; Duraisingh, Manoj T.; Gaudet, Rachelle; Ploegh, Hidde L.
Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:6857-6866, FEB 26 2010
abstract, full text, DOI:10.1074/jbc.M109.072405

Choudhary, Om P.; Ujwal, Rachna; Kowallis, William; Coalson, Rob; Abramson, Jeff; Grabe, Michael
The Electrostatics of VDAC: Implications for Selectivity and Gating
JOURNAL OF MOLECULAR BIOLOGY, 396:580-592, FEB 26 2010
abstract, full text, DOI:10.1016/j.jmb.2009.12.006

Barakat, Khaled; Mane, Jonathan; Friesen, Douglas; Tuszynski, Jack
Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:555-568, FEB 26 2010
abstract, full text, DOI:10.1016/j.jmgm.2009.12.003

Harmon, Christopher W.; Grimm, Ronald L.; McIntire, Theresa M.; Peterson, Mark D.; Njegic, Bosiljka; Angel, Vanessa M.; Alshawa, Ahmad; Underwood, Joelle S.; Tobias, Douglas J.; Gerber, R. Benny; Gordon, Mark S.; Hemminger, John C.; Nizkorodov, Sergey A.
Hygroscopic Growth and Deliquescence of NaCl Nanoparticles Mixed with Surfactant SDS
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2435-2449, FEB 25 2010
abstract, full text, DOI:10.1021/jp909661q

Cheluvaraja, S.; Ortoleva, P.
Thermal nanostructure: An order parameter multiscale ensemble approach
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 075102, FEB 21 2010
abstract, full text, DOI:10.1063/1.3316793

Pfaendtner, Jim; Lyman, Edward; Pollard, Thomas D.; Voth, Gregory A.
Structure and Dynamics of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 396:252-263, FEB 19 2010
abstract, full text, DOI:10.1016/j.jmb.2009.11.034

Liu, Jian; Fan, Jianfen; Tang, Min; Zhou, Weiqun
Molecular Dynamics Simulation for the Structure of the Water Chain in a Transmembrane Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY A, 114:2376-2383, FEB 18 2010
abstract, full text, DOI:10.1021/jp910624z

Pedersen, Ulf R.; Peters, Gunther H.; Schroder, Thomas B.; Dyre, Jeppe C.
Correlated Volume-Energy Fluctuations of Phospholipid Membranes: A Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2124-2130, FEB 18 2010
abstract, full text, DOI:10.1021/jp9086865

Furini, Simone; Domene, Carmen; Cavalcanti, Silvio
Insights into the Sliding Movement of the Lac Repressor Nonspecifically Bound to DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2238-2245, FEB 18 2010
abstract, full text, DOI:10.1021/jp906504m

Waegele, Matthias M.; Gai, Feng
Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:781-786, FEB 18 2010
abstract, full text, DOI:10.1021/jz900429z

Kim, Hyun Jin; Choi, Moo Young; Kim, Hyung J.; Llinas, Miguel
Conformational Dynamics and Ligand Binding in the Multi-Domain Protein PDC109
PLOS ONE, 5 Art. No. e9180, FEB 18 2010
abstract, full text, DOI:10.1371/journal.pone.0009180

Zhang, Hao; Wang, Peng; Papangelopoulos, Nikitas; Xu, Ying; Sette, Alessandro; Bourne, Philip E.; Lund, Ole; Ponomarenko, Julia; Nielsen, Morten; Peters, Bjoern
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
PLOS ONE, 5 Art. No. e9272, FEB 17 2010
abstract, full text, DOI:10.1371/journal.pone.0009272

Enkavi, Giray; Tajkhorshid, Emad
Simulation of Spontaneous Substrate Binding Revealing the Binding Pathway and Mechanism and Initial Conformational Response of GlpT
BIOCHEMISTRY, 49:1105-1114, FEB 16 2010
abstract, full text, DOI:10.1021/bi901412a

Hartshorn, Christopher M.; Jewett, Cayla M.; Brozik, James A.
Molecular Effects of a Nanocrystalline Quartz Support upon Planar Lipid Bilayers
LANGMUIR, 26:2609-2617, FEB 16 2010
abstract, full text, DOI:10.1021/la904308g

Latawiec, Diane; Herrera, Fernando; Bek, Alpan; Losasso, Valeria; Candotti, Michela; Benetti, Federico; Carlino, Elvio; Kranjc, Agata; Lazzarino, Marco; Gustincich, Stefano; Carloni, Paolo; Legname, Giuseppe
Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs
PLOS ONE, 5 Art. No. e9234, FEB 16 2010
abstract, full text, DOI:10.1371/journal.pone.0009234

Wang, Yi; Tajkhorshid, Emad
Nitric oxide conduction by the brain aquaporin AQP4
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:661-670, FEB 15 2010
abstract, full text, DOI:10.1002/prot.22595

Zhang Jilong; Hou Ruizhe; Li Zhuo; Zheng Qingchuan; Zhang Hongxing
Homology Modeling of Human Extracellular Signal-regulated Kinase 1 and Docking and Reconstitution of Its Inhibitors
ACTA CHIMICA SINICA, 68:222-226, FEB 14 2010
abstract, full text

Gu, Feifei; Jones, Martin K.; Chen, Jianguo; Patterson, James C.; Catte, Andrea; Jerome, W. Gray; Li, Ling; Segrest, Jere P.
Structures of Discoidal High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:4652-4665, FEB 12 2010
abstract, full text, DOI:10.1074/jbc.M109.069914

Freire, Mara G.; Neves, Catarina M. S. S.; Silva, Artur M. S.; Santos, Luis M. N. B. F.; Marrucho, Isabel M.; Rebelo, Luis P. N.; Shah, Jindal K.; Maginn, Edward J.; Coutinho, Joao A. P.
H-1 NMR and Molecular Dynamics Evidence for an Unexpected Interaction on the Origin of Salting-In/Salting-Out Phenomena
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2004-2014, FEB 11 2010
abstract, full text, DOI:10.1021/jp9095634

Sterpone, Fabio; Stirnemann, Guillaume; Hynes, James T.; Laage, Damien
Water Hydrogen-Bond Dynamics around Amino Acids: The Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2083-2089, FEB 11 2010
abstract, full text, DOI:10.1021/jp9119793

Mori, Takaharu; Ishitani, Ryuichiro; Tsukazaki, Tomoya; Nureki, Osamu; Sugita, Yuji
Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon
BIOCHEMISTRY, 49:945-950, FEB 9 2010
abstract, full text, DOI:10.1021/bi901594w

Holst, Birgitte; Nygaard, Rie; Valentin-Hansen, Louise; Bach, Anders; Engelstoft, Maja S.; Petersen, Pia S.; Frimurer, Thomas M.; Schwartz, Thue W.
A Conserved Aromatic Lock for the Tryptophan Rotameric Switch in TM-VI of Seven-transmembrane Receptors
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:3973-3985, FEB 5 2010
abstract, full text, DOI:10.1074/jbc.M109.064725

Guzman, Dora L.; Randall, Arlo; Baldi, Pierre; Guan, Zhibin
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:1989-1994, FEB 2 2010
abstract, full text, DOI:10.1073/pnas.0905796107

Gannon, G.; Greer, J. C.; Larsson, J. A.; Thompson, D.
Molecular Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer Formation
ACS NANO, 4:921-932, FEB 2010
abstract, full text, DOI:10.1021/nn901821h

Costache, Aurora D.; Ghosh, Jayeeta; Knight, Doyle D.; Kohn, Joachim
Computational Methods for the Development of Polymeric Biomaterials
ADVANCED ENGINEERING MATERIALS, 12:B3-B17, FEB 2010
abstract, full text, DOI:10.1002/adem.200980020

Michel Espinoza-Fonseca, L.; Wong-Ramirez, Carlos; Trujillo-Ferrara, Jose G.
Tyr74 is essential for the formation, stability and function of Plasmodium falciparum triosephosphate isomerase dimer
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 494:46-57, FEB 1 2010
abstract, full text, DOI:10.1016/j.abb.2009.11.009

Qin, Wu; Li, Xin; Bian, Wen-Wen; Fan, Xiu-Juan; Qi, Jing-Yao
Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces
BIOMATERIALS, 31:1007-1016, FEB 2010
abstract, full text, DOI:10.1016/j.biomaterials.2009.10.013

Deeb, Omar; Cecilia Rosales-Hernandez, Martha; Gomez-Castro, Carlos; Garduno-Juarez, Ramon; Correa-Basurto, Jose
Exploration of Human Serum Albumin Binding Sites by Docking and Molecular Dynamics Flexible Ligand-Protein Interactions
BIOPOLYMERS, 93:161-170, FEB 2010
abstract, full text, DOI:10.1002/bip.21314

Stopa, Barbara; Piekarska, Barbara; Konieczny, Leszek; Krol, Marcin; Rybarska, Janina; Jagusiak, Anna; Spolnik, Pawel; Roterman, Irena; Urbanowicz, Barbara; Piwowar, Piotr; Lewinski, Krzysztof
Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered under the influence of an electric field
CENTRAL EUROPEAN JOURNAL OF CHEMISTRY, 8:41-50, FEB 2010
abstract, full text, DOI:10.2478/s11532-009-0107-y

Abate, Carmen; Elenewski, Justin; Niso, Mauro; Berardi, Francesco; Colabufo, Nicola Antonio; Azzariti, Amalia; Perrone, Roberto; Glennon, Richard A.
Interaction of the sigma(2) Receptor Ligand PB28 with the Human Nucleosome: Computational and Experimental Probes of Interaction with the H2A/H2B Dimer
CHEMMEDCHEM, 5:268-273, FEB 2010
abstract, full text, DOI:10.1002/cmdc.200900402

Devireddy, Ram V.
Statistical thermodynamics of biomembranes
CRYOBIOLOGY, 60:80-90, FEB 2010
abstract, full text, DOI:10.1016/j.cryobiol.2009.05.001

Park, Jin Woo; Jo, Won Ho
Computational design of novel, high-affinity neuraminidase inhibitors for H5N1 avian influenza virus
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:536-541, FEB 2010
abstract, full text, DOI:10.1016/j.ejmech.2009.10.040

Tuszynska, Irina; Bujnicki, Janusz M.
Predicting Atomic Details of the Unfolding Pathway for YibK, a Knotted Protein from the SPOUT Superfamily
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:511-520, FEB 2010
abstract, full text

Bjelkmar, Par; Larsson, Per; Cuendet, Michel A.; Hess, Berk; Lindahl, Erik
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:459-466, FEB 2010
abstract, full text, DOI:10.1021/ct900549r

Ko, Youn Jo; Jo, Won Ho
Chloride Ion Conduction Without Water Coordination in the Pore of ClC Protein
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:603-611, FEB 2010
abstract, full text, DOI:10.1002/jcc.21432

Gorantla, Sandeep; Avdoshenko, Stanislav; Boerrnert, Felix; Bachmatiuk, Alicja; Dimitrakopoulou, Maria; Schaeffel, Franziska; Schoenfelder, Ronny; Thomas, Juergen; Gemming, Thomas; Warner, Jamie H.; Cuniberti, Gianaurelio; Eckert, Juergen; Buechner, Bernd; Ruemmeli, Mark H.
Enhanced pi-pi interactions between a C-60 fullerene and a buckle bend on a double-walled carbon nanotube
NANO RESEARCH, 3:92-97, FEB 2010
abstract, full text, DOI:10.1007/s12274-010-1012-6

Postila, Pekka A.; Swanson, Geoffrey T.; Pentikainen, Olli T.
Exploring kainate receptor pharmacology using molecular dynamics simulations
NEUROPHARMACOLOGY, 58:515-527, FEB 2010
abstract, full text, DOI:10.1016/j.neuropharm.2009.08.019

Kanth, J. Maruthi Pradeep; Vemparala, Satyavani; Anishetty, Ramesh
Long-distance correlations in molecular orientations of liquid water and shape-dependent hydrophobic force
PHYSICAL REVIEW E, 81 Art. No. 021201, FEB 2010
abstract, full text, DOI:10.1103/PhysRevE.81.021201

Salimi, Neema L.; Ho, Bosco; Agard, David A.
Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable alpha-Lytic Protease
PLOS COMPUTATIONAL BIOLOGY, 6 Art. No. e1000689, FEB 2010
abstract, full text, DOI:10.1371/journal.pcbi.1000689

Rodrigues, J. Rui; Simoes, Carlos J. V.; Silva, Candida G.; Brito, Rui M. M.
Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations
PROTEIN SCIENCE, 19:202-219, FEB 2010
abstract, full text, DOI:10.1002/pro.289

Eichenbaum, Kenneth D.; Rodriguez, Yoel; Mezei, Mihaly; Osman, Roman
The energetics of the acetylation switch in p53-mediated transcriptional activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:447-456, FEB 1 2010
abstract, full text, DOI:10.1002/prot.22565

Basse, Nicolas; Kaar, Joel L.; Settanni, Giovanni; Joerger, Andreas C.; Rutherford, Trevor J.; Fersht, Alan R.
Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant
CHEMISTRY & BIOLOGY, 17:46-56, JAN 29 2010
abstract, full text, DOI:10.1016/j.chembiol.2009.12.011

Weng, Jing-Wei; Fan, Kang-Nian; Wang, Wen-Ning
The Conformational Transition Pathway of ATP Binding Cassette Transporter MsbA Revealed by Atomistic Simulations
JOURNAL OF BIOLOGICAL CHEMISTRY, 285 Art. No. 3053, JAN 29 2010
abstract, full text, DOI:10.1074/jbc.M109.056432

Floquet, Nicolas; MiKadmi, Celine; Perahia, David; Gagne, Didier; Berge, Gilbert; Marie, Jacky; Baneres, Jean-Louis; Galleyrand, Jean-Claude; Fehrentz, Jean-Alain; Martinez, Jean
Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR)
JOURNAL OF MOLECULAR BIOLOGY, 395:769-784, JAN 29 2010
abstract, full text, DOI:10.1016/j.jmb.2009.09.051

Ovchinnikov, Victor; Trout, Bernhardt L.; Karplus, Martin
Mechanical Coupling in Myosin V: A Simulation Study
JOURNAL OF MOLECULAR BIOLOGY, 395:815-833, JAN 29 2010
abstract, full text, DOI:10.1016/j.jmb.2009.10.029

Kuroda, Daniel G.; Vorobyev, Dmitriy Yu.; Hochstrasser, Robin M.
Ultrafast relaxation and 2D IR of the aqueous trifluorocarboxylate ion
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 044501, JAN 28 2010
abstract, full text, DOI:10.1063/1.3285265

Yang, Lu; Fishbine, Brian H.; Migliori, Albert; Pratt, Lawrence R.
Dielectric saturation of liquid propylene carbonate in electrical energy storage applications
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 044701, JAN 28 2010
abstract, full text, DOI:10.1063/1.3294560

Maekawa, Hiroaki; Ge, Nien-Hui
Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1434-1446, JAN 28 2010
abstract, full text, DOI:10.1021/jp908695g

Martinez, Leandro; Souza, Paulo C. T.; Garcia, Wanius; Batista, Fernanda A. H.; Portugal, Rodrigo V.; Nascimento, Alessandro S.; Nakahira, Marcel; Lima, Luis M. T. R.; Polikarpov, Igor; Skaf, Munir S.
On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1529-1540, JAN 28 2010
abstract, full text, DOI:10.1021/jp911554p

Grimm, Ronald L.; Tobias, Douglas J.; Hemminger, John C.
D2O Water Interaction with Textured Carboxylic Acid-Terminated Monolayer Surfaces Characterized by Temperature-Programmed Desorption and Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 114:1570-1579, JAN 28 2010
abstract, full text, DOI:10.1021/jp9064642

Landstrom, Jens; Widmalm, Goran
Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect
CARBOHYDRATE RESEARCH, 345:330-333, JAN 26 2010
abstract, full text, DOI:10.1016/j.carres.2009.11.003

Durer, Zeynep A. Oztug; Diraviyam, Karthikeyan; Sept, David; Kudryashov, Dmitri S.; Reisler, Emil
F-Actin Structure Destabilization and DNase I Binding Loop Fluctuations Mutational Cross-Linking and Electron Microscopy Analysis of Loop States and Effects on F-Actin
JOURNAL OF MOLECULAR BIOLOGY, 395:544-557, JAN 22 2010
abstract, full text, DOI:10.1016/j.jmb.2009.11.001

Morriss-Andrews, Alex; Rottler, Joerg; Plotkin, Steven S.
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
JOURNAL OF CHEMICAL PHYSICS, 132 Art. No. 035105, JAN 21 2010
abstract, full text, DOI:10.1063/1.3269994

Titov, Alexey V.; Wang, Boyang; Sint, Kyaw; Kral, Petr
Controllable Synthetic Molecular Channels: Biomimetic Ammonia Switch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1174-1179, JAN 21 2010
abstract, full text, DOI:10.1021/jp9103933

Sul, Soohwan; Feng, Yuan; Le, Uyen; Tobias, Douglas J.; Ge, Nien-Hui
Interactions of Tyrosine in Leu-Enkephalin at a Membrane-Water Interface: An Ultrafast Two-Dimensional Infrared Study Combined with Density Functional Calculations and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1180-1190, JAN 21 2010
abstract, full text, DOI:10.1021/jp9105844

Goldsmith, Jacob; Martens, Craig C.
Molecular Dynamics Simulation of Salt Rejection in Model Surface-Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:528-535, JAN 21 2010
abstract, full text, DOI:10.1021/jz900173w

Lupyan, Dmitry; Mezei, Mihaly; Logothetis, Diomedes E.; Osman, Roman
A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2
BIOPHYSICAL JOURNAL, 98:240-247, JAN 20 2010
abstract, full text, DOI:10.1016/j.bpj.2009.09.063

Gonnet, Pedro
Using piecewise polynomials for faster potential function evaluation
JOURNAL OF COMPUTATIONAL PHYSICS, 229:313-324, JAN 20 2010
abstract, full text, DOI:10.1016/j.jcp.2009.09.028

Asthagiri, D.; Dixit, P. D.; Merchant, S.; Paulaitis, M. E.; Pratt, L. R.; Rempe, S. B.; Varma, S.
Ion selectivity from local configurations of ligands in solutions and ion channels
CHEMICAL PHYSICS LETTERS, 485:1-7, JAN 18 2010
abstract, full text, DOI:10.1016/j.cplett.2009.12.013

Armishaw, Christopher J.; Singh, Narender; Medina-Franco, Jose L.; Clark, Richard J.; Scott, Krystle C. M.; Houghten, Richard A.; Jensen, Anders A.
A Synthetic Combinatorial Strategy for Developing alpha-Conotoxin Analogs as Potent alpha(7) Nicotinic Acetylcholine Receptor Antagonists
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:1809-1821, JAN 15 2010
abstract, full text, DOI:10.1074/jbc.M109.071183

Zheng, Jie; Yu, Xiang; Wang, Jingdai; Yang, Jui-Chen; Wang, Qiuming
Molecular Modeling of Two Distinct Triangular Oligomers in Amyloid beta-protein
JOURNAL OF PHYSICAL CHEMISTRY B, 114:463-470, JAN 14 2010
abstract, full text, DOI:10.1021/jp907608s

Henin, Jerome; Brannigan, Grace; Dailey, William P.; Eckenhoff, Roderic; Klein, Michael L.
An Atomistic Model for Simulations of the General Anesthetic Isoflurane
JOURNAL OF PHYSICAL CHEMISTRY B, 114:604-612, JAN 14 2010
abstract, full text, DOI:10.1021/jp9088035

Liu, Lu Tian; Haddadian, Esmael J.; Willenbring, Dan; Xu, Yan; Tang, Pei
Higher Susceptibility to Halothane Modulation in Open- Than in Closed-Channel alpha 4 beta 2 nAChR Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:626-632, JAN 14 2010
abstract, full text, DOI:10.1021/jp908944e

Agarwal, Manish; Kushwaha, Hemant R.; Chakravarty, Charusita
Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 114:651-659, JAN 14 2010
abstract, full text, DOI:10.1021/jp909090u

Golosov, Andrei A.; Warren, Joshua J.; Beese, Lorena S.; Karplus, Martin
The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis
STRUCTURE, 18:83-93, JAN 13 2010
abstract, full text, DOI:10.1016/j.str.2009.10.014

Krah, Alexander; Pogoryelov, Denys; Meier, Thomas; Faraldo-Gomez, Jose D.
On the Structure of the Proton-Binding Site in the F-o Rotor of Chloroplast ATP Synthases
JOURNAL OF MOLECULAR BIOLOGY, 395:20-27, JAN 8 2010
abstract, full text, DOI:10.1016/j.jmb.2009.10.059

Sept, David; MacKintosh, Fred C.
Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics
PHYSICAL REVIEW LETTERS, 104 Art. No. 018101, JAN 8 2010
abstract, full text, DOI:10.1103/PhysRevLett.104.018101

Zhang, Ji-long; Zheng, Qing-chuan; Zhang, Hong-xing
Unbinding of glucose from human pulmonary surfactant protein D studied by steered molecular dynamics simulations
CHEMICAL PHYSICS LETTERS, 484:338-343, JAN 7 2010
abstract, full text, DOI:10.1016/j.cplett.2009.12.022

Romo, Tod D.; Grossfield, Alan; Pitman, Michael C.
Concerted Interconversion between Ionic Lock Substates of the beta(2) Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics
BIOPHYSICAL JOURNAL, 98:76-84, JAN 6 2010
abstract, full text, DOI:10.1016/j.bpj.2009.09.046

Rodriguez-Ropero, Francisco; Zanuy, David; Aleman, Carlos
Electronic characterization of all-thiophene conducting dendrimers: Molecules and assemblies
POLYMER, 51:308-315, JAN 6 2010
abstract, full text, DOI:10.1016/j.polymer.2009.11.007

Tsybovsky, Yaroslav; Molday, Robert S.; Palczewski, Krzysztof
The ATP-Binding Cassette Transporter ABCA4: Structural and Functional Properties and Role in Retinal Disease
INFLAMMATION AND RETINAL DISEASE: COMPLEMENT BIOLOGY AND PATHOLOGY, 703:105-125, 2010
abstract, full text, DOI:10.1007/978-1-4419-5635-4_8

Huang, Wei; Koop, Matthew J.; Gao, Qi; Panda, Dhabaleswar K.
Virtual Machine Aware Communication Libraries for High Performance Computing
2007 ACM/IEEE SC07 CONFERENCE, 228-239, 2010
abstract, full text

Alam, Sadaf R.; Kuehn, Jeffery A.; Barrett, Richard F.; Larkin, Jeff M.; Worley, Patrick H.; Fahey, Mark R.; Sankaran, Ramanan
Cray XT4: An Early Evaluation for Petascale Scientific Simulation
2007 ACM/IEEE SC07 CONFERENCE, 271-282, 2010
abstract, full text

Zuo, Guangchao; Shen, Rong; Ma, Shaojie; Guo, Wanlin
Transport Properties of Single-File Water Molecules inside a Carbon Nanotube Biomimicking Water Channel
ACS NANO, 4:205-210, JAN 2010
abstract, full text, DOI:10.1021/nn901334w

Titov, Alexey V.; Kral, Petr; Pearson, Ryan
Sandwiched Graphene-Membrane Superstructures
ACS NANO, 4:229-234, JAN 2010
abstract, full text, DOI:10.1021/nn9015778

Al-Hilli, Safaa; Willander, Magnus
ZNO NANO-STRUCTURES FOR BIOSENSING APPLICATIONS: MOLECULAR DYNAMICS SIMULATIONS
ADVANCES IN NANOTECHNOLOGY, VOLUME 4, 4:123-153, 2010
abstract, full text

Xu, Dong; Williamson, Mark J.; Walker, Ross C.
Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 6, 6:3-19, 2010
abstract, full text, DOI:10.1016/S1574-1400(10)06001-9

Lee, Tai-Sung; Giambasu, George M.; York, Darrin M.
Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 6, 6:169-200, 2010
abstract, full text, DOI:10.1016/S1574-1400(10)06010-X

Langham, Allison; Kaznessis, Yiannis N.
Molecular Simulations of Antimicrobial Peptides
ANTIMICROBIAL PEPTIDES: METHODS AND PROTOCOLS, 618:267-285, 2010
abstract, full text, DOI:10.1007/978-1-60761-594-1_17

Norata, Giuseppe Danilo; Garlaschelli, Katia; Grigore, Liliana; Raselli, Sara; Tramontana, Simona; Meneghetti, Fiorella; Artali, Roberto; Noto, Davide; Cefalu, Angelo Baldassare; Buccianti, Gherardo; Averna, Maurizio; Catapano, Alberico Luigi
Effects of PCSK9 variants on common carotid artery intima media thickness and relation to ApoE alleles
ATHEROSCLEROSIS, 208:177-182, JAN 2010
abstract, full text, DOI:10.1016/j.atherosclerosis.2009.06.023

Liu, Ming S.; Todd, Billy D.; Sadus, Richard J.
Allosteric Conformational Transition in Adenylate Kinase: Dynamic Correlations and Implication for Allostery
AUSTRALIAN JOURNAL OF CHEMISTRY, 63:405-412, 2010
abstract, full text, DOI:10.1071/CH09449

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Testa, Bernard
In silico prediction of human carboxylesterase-1 (hCES1) metabolism combining docking analyses and MD simulations
BIOORGANIC & MEDICINAL CHEMISTRY, 18:320-329, JAN 1 2010
abstract, full text, DOI:10.1016/j.bmc.2009.10.052

Topal, Kevser Gocmen; Atilgan, Canan; Demir, Ayhan S.; Aviyente, Viktorya
Understanding the Mode of Action of ThDP in Benzoylformate Decarboxylase
BIOPOLYMERS, 93:32-46, JAN 2010
abstract, full text, DOI:10.1002/bip.21291

Miao, Yinglong; Ortoleva, Peter J.
Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation
BIOPOLYMERS, 93:61-73, JAN 2010
abstract, full text, DOI:10.1002/bip.21299

Schneider, Olaf; Sternberg, Ulrich; Vondrous, Alexander
PARALLEL MOLECULAR DYNAMICS SIMULATION USING A HYBRID FORCE FIELD WITH QUANTUM CHEMICAL CHARGE CALCULATIONS
CLUSTER COMPUTING AND MULTI-HOP NETWORK RESEARCH, 73-90, 2010
abstract, full text

Buehler, Markus J.
Computational Scale Linking in Biological Protein Materials
COMPUTATIONAL MODELING IN BIOMECHANICS, 491-531, 2010
abstract, full text, DOI:10.1007/978-90-481-3575-2_17

Petridis, Loukas; Xu, Jiancong; Crowley, Michael F.; Smith, Jeremy C.; Cheng, Xiaolin
Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes
COMPUTATIONAL MODELING IN LIGNOCELLULOSIC BIOFUEL PRODUCTION, 1052:55-73, 2010
abstract, full text

McCabe, Clare; Zhao, Xiongce; Adney, William S.; Himmel, Michael E.
Energy Storage in Cellulase Linker Peptides?
COMPUTATIONAL MODELING IN LIGNOCELLULOSIC BIOFUEL PRODUCTION, 1052:119-134, 2010
abstract, full text

Beckham, Gregg T.; Peters, Baron
New Methods To Find Accurate Reaction Coordinates by Path Sampling
COMPUTATIONAL MODELING IN LIGNOCELLULOSIC BIOFUEL PRODUCTION, 1052:299-332, 2010
abstract, full text

Chumningan, Sansai; Pornputtapong, Natapol; Laoteng, Kobkul; Cheevadhanarak, Supapon; Thammarongtham, Chinae
3D Structure Modeling of a Transmembrane Protein, Fatty Acid Elongase
COMPUTATIONAL SYSTEMS-BIOLOGY AND BIOINFORMATICS, 115:36-45, 2010
abstract, full text, DOI:10.1007/978-3-642-16750-8_4

Amaro, Rommie E.; Li, Wilfred W.
Emerging Methods for Ensemble-Based Virtual Screening
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 10:3-13, JAN 2010
abstract, full text

Vohra, Shabana; Hall, Benjamin A.; Holdbrook, Daniel A.; Khalid, Syma; Biggin, Philip C.
Bookshelf: a simple curation system for the storage of biomolecular simulation data
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, Art. No. baq033, 2010
abstract, full text, DOI:10.1093/database/baq033

EzzEldin, Hussein M.; Solares, Santiago D.
CALCULATION OF ISOTHERMAL INTRINSIC COMPRESSIBILITY AND COMPRESSION OF GVPA PROTEIN IN HALOBACTERIUM SP. NRC-1 USING MOLECULAR MODELING AND DYNAMICS
DETC2009: PROCEEDINGS OF THE ASME INTERNATIONAL DESIGN ENGINEERING TECHNICAL CONFERENCES/COMPUTERS AND INFORMATION IN ENGINEERING CONFERENCE, 389-395, 2010
abstract, full text

Wang, Hao; Laughton, Charles A.
Molecular Modelling Methods to Quantitate Drug-DNA Interactions
DRUG-DNA INTERACTION PROTOCOLS, SECOND EDITION, 613:119-131, 2010
abstract, full text, DOI:10.1007/978-1-60327-418-0_8

Xu, Liang; Zhao, Weijie; Wang, Xicheng
Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:327-336, JAN 2010
abstract, full text, DOI:10.1007/s00249-009-0551-9

Stirnemann, Guillaume; Rossky, Peter J.; Hynes, James T.; Laage, Damien
Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface
FARADAY DISCUSSIONS, 146:263-281, 2010
abstract, full text, DOI:10.1039/b925673c

Karachevtsev, V. A.; Karachevtsev, M. V.; Leontiev, V. S.; Lytvyn, O. S.; Bogorosh, A. T.
Nanohybrid Structures Formed by Carbon Nanotubes with Long Polynucleotide
FULLERENES NANOTUBES AND CARBON NANOSTRUCTURES, 18:531-537, 2010
abstract, full text, DOI:10.1080/1536383X.2010.488532

Coveney, P. V.; Giupponi, G.; Jha, S.; Manos, S.; MacLaren, J.; Pickles, S. M.; Saksena, R. S.; Soddemann, T.; Suter, J. L.; Thyveetil, M.; Zasada, S. J.
Large scale computational science on federated international grids: The role of switched optical networks
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 26:99-110, JAN 2010
abstract, full text, DOI:10.1016/j.future.2008.09.013

Malawski, Maciej; Bartynski, Tomasz; Bubak, Marian
Invocation of operations from script-based Grid applications
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 26:138-146, JAN 2010
abstract, full text, DOI:10.1016/j.future.2009.05.012

Burti, F.; Cacciagrano, D.; Corradini, F.; Merelli, E.; Tesei, L.
BIOSHAPE: a spatial shape-based scale-independent simulation environment for biological systems
ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, 1:827-835, 2010
abstract, full text, DOI:10.1016/j.procs.2010.04.090

Zasada, S. J.; Coveney, P. V.
Computational Biomedicine: The Role of Workflow Tools
ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, 1:2747-2755, 2010
abstract, full text, DOI:10.1016/j.procs.2010.04.309

Ourmazd, Abbas; Schwander, Peter; Phillips, George N., Jr.
Structure from Random Snapshots
IMAGE RECONSTRUCTION FROM INCOMPLETE DATA VI, 7800 Art. No. 780002, 2010
abstract, full text, DOI:10.1117/12.860772

Sikdar, Debashis; Katti, Dinesh R.; Katti, Kalpana S.; Bhowmik, Rahul
TAILORING CRYSTALLINITY AND NANOMECHANICAL PROPERTIES OF CLAY POLYMER NANOCOMPOSITES: A MOLECULAR DYNAMICS STUDY
INTERNATIONAL JOURNAL FOR MULTISCALE COMPUTATIONAL ENGINEERING, 8:561-584, 2010
abstract, full text

Blayney, Jaine K.; Ojha, Piyush C.; Shapcott, Mary
Predicting three-dimensional structure of protein fragments from dihedral angle propensities and molecular dynamics
International Journal of Computational Biology and Drug Design, 3:146-163, 2010
abstract, full text

Yakubovich, Alexander V.; Solov'yov, Andrey V.; Greiner, Walter
Conformational Changes in Polypeptides and Proteins
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 110:257-269, JAN 2010
abstract, full text, DOI:10.1002/qua.22268

Henin, Jerome; Fiorin, Giacomo; Chipot, Christophe; Klein, Michael L.
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:35-47, JAN 2010
abstract, full text, DOI:10.1021/ct9004432

Dubey, Devendra K.; Tomar, Vikas
Effect of changes in tropocollagen residue sequence and hydroxyapatite mineral texture on the strength of ideal nanoscale tropocollagen-hydroxyapatite biomaterials
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN MEDICINE, 21:161-171, JAN 2010
abstract, full text, DOI:10.1007/s10856-009-3837-7

Mernea, M.; Calborean, O.; Dinca, M. P.; Leca, A.; Apostol, D.; Dascalu, T.; Mihailescu, D.
The simulation of bovine serum albumin vibration spectrum in THz domain
JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 12:135-140, JAN 2010
abstract, full text

Luo, Yun; Roux, Benoit
Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:183-189, JAN 2010
abstract, full text, DOI:10.1021/jz900079w

Shestakov, I.A.; Vakhrouchev, A.V.; Fedotov, A.Y.
Mathematical model combined nanomotor
Khimicheskaya fizika i mezoskopiya, 12:467-473, 2010
abstract, full text

Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Tita, Andrei; Leca, Aurel; Dascalu, Traian; Mihailescu, Dan Florin
Protein association investigated by THz spectroscopy and molecular modeling
LASER APPLICATIONS IN LIFE SCIENCES, 7376 Art. No. 73760O, 2010
abstract, full text, DOI:10.1117/12.871159

Zobnina, V.G.; Kosevich, M.V.; Chagovets, V.V.; Boryak, O.A.; Kulyk, A.N.; Gomory, A.
Stable associates of polyether oligomers with chlorine anion as revealed by electrospray mass spectrometry and molecular dynamics
Mass-spektrometriya, 7:225-231, 2010
abstract, full text

Fuchs, Patrick F. J.
Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data
MEMBRANE PROTEIN STRUCTURE DETERMINATION: METHODS AND PROTOCOLS, 654:403-421, 2010
abstract, full text, DOI:10.1007/978-1-60761-762-4_21

Edelkamp, Stefan; Sulewski, Damian
Efficient Explicit-State Model Checking on General Purpose Graphics Processors
MODEL CHECKING SOFTWARE, 6349:106-123, 2010
abstract, full text

Zomot, Elia; Bahar, Ivet
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state
MOLECULAR BIOSYSTEMS, 6:1040-1046, 2010
abstract, full text, DOI:10.1039/b927492h

Schlick, T.
Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Edition
MOLECULAR MODELING AND SIMULATION: AN INTERDISCIPLINARY GUIDE, 2ND EDITION, 21:1-723, 2010
full text, DOI:10.1007/978-1-4419-6351-2

Dieterich, Johannes M.; Hartke, Bernd
OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach
MOLECULAR PHYSICS, 108:279-291, 2010
abstract, full text, DOI:10.1080/00268970903446756

Abroshan, Hadi; Akbarzadeh, Hamed; Taherkhani, Farid; Parsafar, Gholamabbas
Effect of a monomeric sequence on the structure of hydrated Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamic study
MOLECULAR PHYSICS, 108:3393-3404, 2010
abstract, full text, DOI:10.1080/00268976.2010.511635

Stavrakoudis, Athanassios
Computational modelling and molecular dynamics simulations of a cyclic peptide mimotope of the CD52 antigen complexed with CAMPATH-1H antibody
MOLECULAR SIMULATION, 36:127-137, 2010
abstract, full text, DOI:10.1080/08927020903124593

Roth, M. W.; Kaspar, M.; Wexler, Carlos; Firlej, L.; Kuchta, B.
Molecular dynamics simulations of submonolayer hexane and pentane films on graphite
MOLECULAR SIMULATION, 36:326-333, 2010
abstract, full text, DOI:10.1080/08927020903437839

Duff, Nathan; Peters, Baron
Mitosis method for directly calculating the interfacial free energy of nuclei
MOLECULAR SIMULATION, 36:498-504, 2010
abstract, full text, DOI:10.1080/08927022.2010.483684

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei
Modelling the viscoelasticity and thermal fluctuations of fluids at the nanoscale
MOLECULAR SIMULATION, 36:552-559, 2010
abstract, full text, DOI:10.1080/08927022.2010.486832

Xu, Ji; Ren, Ying; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai
Molecular dynamics simulation of macromolecules using graphics processing unit
MOLECULAR SIMULATION, 36:1131-1140, 2010
abstract, full text, DOI:10.1080/08927022.2010.506512

Peters, Baron
Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
MOLECULAR SIMULATION, 36:1265-1281, 2010
abstract, full text, DOI:10.1080/08927020903536382

Yin, Ying; Arkhipov, Anton; Schulten, Klaus
Multi-scale Simulations of Membrane Sculpting by N-BAR Domains
MOLECULAR SIMULATIONS AND BIOMEMBRANES: FROM BIOPHYSICS TO FUNCTION, Issue 20, 146-176, 2010
full text, TCBG publications, DOI:10.1039/9781849732154-00146

Wen, Po-Chao; Huang, Zhijian; Enkavi, Giray; Wang, Yi; Gumbart, James; Tajkhorshid, Emad
Molecular Mechanisms of Active Transport Across the Cellular Membrane
MOLECULAR SIMULATIONS AND BIOMEMBRANES: FROM BIOPHYSICS TO FUNCTION, Issue 20, 248-286, 2010
full text, DOI:10.1039/9781849732154-00248

Calderon, Christopher P.; Martinez, Josue G.; Carroll, Raymond J.; Sorensen, Danny C.
P-SPLINES USING DERIVATIVE INFORMATION
MULTISCALE MODELING & SIMULATION, 8:1562-1580, 2010
abstract, full text, DOI:10.1137/090768102

Zhang, Lei; Berlyand, Leonid; Fedorov, Maxim V.; Owhadi, Houman
GLOBAL ENERGY MATCHING METHOD FOR ATOMISTIC-TO-CONTINUUM MODELING OF SELF-ASSEMBLING BIOPOLYMER AGGREGATES
MULTISCALE MODELING & SIMULATION, 8:1958-1980, 2010
abstract, full text, DOI:10.1137/090781619

Aksimentiev, Aleksei
Deciphering ionic current signatures of DNA transport through a nanopore
NANOSCALE, 2:468-483, 2010
abstract, full text, DOI:10.1039/b9nr00275h

Li Sijie; Bai Bofeng
Multi-Vapor Embryos Nucleation Process and Spinodal Analyses of Expandable Superheated Water System
NANOSCALE AND MICROSCALE THERMOPHYSICAL ENGINEERING, 14:174-185, 2010
abstract, full text, DOI:10.1080/15567265.2010.502922

Volkova, E. I.; Suyetin, M. V.; Vakhrushev, A. V.
Temperature Sensitive Nanocapsule of Complex Structural Form for Methane Storage
NANOSCALE RESEARCH LETTERS, 5:205-210, JAN 2010
abstract, full text, DOI:10.1007/s11671-009-9466-8

Ziemys, Arturas; Grattoni, Alessandro; Gill, Jaskaran; Ferrari, Mauro
SILICA NANOCHANNEL SURFACE EFFECT ON MONOSACCHARIDE TRANSPORT
NEMB2010: PROCEEDINGS OF THE ASME FIRST GLOBAL CONGRESS ON NANOENGINEERING FOR MEDICINE AND BIOLOGY - 2010, 301-303, 2010
abstract, full text

Roy, Arijit; Carpentier, Philippe; Bourgeois, Dominique; Field, Martin
Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 9:1342-1350, 2010
abstract, full text, DOI:10.1039/c0pp00141d

Yamamoto, Takenori; Ohnishi, Shuhei
Nano bubbles in liquid of a noble-gas mixture
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:1033-1037, 2010
abstract, full text, DOI:10.1039/b918541k

Schmeer, Georg; Maurer, Alexander
Development of thermodynamic properties of electrolyte solutions with the help of RISM-calculations at the Born-Oppenheimer level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2407-2417, 2010
abstract, full text, DOI:10.1039/b917653e

Abou Hamad, Ibrahim; Novotny, M. A.; Wipf, D. O.; Rikvold, P. A.
A new battery-charging method suggested by molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2740-2743, 2010
abstract, full text, DOI:10.1039/b920970k

Batista, Paulo Ricardo; Robert, Charles Herbert; Marechal, Jean-Didier; Ben Hamida-Rebai, Meriam; Pascutti, Pedro Geraldo; Bisch, Paulo Mascarello; Perahia, David
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2850-2859, 2010
abstract, full text, DOI:10.1039/b919148h

Liang, Haiqing; Li, Zhenyu; Yang, Jinlong
Single-stranded DNA adsorption on chiral molecule coated Au surface: a molecular dynamics study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:4431-4434, 2010
abstract, full text, DOI:10.1039/b923012b

Denysenkov, Vasyl; Prandolini, Mark J.; Gafurov, Marat; Sezer, Deniz; Endeward, Burkhard; Prisner, Thomas F.
Liquid state DNP using a 260 GHz high power gyrotron
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:5786-5790, 2010
abstract, full text, DOI:10.1039/c003697h

Chen, L. Y.; Bastien, D. A.; Espejel, H. E.
Determination of equilibrium free energy from nonequilibrium work measurements
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:6579-6582, 2010
abstract, full text, DOI:10.1039/b926889h

Liu, Ying-Chun; Moore, Joshua D.; Roussel, Thomas J.; Gubbins, Keith E.
Dual diffusion mechanism of argon confined in single-walled carbon nanotube bundles
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:6632-6640, 2010
abstract, full text, DOI:10.1039/b927152j

Broemstrup, Torben; Reuter, Nathalie
How does Proteinase 3 interact with lipid bilayers?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:7487-7496, 2010
abstract, full text, DOI:10.1039/b924117e

Yamamoto, Takenori; Uda, Tsuyoshi; Yamasaki, Takahiro; Ohno, Takahisa
Hydration effect on the optical property of a DNA fiber: First-principles and molecular dynamics studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:9300-9311, 2010
abstract, full text, DOI:10.1039/b924678a

Willenbring, Dan; Xu, Yan; Tang, Pei
The role of structured water in mediating general anesthetic action on alpha 4 beta 2 nAChR
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:10263-10269, 2010
abstract, full text, DOI:10.1039/c003573d

Nemkevich, Alexandra; Buergi, Hans-Beat; Spackman, Mark A.; Corry, Ben
Molecular dynamics simulations of structure and dynamics of organic molecular crystals
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:14916-14929, 2010
abstract, full text, DOI:10.1039/c0cp01409e

Kumar, Sanjay; Li, Mai Suan
Biomolecules under mechanical force
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 486:1-74, JAN 2010
abstract, full text, DOI:10.1016/j.physrep.2009.11.001

Hodak, Miroslav; Bernholc, Jerzy
Insights into prion protein function from atomistic simulations
PRION, 4:13-19, JAN-MAR 2010
abstract, full text

Iliopoulos, Athanasios P.; Michopoulos, John G.; Lambrakos, Samuel G.; Bernstein, Noam
INVERSE MOLECULAR DYNAMICS MODELING PERFORMANCE ON GPU ARCHITECTURES FOR A PROBLEM OF FRACTURE
PROCEEDINGS OF THE ASME INTERNATIONAL DESIGN ENGINEERING TECHNICAL CONFERENCES AND COMPUTERS AND INFORMATION IN ENGINEERING CONFERENCE, DETC 2010, VOL 3, A AND B, 767-775, 2010
abstract, full text

Bellesia, Giovanni; Jewett, Andrew Iain; Shea, Joan-Emma
Sequence periodicity and secondary structure propensity in model proteins
PROTEIN SCIENCE, 19:141-154, JAN 2010
abstract, full text, DOI:10.1002/pro.288

Emperador, Agusti; Meyer, Tim; Orozco, Modesto
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:83-94, JAN 2010
abstract, full text, DOI:10.1002/prot.22563

Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Dinca, Mihai P.; Leca, Aurel; Apostol, Dan; Dascalu, Traian; Mihailescu, Dan
The flexibility of hydrated bovine serum albumin investigated by THz spectroscopy and molecular modeling
ROMOPTO 2009: NINTH CONFERENCE ON OPTICS: MICRO- TO NANOPHOTONICS II, 7469 Art. No. 74690N, 2010
abstract, full text, DOI:10.1117/12.861821

Bajaj, Chandrajit; Zhao, Wenqi
FAST MOLECULAR SOLVATION ENERGETICS AND FORCES COMPUTATION
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 31:4524-4552, 2010
abstract, full text, DOI:10.1137/090746173

He, Yuhui; Scheicher, Ralph H.; Grigoriev, Anton; Ahuja, Rajeev; Long, Shibing; Ji, Zhuoyu; Yu, Zhaoan; Liu, Ming
Fast DNA Sequencing via Transverse Differential Conductance
SISPAD 2010 - 15TH INTERNATIONAL CONFERENCE ON SIMULATION OF SEMICONDUCTOR PROCESSES AND DEVICES, 313-316, 2010
abstract, full text

Luan, Binquan; Aksimentiev, Aleksei
Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
SOFT MATTER, 6:243-246, 2010
abstract, full text, DOI:10.1039/b917973a

Halverson, Jonathan D.; Maldarelli, Charles; Couzis, Alexander; Koplik, Joel
Atomistic simulations of the wetting behavior of nanodroplets of water on homogeneous and phase separated self-assembled monolayers
SOFT MATTER, 6:1297-1307, 2010
abstract, full text, DOI:10.1039/b921840h

Aguilella-Arzo, Marcel; Calero, Carles; Faraudo, Jordi
Simulation of electrokinetics at the nanoscale: inversion of selectivity in a bio-nanochannel
SOFT MATTER, 6:6079-6082, 2010
abstract, full text, DOI:10.1039/c0sm00904k

Katti, Dinesh R.; Katti, Kalpana S.; Pradhan, Shashindra M.
What's up with clay and water molecules? A view into molecular interactions and molecular responses in swelling clays
UNSATURATED SOILS: THEORETICAL AND NUMERICAL ADVANCES IN UNSATURATED SOIL MECHANICS, 531-536, 2010
abstract, full text

Glowacki, David R.; Paci, Emanuele; Shalashilin, Dmitrii V.
Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems
JOURNAL OF PHYSICAL CHEMISTRY B, 113:16603-16611, DEC 31 2009
abstract, full text, DOI:10.1021/jp9074898

Hamaneh, Mehdi Bagheri; Buck, Matthias
Refinement of the Primary Hydration Shell Model for Molecular Dynamics Simulations of Large Proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2635-2644, DEC 30 2009
abstract, full text, DOI:10.1002/jcc.21246

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Yang, Jian
A molecular dynamics study of cryoprotective agent - Water-sodium chloride ternary solutions
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 916:37-46, DEC 30 2009
abstract, full text, DOI:10.1016/j.theochem.2009.09.007

Puklin-Faucher, Eileen; Vogel, Viola
Integrin Activation Dynamics between the RGD-binding Site and the Headpiece Hinge
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:36557-36568, DEC 25 2009
abstract, full text, DOI:10.1074/jbc.M109.041194

Yeung, Natasha; Lin, Ying-Wu; Gao, Yi-Gui; Zhao, Xuan; Russell, Brandy S.; Lei, Lanyu; Miner, Kyle D.; Robinson, Howard; Lu, Yi
Rational design of a structural and functional nitric oxide reductase
NATURE, 462:1079-U144, DEC 24 2009
abstract, full text, DOI:10.1038/nature08620

Yang, Li-Jun; Zou, Jun; Xie, Huan-Zhang; Li, Lin-Li; Wei, Yu-Quan; Yang, Sheng-Yong
Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl
PLOS ONE, 4 Art. No. e8470, DEC 24 2009
abstract, full text, DOI:10.1371/journal.pone.0008470

Anisimov, Victor M.; Bugaenko, Vladislav L.; Cavasotto, Claudio N.
Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution
CHEMPHYSCHEM, 10:3194-3196, DEC 21 2009
full text, DOI:10.1002/cphc.200900535

Voulgarakis, Nikolaos K.; Satish, Siddarth; Chu, Jhih-Wei
Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 234115, DEC 21 2009
abstract, full text, DOI:10.1063/1.3273210

Heyes, Derren J.; Levy, Colin; Lafite, Pierre; Roberts, Ian S.; Goldrick, Marie; Stachulski, Andrew V.; Rossington, Steven B.; Stanford, Deborah; Rigby, Stephen E. J.; Scrutton, Nigel S.; Leys, David
Structure-based Mechanism of CMP-2-keto-3-deoxymanno-octulonic Acid Synthetase CONVERGENT EVOLUTION OF A SUGAR-ACTIVATING ENZYME WITH DNA/RNA POLYMERASES
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:35514-35523, DEC 18 2009
abstract, full text, DOI:10.1074/jbc.M109.056630

McLean, Kirsty J.; Lafite, Pierre; Levy, Colin; Cheesman, Myles R.; Mast, Natalia; Pikuleva, Irina A.; Leys, David; Munro, Andrew W.
The Structure of Mycobacterium tuberculosis CYP125 MOLECULAR BASIS FOR CHOLESTEROL BINDING IN A P450 NEEDED FOR HOST INFECTION
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:35524-35533, DEC 18 2009
abstract, full text, DOI:10.1074/jbc.M109.032706

Chen, Harvey S.; Kolahi, Kevin S.; Mofrad, Mohammad R. K.
Phosphorylation Facilitates the Integrin Binding of Filamin under Force
BIOPHYSICAL JOURNAL, 97:3095-3104, DEC 16 2009
abstract, full text, DOI:10.1016/j.bpj.2009.08.059

Al-Hilli, Safaa; Willander, M.
Ionic current flow through ZnO nanotubes
NANOTECHNOLOGY, 20 Art. No. 505504, DEC 16 2009
abstract, full text, DOI:10.1088/0957-4484/20/50/505504

Wang, Shengjun; Xin, Fengxue; Liu, Xiaoyue; Wang, Yuxiao; An, Zhenyi; Qi, Qingsheng; Wang, Peng George
N-Terminal Deletion of Peptide: N-Glycanase Results in Enhanced Deglycosylation Activity
PLOS ONE, 4 Art. No. e8335, DEC 16 2009
abstract, full text, DOI:10.1371/journal.pone.0008335

Vukovic, Lela; Kral, Petr
Coulombically Driven Rolling of Nanorods on Water
PHYSICAL REVIEW LETTERS, 103 Art. No. 246103, DEC 11 2009
abstract, full text, DOI:10.1103/PhysRevLett.103.246103

Taylor, Derek J.; Devkota, Batsal; Huang, Andrew D.; Topf, Maya; Narayanan, Eswar; Sali, Andrej; Harvey, Stephen C.; Frank, Joachim
Comprehensive Molecular Structure of the Eukaryotic Ribosome
STRUCTURE, 17:1591-1604, DEC 9 2009
abstract, full text, DOI:10.1016/j.str.2009.09.015

Khavrutskii, Ilja V.; Grant, Barry; Taylor, Susan S.; McCammon, J. Andrew
A Transition Path Ensemble Study Reveals a Linchpin Role for Mg2+ during Rate-Limiting ADP Release from Protein Kinase A
BIOCHEMISTRY, 48:11532-11545, DEC 8 2009
abstract, full text, DOI:10.1021/bi901475g

Martinez, Leandro; Nascimento, Alessandro S.; Nunes, Fabio M.; Phillips, Kevin; Aparicio, Ricardo; Dias, Sandra Martha G.; Figueira, Ana Carolina M.; Lin, Jean H.; Nguyen, Phuong; Apriletti, James W.; Neves, Francisco A. R.; Baxter, John D.; Webb, Paul; Skaf, Munir S.; Polikarpov, Igor
Gaining ligand selectivity in thyroid hormone receptors via entropy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:20717-20722, DEC 8 2009
abstract, full text, DOI:10.1073/pnas.0911024106

Kouza, Maksim; Hu, Chin-Kun; Zung, Hoang; Li, Mai Suan
Protein mechanical unfolding: Importance of non-native interactions
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 215103, DEC 7 2009
abstract, full text, DOI:10.1063/1.3272275

Hilder, Tamsyn A.; Gordon, Daniel; Chung, Shin-Ho
Boron Nitride Nanotubes Selectively Permeable to Cations or Anions
SMALL, 5:2870-2875, DEC 4 2009
abstract, full text, DOI:10.1002/smll.200901229

Neumann, Anna; Czub, Jacek; Baginski, Maciej
On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 113:15875-15885, DEC 3 2009
abstract, full text, DOI:10.1021/jp905133f

Daigle, Richard; Rousseau, Julie-Anne; Guertin, Michel; Laguee, Patrick
Theoretical Investigations of Nitric Oxide Channeling in Mycobacterium tuberculosis Truncated Hemoglobin N
BIOPHYSICAL JOURNAL, 97:2967-2977, DEC 2 2009
abstract, full text, DOI:10.1016/j.bpj.2009.09.006

Chandler, Danielle E.; Gumbart, James; Stack, John D.; Chipot, Christophe; Schulten, Klaus
Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s
BIOPHYSICAL JOURNAL, 97:2978-2984, DEC 2 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.09.007

Jang, Hyunbum; Arce, Fernando Teran; Capone, Ricardo; Ramachandran, Srinivasan; Lal, Ratnesh; Nussinov, Ruth
Misfolded Amyloid Ion Channels Present Mobile beta-Sheet Subunits in Contrast to Conventional Ion Channels
BIOPHYSICAL JOURNAL, 97:3029-3037, DEC 2 2009
abstract, full text, DOI:10.1016/j.bpj.2009.09.014

Hsin, Jen; Chipot, Christophe; Schulten, Klaus
A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17096-+, DEC 2 2009
abstract, full text, TCBG publications, DOI:10.1021/ja905903n

Newhouse, E. Irene; Xu, Dong; Markwick, Phineus R. L.; Amaro, Rommie E.; Pao, Hsing C.; Wu, Kevin J.; Alam, Maqsudul; McCammon, J. Andrew; Li, Wilfred W.
Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17430-17442, DEC 2 2009
abstract, full text, DOI:10.1021/ja904052q

Hu, Keke; Tanaka, Takuji
S-1 site residues of Lactococcus lactis prolidase affect substrate specificity and allosteric behaviour
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1794:1715-1724, DEC 2009
abstract, full text, DOI:10.1016/j.bbapap.2009.08.005

Jones, Martin K.; Catte, Andrea; Li, Ling; Segrest, Jere P.
Dynamics of Activation of Lecithin: Cholesterol Acyltransferase by Apolipoprotein A-I
BIOCHEMISTRY, 48:11196-11210, DEC 1 2009
abstract, full text, DOI:10.1021/bi901242k

Genchev, Georgi Z.; Kaellberg, Morten; Guersoy, Gamze; Mittal, Anuradha; Dubey, Lalit; Perisic, Ognjen; Feng, Gang; Langlois, Robert; Lu, Hui
Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics
CELL BIOCHEMISTRY AND BIOPHYSICS, 55:141-152, DEC 2009
abstract, full text, DOI:10.1007/s12013-009-9064-5

Vargas, Diego A.; Zaman, Muhammad H.
Serine at Phosphorylation Site Regulates the Mechanical and Structural Behavior of Fascin
CELLULAR AND MOLECULAR BIOENGINEERING, 2:504-513, DEC 2009
abstract, full text, DOI:10.1007/s12195-009-0091-5

Asses, Yasmine; Leroux, Vincent; Tairi-Kellou, Safia; Dono, Rosanna; Maina, Flavio; Maigret, Bernard
Analysis of c-Met Kinase Domain Complexes: A New Specific Catalytic Site Receptor Model for Defining Binding Modes of ATP-Competitive Ligands
CHEMICAL BIOLOGY & DRUG DESIGN, 74:560-570, DEC 2009
abstract, full text, DOI:10.1111/j.1747-0285.2009.00895.x

Zasada, S. J.; Coveney, P. V.
Virtualizing access to scientific applications with the Application Hosting Environment
COMPUTER PHYSICS COMMUNICATIONS, 180:2513-2525, DEC 2009
abstract, full text, DOI:10.1016/j.cpc.2009.06.008

Arinaminpathy, Yalini; Khurana, Ekta; Engelman, Donald M.; Gerstein, Mark B.
Computational analysis of membrane proteins: the largest class of drug targets
DRUG DISCOVERY TODAY, 14:1130-1135, DEC 2009
abstract, full text, DOI:10.1016/j.drudis.2009.08.006

Caroli Rezende, Marcos; Onate, Ruben; Nunez, Gabriel; Dominguez, Moises; Mascayano, Carolina
Lipophilic contributions to the solvatochromism of analogous betaines
DYES AND PIGMENTS, 83:391-395, DEC 2009
abstract, full text, DOI:10.1016/j.dyepig.2009.06.011

Stavrakoudis, Athanassios
Conformational Studies of the 313-320 and 313-332 Peptide Fragments Derived from the alpha(IIb) Subunit of Integrin Receptor with Molecular Dynamics Simulations
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:263-272, DEC 2009
abstract, full text, DOI:10.1007/s10989-009-9187-y

Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C.
CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 109:3767-3772, DEC 2009
abstract, full text, DOI:10.1002/qua.22372

Park, Jin Woo; Jo, Won Ho
Infiltration of Water Molecules into the Oseltamivir-Binding Site of H274Y Neuraminidase Mutant Causes Resistance to Oseltamivir
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2735-2741, DEC 2009
abstract, full text, DOI:10.1021/ci900348n

Fadouloglou, Vasiliki E.; Stavrakoudis, Athanassios; Bouriotis, Vassilis; Kokkinidis, Michael; Glykos, Nicholas M.
Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:3299-3311, DEC 2009
abstract, full text, DOI:10.1021/ct9002338

Khafizov, Kamil
GoLoco motif proteins binding to G alpha(i1): insights from molecular simulations
JOURNAL OF MOLECULAR MODELING, 15:1491-1499, DEC 2009
abstract, full text, DOI:10.1007/s00894-009-0516-z

Garzon, Diana; Bond, Peter J.; Faraldo-Gomez, Jose D.
Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens
MOLECULAR IMMUNOLOGY, 47:253-260, DEC 2009
abstract, full text, DOI:10.1016/j.molimm.2009.09.029

Paliy, Maxim; Melnik, Roderick; Shapiro, Bruce A.
Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization
PHYSICAL BIOLOGY, 6 Art. No. 046003, DEC 2009
abstract, full text, DOI:10.1088/1478-3975/6/4/046003

Chae, Keun; Kieslich, Chris A.; Morikis, Dimitrios; Kim, Seung-Chul; Lord, Elizabeth M.
A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization
PLANT CELL, 21:3902-3914, DEC 2009
abstract, full text, DOI:10.1105/tpc.109.070854

Liu, Lin; Koharudin, Leonardus M. I.; Gronenborn, Angela M.; Bahar, Ivet
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:927-939, DEC 2009
abstract, full text, DOI:10.1002/prot.22518

Martinez, Leandro; Laine, Elodie; Malliavin, Therese E.; Nilges, Michael; Blondel, Arnaud
ATP conformations and ion binding modes in the active site of anthrax edema factor: A computational analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:971-983, DEC 2009
abstract, full text, DOI:10.1002/prot.22523

Li Bo; Zhu Hao-Miao; Wang Ying; Zhao Bo; Li Li; Shen Jian
Molecular Dynamics Simulation of the Effect of Different Materials Surface on Natural Behavior of Nine Peptides of Coagulation Factor XII
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 30:23-28, NOV 30 2009
abstract, full text

Delalande, Olivier; Ferey, Nicolas; Grasseau, Gilles; Baaden, Marc
Complex Molecular Assemblies at Hand via Interactive Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2375-2387, NOV 30 2009
abstract, full text, DOI:10.1002/jcc.21235

Krepkiy, Dmitriy; Mihailescu, Mihaela; Freites, J. Alfredo; Schow, Eric V.; Worcester, David L.; Gawrisch, Klaus; Tobias, Douglas J.; White, Stephen H.; Swartz, Kenton J.
Structure and hydration of membranes embedded with voltage-sensing domains
NATURE, 462:473-U168, NOV 26 2009
abstract, full text, DOI:10.1038/nature08542

Vagenende, Vincent; Yap, Miranda G. S.; Trout, Bernhardt L.
Mechanisms of Protein Stabilization and Prevention of Protein Aggregation by Glycerol
BIOCHEMISTRY, 48:11084-11096, NOV 24 2009
abstract, full text, DOI:10.1021/bi900649t

Arkhipov, Anton; Yin, Ying; Schulten, Klaus
Membrane-Bending Mechanism of Amphiphysin N-BAR Domains
BIOPHYSICAL JOURNAL, 97:2727-2735, NOV 18 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.08.051

Cui, Haosheng; Ayton, Gary S.; Voth, Gregory A.
Membrane Binding by the Endophilin N-BAR Domain
BIOPHYSICAL JOURNAL, 97:2746-2753, NOV 18 2009
abstract, full text, DOI:10.1016/j.bpj.2009.08.043

Krammer, Eva-Maria; Ravaud, Stephanie; Dehez, Francois; Frelet-Barrand, Annie; Pebay-Peyroula, Eva; Chipot, Christophe
High-Chloride Concentrations Abolish the Binding of Adenine Nucleotides in the Mitochondrial ADP/ATP Carrier Family
BIOPHYSICAL JOURNAL, 97:L25-L27, NOV 18 2009
abstract, full text, DOI:10.1016/j.bpj.2009.08.047

Halverson, Jonathan D.; Maldarelli, Charles; Couzis, Alexander; Koplik, Joel
Wetting of hydrophobic substrates by nanodroplets of aqueous trisiloxane and alkyl polyethoxylate surfactant solutions
CHEMICAL ENGINEERING SCIENCE, 64:4657-4667, NOV 16 2009
abstract, full text, DOI:10.1016/j.ces.2009.05.010

Tournassat, Christophe; Chapron, Yves; Leroy, Philippe; Bizi, Mohamed; Boulahya, Faiza
Comparison of molecular dynamics simulations with triple layer and modified Gouy-Chapman models in a 0.1 M NaCl-montmorillonite system
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 339:533-541, NOV 15 2009
abstract, full text, DOI:10.1016/j.jcis.2009.06.051

Gorecki, Adam; Szypowski, Marcin; Dlugosz, Maciej; Trylska, Joanna
RedMD-Reduced Molecular Dynamics Package
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2364-2373, NOV 15 2009
abstract, full text, DOI:10.1002/jcc.21223

Carotti, Andrea; Macchiarulo, Antonio; Giacche, Nicola; Pellicciari, Roberto
Targeting the conformational transitions of MDM2 and MDMX: Insights into key residues affecting p53 recognition
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:524-535, NOV 15 2009
abstract, full text, DOI:10.1002/prot.22464

Gumbart, James; Wiener, Michael C.; Tajkhorshid, Emad
Coupling of Calcium and Substrate Binding through Loop Alignment in the Outer-Membrane Transporter BtuB
JOURNAL OF MOLECULAR BIOLOGY, 393:1129-1142, NOV 13 2009
abstract, full text, DOI:10.1016/j.jmb.2009.09.004

Rodriguez-Ropero, Francisco; Canales, Manel; Zanuy, David; Zhang, Afang; Schlueter, Dieter; Aleman, Carlos
Helical Dendronized Polymers with Chiral Second-Generation Dendrons: Atomistic View and Driving Forces for Structure Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14868-14876, NOV 12 2009
abstract, full text, DOI:10.1021/jp903782f

Gumbart, James; Trabuco, Leonardo G.; Schreiner, Eduard; Villa, Elizabeth; Schulten, Klaus
Regulation of the Protein-Conducting Channel by a Bound Ribosome
STRUCTURE, 17:1453-1464, NOV 11 2009
abstract, full text, TCBG publications, DOI:10.1016/j.str.2009.09.010

Knapp, James E.; Pahl, Reinhard; Cohen, Jordi; Nichols, Jeffry C.; Schulten, Klaus; Gibson, Quentin H.; Srajer, Vukica; Royer, William E., Jr.
Ligand Migration and Cavities within Scapharca Dimeric Hbl: Studies by Time-Resolved Crystallography, Xe Binding, and Computational Analysis
STRUCTURE, 17:1494-1504, NOV 11 2009
abstract, full text, TCBG publications, DOI:10.1016/j.str.2009.09.004

Li Si-Jie; Bai Bo-Feng
Multi-vapor embryos nucleation process and spinodal temperature analysis of expandable superheated water system
ACTA PHYSICA SINICA, 58:7596-7602, NOV 2009
abstract, full text

Moretti, Sonia; De Falco, Valentina; Tamburrino, Anna; Barbi, Flavia; Tavano, Maria; Avenia, Nicola; Santeusanio, Fausto; Santoro, Massimo; Macchiarulo, Antonio; Puxeddu, Efisio
Insights into the molecular function of the inactivating mutations of B-Raf involving the DFG motif
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1793:1634-1645, NOV 2009
abstract, full text, DOI:10.1016/j.bbamcr.2009.09.001

Sharma, Gaurav; Rege, Kaushal; Budil, David E.; Yarmush, Martin; Mavroidis, Constantinos
Biological Force Measurement in a Protein-Based Nanoactuator
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 8:684-691, NOV 2009
abstract, full text, DOI:10.1109/TNANO.2009.2023517

Krone, Michael; Bidmon, Katrin; Ertl, Thomas
Interactive Visualization of Molecular Surface Dynamics
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 15:1391-1398, NOV-DEC 2009
abstract, full text

Hong, Seung Do; Ha, Man Yeong; Balachandar, S.
Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 339:187-195, NOV 1 2009
abstract, full text, DOI:10.1016/j.jcis.2009.07.048

Sekhar, P. Nataraj; Reddy, L. Ananda; De Maeyer, Marc; Kumar, K. Praveen; Srinivasulu, Y. S.; Sunitha, M. S. L.; Sphoorthi, I. S. N.; Jayasree, G.; Rao, A. Maruthi; Kothekar, V. S.; Narayana, P. V. B. S.; Kishor, P. B. Kavi
Genome wide analysis and comparative docking studies of new diaryl furan derivatives against human cyclooxygenase-2, lipoxygenase, thromboxane synthase and prostacyclin synthase enzymes involved in inflammatory pathway
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:313-329, NOV 2009
abstract, full text, DOI:10.1016/j.jmgm.2009.08.010

Lin, Jianping; Buettner, Ralf; Yuan, Yate-Ching; Yip, Richard; Horne, David; Jove, Richard; Vaidehi, Nagarajan
Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:347-356, NOV 2009
abstract, full text, DOI:10.1016/j.jmgm.2009.08.013

Wang, Shichen; Yang, Shuo; Yin, Yuejia; Xi, Jinghui; Li, Shanyu; Hao, Dongyun
Molecular dynamics simulations reveal the disparity in specific recognition of GCC-box by AtERFs transcription factors super family in Arabidopsis
JOURNAL OF MOLECULAR RECOGNITION, 22:474-479, NOV-DEC 2009
abstract, full text, DOI:10.1002/jmr.965

Ziemys, Arturas; Ferrari, Mauro; Cavasotto, Claudio N.
Molecular Modeling of Glucose Diffusivity in Silica Nanochannels
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 9:6349-6359, NOV 2009
abstract, full text, DOI:10.1166/jnn.2009.1822

Patra, Niladri; Wang, Boyang; Kral, Petr
Nanodroplet Activated and Guided Folding of Graphene Nanostructures
NANO LETTERS, 9:3766-3771, NOV 2009
abstract, full text, DOI:10.1021/nl9019616

Suyetin, M. V.; Vakhrushev, A. V.
Nanocapsule for Safe and Effective Methane Storage
NANOSCALE RESEARCH LETTERS, 4:1267-1270, NOV 2009
abstract, full text, DOI:10.1007/s11671-009-9391-x

Palmai, Zoltan; Chaloin, Laurent; Lionne, Corinne; Fidy, Judit; Perahia, David; Balog, Erika
Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:319-329, NOV 1 2009
abstract, full text, DOI:10.1002/prot.22437

Pickholz, Monica; Fraceto, Leonardo Fernandes; de Paula, Eneida
Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study
SYNTHETIC METALS, 159:2157-2158, NOV 2009
abstract, full text, DOI:10.1016/j.synthmet.2009.07.034

Pentikainen, Ulla; Ylanne, Jari
The Regulation Mechanism for the Auto-Inhibition of Binding of Human Filamin A to Integrin
JOURNAL OF MOLECULAR BIOLOGY, 393:644-657, OCT 30 2009
abstract, full text, DOI:10.1016/j.jmb.2009.08.035

Hajjar, Eric; Dejaegere, Annick; Reuter, Nathalie
Challenges in pK(a) Predictions for Proteins: The case of Asp213 in Human Proteinase 3
JOURNAL OF PHYSICAL CHEMISTRY A, 113:11783-11792, OCT 29 2009
abstract, full text, DOI:10.1021/jp902930u

Olivier, Y.; Muccioli, L.; Lemaur, V.; Geerts, Y. H.; Zannoni, C.; Cornil, J.
Theoretical Characterization of the Structural and Hole Transport Dynamics in Liquid-Crystalline Phthalocyanine Stacks
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14102-14111, OCT 29 2009
abstract, full text, DOI:10.1021/jp9061169

Mori, Takaharu; Okamoto, Yuko
Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 165103, OCT 28 2009
abstract, full text, DOI:10.1063/1.3247578

Xu, Wei; Cai, Ping; Yan, Ming; Xu, Lin; Ouyang, Ping-kai
Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
CHINESE JOURNAL OF CHEMICAL PHYSICS, 22:467-472, OCT 27 2009
abstract, full text, DOI:10.1088/1674-0068/22/05/467-472

Lafleur, Karine; Huang, Danzhi; Zhou, Ting; Caflisch, Amedeo; Nevado, Cristina
Structure-Based Optimization of Potent and Selective Inhibitors of the Tyrosine Kinase Erythropoietin Producing Human Hepatocellular Carcinoma Receptor B4 (EphB4)
JOURNAL OF MEDICINAL CHEMISTRY, 52:6433-6446, OCT 22 2009
abstract, full text, DOI:10.1021/jm9009444

Pantano, Diego A.; Klein, Michael L.
Characterization of Membrane-Protein Interactions for the Leucine Transporter from Aquifex aeolicus by Molecular Dynamics Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13715-13722, OCT 22 2009
abstract, full text, DOI:10.1021/jp901840u

Legge, F. S.; Binger, K. J.; Griffin, M. D. W.; Howlett, G. J.; Scanlon, D.; Treutlein, H.; Yarovsky, I.
Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14006-14014, OCT 22 2009
abstract, full text, DOI:10.1021/jp903842u

Freddolino, Peter L.; Schulten, Klaus
Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding
BIOPHYSICAL JOURNAL, 97:2338-2347, OCT 21 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.08.012

Dendzik, Z.; Gorny, K.; Gburski, Z.
Cooperative dipolar relaxation of a glycerol molecular cluster in nanoscale confinement-a computer simulation study
JOURNAL OF PHYSICS-CONDENSED MATTER, 21 Art. No. 425101, OCT 21 2009
abstract, full text, DOI:10.1088/0953-8984/21/42/425101

Wang, Tianjiao; Hoy, Julie A.; Lamm, Monica H.; Nilsen-Hamilton, Marit
Computational and Experimental Analyses Converge to Reveal a Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:14747-14755, OCT 21 2009
abstract, full text, DOI:10.1021/ja902719q

Mustata, Mirela; Capone, Ricardo; Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Lal, Ratnesh; Nussinov, Ruth
K3 Fragment of Amyloidogenic beta(2)-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:14938-14945, OCT 21 2009
abstract, full text, DOI:10.1021/ja9049299

Materese, Christopher K.; Savelyev, Alexey; Papoian, Garegin A.
Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:15005-15013, OCT 21 2009
abstract, full text, DOI:10.1021/ja905376q

Tarrago, Teresa; Martin-Benito, Jaime; Sabido, Eduard; Claasen, Birgit; Madurga, Sergio; Gairi, Margarida; Valpuesta, Jose M.; Giralt, Ernest
A new side opening on prolyl oligopeptidase revealed by electron microscopy
FEBS LETTERS, 583:3344-3348, OCT 20 2009
abstract, full text, DOI:10.1016/j.febslet.2009.09.036

Fatmi, M. Qaiser; Ai, Rizi; Chang, Chia-en A.
Synergistic Regulation and Ligand-Induced Conformational Changes of Tryptophan Synthase
BIOCHEMISTRY, 48:9921-9931, OCT 20 2009
abstract, full text, DOI:10.1021/bi901358j

Dixit, Anshuman; Yi, Lin; Gowthaman, Ragul; Torkamani, Ali; Schork, Nicholas J.; Verkhivker, Gennady M.
Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases
PLOS ONE, 4 Art. No. e7485, OCT 16 2009
abstract, full text, DOI:10.1371/journal.pone.0007485

Xu, Liang; Liu, Xin; Zhao, Weijie; Wang, Xicheng
Locally Enhanced Sampling Study of Dioxygen Diffusion Pathways in Homoprotocatechuate 2,3-Dioxygenase
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13596-13603, OCT 15 2009
abstract, full text, DOI:10.1021/jp902597t

Lee, Eric H.; Hsin, Jen; Sotomayor, Marcos; Comellas, Gemma; Schulten, Klaus
Discovery Through the Computational Microscope
STRUCTURE, 17:1295-1306, OCT 14 2009
abstract, full text, TCBG publications, DOI:10.1016/j.str.2009.09.001

Zhong, Wenyu; Guo, Wanlin
Mixed modes in opening of KcsA potassium channel from a targeted molecular dynamics simulation
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 388:86-90, OCT 9 2009
abstract, full text, DOI:10.1016/j.bbrc.2009.07.123

Lvov, Anatoli; Greitzer, Dafna; Berlin, Shai; Chikvashvili, Dodo; Tsuk, Sharon; Lotan, Ilana; Michaelevski, Izhak
Rearrangements in the Relative Orientation of Cytoplasmic Domains Induced by a Membrane-anchored Protein Mediate Modulations in Kv Channel Gating
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:28276-28291, OCT 9 2009
abstract, full text, DOI:10.1074/jbc.M109.028761

Cavallari, Manuela; Garbesi, Anna; Di Felice, Rosa
Porphyrin Intercalation in G4-DNA Quadruplexes by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13152-13160, OCT 8 2009
abstract, full text, DOI:10.1021/jp9039226

Pezeshki, Soroosh; Chimerel, Catalin; Bessonov, Andrey N.; Winterhalter, Mathias; Kleinekathoefer, Ulrich
Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF
BIOPHYSICAL JOURNAL, 97:1898-1906, OCT 7 2009
abstract, full text, DOI:10.1016/j.bpj.2009.07.018

Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.; Di Ventra, Massimiliano
Effect of Noise on DNA Sequencing via Transverse Electronic Transport
BIOPHYSICAL JOURNAL, 97:1990-1996, OCT 7 2009
abstract, full text, DOI:10.1016/j.bpj.2009.06.055

Arkhipov, Anton; Roos, Wouter H.; Wuite, Gijs J. L.; Schulten, Klaus
Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids
BIOPHYSICAL JOURNAL, 97:2061-2069, OCT 7 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.07.039

Okan, Osman Burak; Atilgan, Ali Rana; Atilgan, Canan
Nanosecond Motions in Proteins Impose Bounds on the Timescale Distributions of Local Dynamics
BIOPHYSICAL JOURNAL, 97:2080-2088, OCT 7 2009
abstract, full text, DOI:10.1016/j.bpj.2009.07.036

Fogolari, Federico; Haridas, Haritha; Corazza, Alessandra; Viglino, Paolo; Cora, Davide; Caselle, Michele; Esposito, Gennaro; Xodo, Luigi E.
Molecular models for intrastrand DNA G-quadruplexes
BMC STRUCTURAL BIOLOGY, 9 Art. No. 64, OCT 7 2009
abstract, full text, DOI:10.1186/1472-6807-9-64

Cho, Hyung Min; Chu, Jhih-Wei
Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 134107, OCT 7 2009
abstract, full text, DOI:10.1063/1.3238547

Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho
Generalized Langevin models of molecular dynamics simulations with applications to ion channels
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 134102, OCT 7 2009
abstract, full text, DOI:10.1063/1.3233945

Shih, Amy Y.; Sligar, Stephen G.; Schulten, Klaus
Maturation of high-density lipoproteins
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 6:863-871, OCT 6 2009
abstract, full text, TCBG publications, DOI:10.1098/rsif.2009.0173

Metcalf, Douglas G.; Kulp, Dan W.; Bennett, Joel S.; DeGrado, William F.
Multiple Approaches Converge on the Structure of the Integrin alpha IIb/beta 3 Transmembrane Heterodimer
JOURNAL OF MOLECULAR BIOLOGY, 392:1087-1101, OCT 2 2009
abstract, full text, DOI:10.1016/j.jmb.2009.06.032

Hilder, Tamsyn A.; Gordon, Daniel; Chung, Shin-Ho
Salt Rejection and Water Transport Through Boron Nitride Nanotubes
SMALL, 5:2183-2190, OCT 2 2009
abstract, full text, DOI:10.1002/smll.200900349

Perlmutter, Jason D.; Sachs, Jonathan N.
Experimental verification of lipid bilayer structure through multi-scale modeling
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:2284-2290, OCT 2009
abstract, full text, DOI:10.1016/j.bbamem.2009.07.006

Kaila, Ville R. I.; Verkhovsky, Michael I.; Hummer, Gerhard; Wikstrom, Marten
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1787:1205-1214, OCT 2009
abstract, full text, DOI:10.1016/j.bbabio.2009.04.008

Monfregola, Luca; Vitale, Rosa Maria; Amodeo, Pietro; De Luca, Stefania
A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: A proof of concept on HER2 receptor
BIOORGANIC & MEDICINAL CHEMISTRY, 17:7015-7020, OCT 1 2009
abstract, full text, DOI:10.1016/j.bmc.2009.08.004

Phillips, James C.; Stone, John E.
Probing Biomolecular Machines with Graphics Processors
COMMUNICATIONS OF THE ACM, 52:34-41, OCT 2009
full text, DOI:10.1145/1562764.1562780

Bonomi, Massimiliano; Branduardi, Davide; Bussi, Giovanni; Camilloni, Carlo; Provasi, Davide; Raiteri, Paolo; Donadio, Davide; Marinelli, Fabrizio; Pietrucci, Fabio; Broglia, Ricardo A.; Parrinello, Michele
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
COMPUTER PHYSICS COMMUNICATIONS, 180:1961-1972, OCT 2009
abstract, full text, DOI:10.1016/j.cpc.2009.05.011

Penev, Evgeni S.; Lampoudi, Sotiria; Shea, Joan-Emma
TiREX: Replica-exchange molecular dynamics using TINKER
COMPUTER PHYSICS COMMUNICATIONS, 180:2013-2019, OCT 2009
abstract, full text, DOI:10.1016/j.cpc.2009.06.005

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Sekar, K.
An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II (Human): Recognition of Cofactor and Substrate to Catalytic Arg 322
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:149-158, OCT 2009
abstract, full text

Dagliyan, Onur; Kavakli, I. Halil; Turkay, Metin
Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC(50) Using Common Molecular Descriptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2403-2411, OCT 2009
abstract, full text, DOI:10.1021/ci00247t

Roopra, Sanjit; Knapp, Bernhard; Omasits, Ulrich; Schreiner, Wolfgang
jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2412-2417, OCT 2009
abstract, full text, DOI:10.1021/ci90024817

Maragliano, Luca; Vanden-Eijnden, Eric; Roux, Benoit
Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2589-2594, OCT 2009
abstract, full text, DOI:10.1021/ct900279z

Schulz, Roland; Lindner, Benjamin; Petridis, Loukas; Smith, Jeremy C.
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2798-2808, OCT 2009
abstract, full text, DOI:10.1021/ct900292r

Soriano-Ursua, Marvin A.; Trujillo-Ferrara, Jose G.; Correa-Basurto, Jose
Homology modeling and flex-ligand docking studies on the guinea pig beta(2) adrenoceptor: structural and experimental similarities differences with the human beta(2)
JOURNAL OF MOLECULAR MODELING, 15:1203-1211, OCT 2009
abstract, full text, DOI:10.1007/s00894-009-0480-7

Walker, Kristin D.; Causgrove, Timothy P.
Contribution of arginine-glutamate salt bridges to helix stability
JOURNAL OF MOLECULAR MODELING, 15:1213-1219, OCT 2009
abstract, full text, DOI:10.1007/s00894-009-0482-5

Trivedi, Maulik; Davis, R. Andrew; Shabaik, Yumna; Roy, Ambrish; Verkhivker, Gennady; Laurence, Jennifer S.; Middaugh, C. Russell; Siahaan, Teruna J.
The Role of Covalent Dimerization on the Physical and Chemical Stability of the EC1 Domain of Human E-Cadherin
JOURNAL OF PHARMACEUTICAL SCIENCES, 98:3562-3574, OCT 2009
abstract, full text, DOI:10.1002/jps.21686

Pomata, Matias H. H.; Sonoda, Milton T.; Skaf, Munir S.; Elola, M. Dolores
Anomalous Dynamics of Hydration Water in Carbohydrate Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12999-13006, OCT 1 2009
abstract, full text, DOI:10.1021/jp904019c

Fishelovitch, Dan; Shaik, Sason; Wolfson, Haim J.; Nussinov, Ruth
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13018-13025, OCT 1 2009
abstract, full text, DOI:10.1021/jp810386z

Foley, Meredith C.; Schlick, Tamar
Relationship Between Conformational Changes in Pol lambda's Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13035-13047, OCT 1 2009
abstract, full text, DOI:10.1021/jp903172x

Dubey, Devendra K.; Tomar, Vikas
Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen-hydroxyapatite biomaterials
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS, 57:1702-1717, OCT 2009
abstract, full text, DOI:10.1016/j.jmps.2009.07.002

Talbert-Slagle, Kristina; Marlatt, Sara; Barrera, Francisco N.; Khurana, Ekta; Oates, Joanne; Gerstein, Mark; Engelman, Donald M.; Dixon, Ann M.; DiMaio, Daniel
Artificial Transmembrane Oncoproteins Smaller than the Bovine Papillomavirus E5 Protein Redefine Sequence Requirements for Activation of the Platelet-Derived Growth Factor beta Receptor
JOURNAL OF VIROLOGY, 83:9773-9785, OCT 2009
abstract, full text, DOI:10.1128/JVI.00946-09

Trabuco, Leonardo G.; Villa, Elizabeth; Schreiner, Eduard; Harrison, Christopher B.; Schulten, Klaus
Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
METHODS, 49:174-180, OCT 2009
abstract, full text, TCBG publications, DOI:10.1016/j.ymeth.2009.04.005

Ahn, Kwang H.; Bertalovitz, Alexander C.; Mierke, Dale F.; Kendall, Debra A.
Dual Role of the Second Extracellular Loop of the Cannabinoid Receptor 1: Ligand Binding and Receptor Localization
MOLECULAR PHARMACOLOGY, 76:833-842, OCT 2009
abstract, full text, DOI:10.1124/mol.109.057356

Huang, Wei; Kim, Joohyun; Jha, Shantenu; Aboul-ela, Fareed
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
NUCLEIC ACIDS RESEARCH, 37:6528-6539, OCT 2009
abstract, full text, DOI:10.1093/nar/gkp664

Lim, M. C. G.; Zhong, Z. W.
Effects of fluid flow on the oligonucleotide folding in single-walled carbon nanotubes
PHYSICAL REVIEW E, 80 Art. No. 041915, OCT 2009
abstract, full text, DOI:10.1103/PhysRevE.80.041915

Atilgan, Canan; Atilgan, Ali Rana
Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000544, OCT 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000544

Baris, Ibrahim; Tuncel, Aytug; Ozber, Natali; Keskin, Ozlem; Kavakli, Ibrahim Halil
Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000546, OCT 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000546

Liu, Jin; Nussinov, Ruth
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000527, OCT 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000527

Gutowski, Keith E.; Gurkan, Burcu; Maginn, Edward J.
Force field for the atomistic simulation of the properties of hydrazine, organic hydrazine derivatives, and energetic hydrazinium ionic liquids
PURE AND APPLIED CHEMISTRY, 81:1799-1828, OCT 2009
abstract, full text, DOI:10.1351/PAC-CON-08-09-24

Moraru, Alexandra; Svab, Istvan; Mihailescu, Dan Florin
CHARMM FORCE FIELD PARAMETERIZATION OF BACTERIAL LIPOPOLYSACCHARIDES
REVUE ROUMAINE DE CHIMIE, 54:799-+, OCT 2009
abstract, full text

Lin, Ying-Wu; Nie, Chang-Ming; Liao, Li-Fu
Folding behaviors of apocytochrome b(5) and its mutants: Insights from high temperature molecular dynamics simulations
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 910:154-162, SEP 30 2009
abstract, full text, DOI:10.1016/j.theochem.2009.06.036

Taskent-Sezgin, Humeyra; Chung, Juah; Patsalo, Vadim; Miyake-Stoner, Shigeki J.; Miller, Andrew M.; Brewer, Scott H.; Mehl, Ryan A.; Green, David F.; Raleigh, Daniel P.; Carrico, Isaac
Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study
BIOCHEMISTRY, 48:9040-9046, SEP 29 2009
abstract, full text, DOI:10.1021/bi900938z

De Angeli, Alexis; Moran, Oscar; Wege, Stefanie; Filleur, Sophie; Ephritikhine, Genevieve; Thomine, Sebastien; Barbier-Brygoo, Helene; Gambale, Franco
ATP Binding to the C Terminus of the Arabidopsis thaliana Nitrate/Proton Antiporter, AtCLCa, Regulates Nitrate Transport into Plant Vacuoles
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:26526-26532, SEP 25 2009
abstract, full text, DOI:10.1074/jbc.M109.005132

Tsai, Ching-Wei; Hsu, Ning-Yi; Wang, Chang-Hsu; Lu, Chia-Yu; Chang, Yung; Tsai, Hui-Hsu Gavin; Ruaan, Rouh-Chyu
Coupling Molecular Dynamics Simulations with Experiments for the Rational Design of Indolicidin-Analogous Antimicrobial Peptides
JOURNAL OF MOLECULAR BIOLOGY, 392:837-854, SEP 25 2009
abstract, full text, DOI:10.1016/j.jmb.2009.06.071

Furini, Simone; Domene, Carmen
Atypical mechanism of conduction in potassium channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:16074-16077, SEP 22 2009
abstract, full text, DOI:10.1073/pnas.0903226106

Bellesia, Giovanni; Shea, Joan-Emma
Diversity of kinetic pathways in amyloid fibril formation
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 111102, SEP 21 2009
abstract, full text, DOI:10.1063/1.3216103

Garate, Jose-Antonio; English, Niall J.; MacElroy, J. M. D.
Static and alternating electric field and distance-dependent effects on carbon nanotube-assisted water self-diffusion across lipid membranes
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 114508, SEP 21 2009
abstract, full text, DOI:10.1063/1.3227042

Zhang, Haoming; Kenaan, Cesar; Hamdane, Djemel; Hoa, Gaston Hui Bon; Hollenberg, Paul F.
Effect of Conformational Dynamics on Substrate Recognition and Specificity as Probed by the Introduction of a de Novo Disulfide Bond into Cytochrome P450 2B1
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25678-25686, SEP 18 2009
abstract, full text, DOI:10.1074/jbc.M109.032748

Carpena, Xavier; Vidossich, Pietro; Schroettner, Klarissa; Calisto, Barbara M.; Banerjee, Srijib; Stampler, Johanna; Soudi, Monika; Furtmueller, Paul G.; Rovira, Carme; Fita, Ignacio; Obinger, Christian
Essential Role of Proximal Histidine-Asparagine Interaction in Mammalian Peroxidases
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25929-25937, SEP 18 2009
abstract, full text, DOI:10.1074/jbc.M109.002154

Shukla, Diwakar; Shinde, Chetan; Trout, Bernhardt L.
Molecular Computations of Preferential Interaction Coefficients of Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12546-12554, SEP 17 2009
abstract, full text, DOI:10.1021/jp810949t

Roy, Arijit; Taraphder, Srabani
Transition Path Sampling Study of the Conformational Fluctuation of His-64 in Human Carbonic Anhydrase II
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12555-12564, SEP 17 2009
abstract, full text, DOI:10.1021/jp9010982

Liu, Lu Tian; Willenbring, Dan; Xu, Yan; Tang, Pei
General Anesthetic Binding to Neuronal alpha 4 beta 2 Nicotinic Acetylcholine Receptor and Its Effects on Global Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12581-12589, SEP 17 2009
abstract, full text, DOI:10.1021/jp9039513

Law, Richard J.; Lightstone, Felice C.
Modeling Neuronal Nicotinic and GABA Receptors: Important Interface Salt-Links and Protein Dynamics
BIOPHYSICAL JOURNAL, 97:1586-1594, SEP 16 2009
abstract, full text, DOI:10.1016/j.bpj.2009.06.044

Gokhan-Kelekci, Nesrin; Simsek, O. Ozgun; Ercan, Ayse; Yelekci, Kemal; Sahin, Z. Sibel; Isik, Samil; Ucar, Guelberk; Bilgin, A. Altan
Synthesis and molecular modeling of some novel hexahydroindazole derivatives as potent monoamine oxidase inhibitors
BIOORGANIC & MEDICINAL CHEMISTRY, 17:6761-6772, SEP 15 2009
abstract, full text, DOI:10.1016/j.bmc.2009.07.033

Orgel, Joseph P. R. O.; Eid, Aya; Antipova, Olga; Bella, Jordi; Scott, John E.
Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding
PLOS ONE, 4 Art. No. e7028, SEP 15 2009
abstract, full text, DOI:10.1371/journal.pone.0007028

Kajander, Tommi; Sachs, Jonathan N.; Goldman, Adrian; Regan, Lynne
Electrostatic Interactions of Hsp-organizing Protein Tetratricopeptide Domains with Hsp70 and Hsp90 COMPUTATIONAL ANALYSIS AND PROTEIN ENGINEERING
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25364-25374, SEP 11 2009
abstract, full text, DOI:10.1074/jbc.M109.033894

Lee, Tai-Sung; Ma, Wanlong; Zhang, Xi; Kantarjian, Hagop; Albitar, Maher
Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations
BMC STRUCTURAL BIOLOGY, 9 Art. No. 58, SEP 10 2009
abstract, full text, DOI:10.1186/1472-6807-9-58

Wang Teng; Sun Hong-Wei; Chen Lan; Shen Rong-Xin; Lai Cheng-Ming
Docking and Molecular Dynamics Simulation Studies of Interaction Between Arabidopsis TIR1 and Auxin IAA
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 30:1835-1838, SEP 10 2009
abstract, full text

Kubiak, Karina; Mulheran, Paul A.
Molecular Dynamics Simulations of Hen Egg White Lysozyme Adsorption at a Charged Solid Surface
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12189-12200, SEP 10 2009
abstract, full text, DOI:10.1021/jp901521x

Homouz, Dirar; Hoffman, Byron; Cheung, Margaret S.
Hydrophobic Interactions of Hexane in Nanosized Water Droplets
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12337-12342, SEP 10 2009
abstract, full text, DOI:10.1021/jp907318d

Lee, One-Sun; Schatz, George C.
Interaction between DNAs on a Gold Surface
JOURNAL OF PHYSICAL CHEMISTRY C, 113:15941-15947, SEP 10 2009
abstract, full text, DOI:10.1021/jp905469q

Wang, Jianping; Cai, Kaicong; Ma, Xiaoyan
Ultrafast Structural Dynamics of Biomolecules Examined by Multiple-Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony
CHEMPHYSCHEM, 10:2242-2250, SEP 9 2009
abstract, full text, DOI:10.1002/cphc.200900301

Newstead, Simon; Fowler, Philip W.; Bilton, Paul; Carpenter, Elisabeth P.; Sadler, Peter J.; Campopiano, Dominic J.; Sansom, Mark S. P.; Iwata, So
Insights into How Nucleotide-Binding Domains Power ABC Transport
STRUCTURE, 17:1213-1222, SEP 9 2009
abstract, full text, DOI:10.1016/j.str.2009.07.009

Balius, Trent E.; Rizzo, Robert C.
Quantitative Prediction of Fold Resistance for Inhibitors of EGFR
BIOCHEMISTRY, 48:8435-8448, SEP 8 2009
abstract, full text, DOI:10.1021/bi900729a

Takeda, Takako; Klimov, Dmitri K.
Side Chain Interactions Can Impede Amyloid Fibril Growth: Replica Exchange Simulations of A beta Peptide Mutant
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11848-11857, SEP 3 2009
abstract, full text, DOI:10.1021/jp904070w

Sengupta, Neelanjana; Maekawa, Hiroaki; Zhuang, Wei; Toniolo, Claudio; Mukamel, Shaul; Tobias, Douglas J.; Ge, Nien-Hui
Sensitivity of 2D IR Spectra to Peptide Helicity: A Concerted Experimental and Simulation Study of an Octapeptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12037-12049, SEP 3 2009
abstract, full text, DOI:10.1021/jp901504r

Law, Christopher J.; Enkavi, Giray; Wang, Da-Neng; Tajkhorshid, Emad
Structural Basis of Substrate Selectivity in the Glycerol-3-Phosphate: Phosphate Antiporter GlpT
BIOPHYSICAL JOURNAL, 97:1346-1353, SEP 2 2009
abstract, full text, DOI:10.1016/j.bpj.2009.06.026

Sarkar, Krishnarjun; Meister, Konrad; Sethi, Anurag; Gruebele, Martin
Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe
BIOPHYSICAL JOURNAL, 97:1418-1427, SEP 2 2009
abstract, full text, DOI:10.1016/j.bpj.2009.06.035

Dubey, Devendra K.; Tomar, Vikas
Role of the nanoscale interfacial arrangement in mechanical strength of tropocollagen-hydroxyapatite-based hard biomaterials
ACTA BIOMATERIALIA, 5:2704-2716, SEP 2009
abstract, full text, DOI:10.1016/j.actbio.2009.02.035

Shi, Wei; Maginn, Edward J.
Molecular Simulation of Ammonia Absorption in the Ionic Liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N])
AICHE JOURNAL, 55:2414-2421, SEP 2009
abstract, full text, DOI:10.1002/aic.11910

Qureshi, Shabir H.; Yang, Likui; Manithody, Chandrashekhara; Iakhiaev, Alexei V.; Rezaie, Alireza R.
Mutagenesis Studies toward Understanding Allostery In Thrombin
BIOCHEMISTRY, 48:8261-8270, SEP 1 2009
abstract, full text, DOI:10.1021/bi900921t

Li, Xiaochuan; Nevels, Kerrick J.; Gryczynski, Zygmunt; Gryczynski, Ignacy; Pusztai-Carey, Marianne; Xie, Dexuan; Butko, Peter
A molecular dynamics model of the Bt toxin Cyt1A and its validation by resonance energy transfer
BIOPHYSICAL CHEMISTRY, 144:53-61, SEP 2009
abstract, full text, DOI:10.1016/j.bpc.2009.06.005

Liu, Ming; Cong, Xiao Jing; Li, Ping; Tan, Jian Jun; Chen, Wei Zu; Wang, Cun Xin
Study on the Inhibitory Mechanism and Binding Mode of the Hydroxycoumarin Compound NSC158393 to HIV-1 Integrase by Molecular Modeling
BIOPOLYMERS, 91:700-709, SEP 2009
abstract, full text, DOI:10.1002/bip.21211

Nishizawa, Kazuhisa
Molecular Dynamics Simulations of Kv Channels and Gating-Modifier Peptide Toxins
CURRENT COMPUTER-AIDED DRUG DESIGN, 5:155-173, SEP 2009
abstract, full text

Song, Chen; Corry, Ben
Computational study of the transmembrane domain of the acetylcholine receptor
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 38:961-970, SEP 2009
abstract, full text, DOI:10.1007/s00249-009-0476-3

Codutti, Luca; Picotti, Paola; Marin, Oriano; Dewilde, Sylvia; Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Moens, Luc; Esposito, Gennaro; Fontana, Angelo
Conformational stability of neuroglobin helix F - possible effects on the folding pathway within the globin family
FEBS JOURNAL, 276:5177-5190, SEP 2009
abstract, full text, DOI:10.1111/j.1742-4658.2009.07214.x

Bulo, Rosa E.; Ensing, Bernd; Sikkema, Jetze; Visscher, Lucas
Toward a Practical Method for Adaptive QM/MM Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2212-2221, SEP 2009
abstract, full text, DOI:10.1021/ct900148e

Cerutti, David S.; Duke, Robert E.; Darden, Thomas A.; Lybrand, Terry P.
Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2322-2338, SEP 2009
abstract, full text, DOI:10.1021/ct9001015

Harvey, M. J.; De Fabritiis, G.
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2371-2377, SEP 2009
abstract, full text, DOI:10.1021/ct900275y

Sakuraba, Shun; Kitao, Akio
Multiple Markov Transition Matrix Method: Obtaining the Stationary Probability Distribution from Multiple Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1850-1858, SEP 2009
abstract, full text, DOI:10.1002/jcc.21186

Yongye, Austin B.; Li, Yangmei; Giulianotti, Marc A.; Yu, Yongping; Houghten, Richard A.; Martinez-Mayorga, Karina
Modeling of peptides containing D-amino acids: implications on cyclization
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 23:677-689, SEP 2009
abstract, full text, DOI:10.1007/s10822-009-9295-y

Banerjee, Amit Kumar; Arora, Neelima; Murty, U. S. N.
Structural model of the Plasmodium falciparum Thioredoxin reductase: a novel target for antimalarial drugs
JOURNAL OF VECTOR BORNE DISEASES, 46:171-183, SEP 2009
abstract, full text

Suyetin, M. V.; Vakhrushev, A. V.
Temperature-sensitive nanocapsules for methane storage
MICRO & NANO LETTERS, 4:172-176, SEP 2009
abstract, full text, DOI:10.1049/mnl.2009.0031

Menor, S. A.; de Graff, Adam M. R.; Thorpe, M. F.
Hierarchical plasticity from pair distance fluctuations
PHYSICAL BIOLOGY, 6 Art. No. 036017, SEP 2009
abstract, full text, DOI:10.1088/1478-3975/6/3/036017

Czajkowsky, Daniel M.; Shao, Zhifeng
The human IgM pentamer is a mushroom-shaped molecule with a flexural bias
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:14960-14965, SEP 1 2009
abstract, full text, DOI:10.1073/pnas.0903805106

Yount, Nannette Y.; Kupferwasser, Deborah; Spisni, Alberto; Dutz, Stephen M.; Ramjan, Zachary H.; Sharma, Shantanu; Waring, Alan J.; Yeaman, Michael R.
Selective reciprocity in antimicrobial activity versus cytotoxicity of hBD-2 and crotamine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:14972-14977, SEP 1 2009
abstract, full text, DOI:10.1073/pnas.0904465106

Mustafa, Morad; Henderson, Douglas J.; Busath, David D.
Free-energy profiles for ions in the influenza M-2-TMD channel
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76:794-807, SEP 2009
abstract, full text, DOI:10.1002/prot.22376

Gaillard, Thomas; Dejaegere, Annick; Stote, Roland H.
Dynamics of beta 3 integrin I-like and Hybrid domains: Insight from simulations on the mechanism of transition between open and closed forms
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76:977-994, SEP 2009
abstract, full text, DOI:10.1002/prot.22404

Fu, Yi; Ding, Yanrui; Chen, Zhiguo; Xu, Wenbo
Exploring Unfolding Pathway of CGTase: Insight from Molecular Dynamics Simulation
RIVISTA DI BIOLOGIA-BIOLOGY FORUM, 102:347-364, SEP-DEC 2009
abstract, full text

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit
MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch
RNA-A PUBLICATION OF THE RNA SOCIETY, 15:1673-1692, SEP 2009
abstract, full text, DOI:10.1261/rna.1675809

Dubey, Devendra K.; Tomar, Vikas
Role of hydroxyapatite crystal shape in nanoscale mechanical behavior of model tropocollagen-hydroxyapatite hard biomaterials
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 29:2133-2140, AUG 31 2009
abstract, full text, DOI:10.1016/j.msec.2009.04.015

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Bhattacharya, S.
Role of the conserved water molecules in the binding of inhibitor to IMPDH-II (human): A study on the water mimic inhibitor design
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 908:31-39, AUG 30 2009
abstract, full text, DOI:10.1016/j.theochem.2009.04.037

Vagenende, Vincent; Yap, Miranda G. S.; Trout, Bernhardt L.
Molecular Anatomy of Preferential Interaction Coefficients by Elucidating Protein Solvation in Mixed Solvents: Methodology and Application for Lysozyme in Aqueous Glycerol
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11743-11753, AUG 27 2009
abstract, full text, DOI:10.1021/jp903413v

Santaniello, Enzo; Casati, Silvana; Ciuffreda, Pierangela; Meroni, Giuseppe; Pedretti, Alessandro; Vistoli, Giulio
A molecular modelling approach to rationalize the stereochemical outcome of the Burkholderia cepacia lipase-catalyzed transesterification of aromatic primary alcohols with vinyl esters with different chain lengths in chloroform
TETRAHEDRON-ASYMMETRY, 20:1833-1836, AUG 26 2009
abstract, full text, DOI:10.1016/j.tetasy.2009.07.024

Aleman, Carlos; Betran, Oscar; Casanovas, Jordi; Houk, K. N.; Hall, H. K., Jr.
Thermodynamic Control of the Polymerizability of Five-, Six-, and Seven-Membered Lactones
JOURNAL OF ORGANIC CHEMISTRY, 74:6237-6244, AUG 21 2009
abstract, full text, DOI:10.1021/jo9010969

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Polymorphism of Alzheimer's A beta(17-42) (p3) Oligomers: The Importance of the Turn Location and Its Conformation
BIOPHYSICAL JOURNAL, 97:1168-1177, AUG 19 2009
abstract, full text, DOI:10.1016/j.bpj.2009.05.042

Chennamsetty, Naresh; Helk, Bernhard; Voynov, Vladimir; Kayser, Veysel; Trout, Bernhardt L.
Aggregation-Prone Motifs in Human Immunoglobulin G
JOURNAL OF MOLECULAR BIOLOGY, 391:404-413, AUG 14 2009
abstract, full text, DOI:10.1016/j.jmb.2009.06.028

Meier, Thomas; Krah, Alexander; Bond, Peter J.; Pogoryelov, Denys; Diederichs, Kay; Faraldo-Gomez, Jose D.
Complete Ion-Coordination Structure in the Rotor Ring of Na+-Dependent F-ATP Synthases
JOURNAL OF MOLECULAR BIOLOGY, 391:498-507, AUG 14 2009
abstract, full text, DOI:10.1016/j.jmb.2009.05.082

Bagchi, Sayan; Falvo, Cyril; Mukamel, Shaul; Hochstrasser, Robin M.
2D-IR Experiments and Simulations of the Coupling between Amide-I and Ionizable Side Chains in Proteins: Application to the Villin Headpiece
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11260-11273, AUG 13 2009
abstract, full text, DOI:10.1021/jp900245s

Mamonov, Artem B.; Bhatt, Divesh; Cashman, Derek J.; Ding, Ying; Zuckerman, Daniel M.
General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models
JOURNAL OF PHYSICAL CHEMISTRY B, 113:10891-10904, AUG 6 2009
abstract, full text, DOI:10.1021/jp901322v

Pfaendtner, Jim; Branduardi, Davide; Parrinello, Michele; Pollard, Thomas D.; Voth, Gregory A.
Nucleotide-dependent conformational states of actin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:12723-12728, AUG 4 2009
abstract, full text, DOI:10.1073/pnas.0902092106

Verde, Ana Vila; Acres, Jacqueline M.; Maranas, Janna K.
Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 10:2118-2128, AUG 2009
abstract, full text, DOI:10.1021/bm9002464

Rodriguez-Ropero, Francisco; Zanuy, David; Assfeld, Xavier; Aleman, Carlos
Modeling an Electronic Conductor Based on Natural Peptide Sequences
BIOMACROMOLECULES, 10:2338-2343, AUG 2009
abstract, full text, DOI:10.1021/bm900524v

Butler, Kyle V.; He, Rong; McLaughlin, Kathryn; Vistoli, Giulio; Langley, Brett; Kozikowski, Alan P.
Stereoselective HDAC Inhibition from Cysteine-Derived Zinc-Binding Groups
CHEMMEDCHEM, 4:1292-1301, AUG 2009
abstract, full text, DOI:10.1002/cmdc.200900088

Martin, Hugh S. C.; Jha, Shantenu; Howorka, Stefan; Coveney, Peter V.
Determination of Free Energy Profiles for the Translocation of Polynucleotides through alpha-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2135-2148, AUG 2009
abstract, full text, DOI:10.1021/ct9000894

Ramya, L.; Gautham, N.
Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2180-2190, AUG 2009
abstract, full text, DOI:10.1021/ct9000087

Bonomi, M.; Barducci, A.; Parrinello, M.
Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1615-1621, AUG 2009
abstract, full text, DOI:10.1002/jcc.21305

Oberhofer, Harald; Dellago, Christoph
Efficient Extraction of Free Energy Profiles From Nonequilibrium Experiments
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1726-1736, AUG 2009
abstract, full text, DOI:10.1002/jcc.21290

Kaestner, Johannes; Loeffler, Hannes H.; Roberts, Selene K.; Martin-Fernandez, Marisa L.; Winn, Martyn D.
Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 167:117-128, AUG 2009
abstract, full text, DOI:10.1016/j.jsb.2009.04.007

Jasuja, Ravi; Ulloor, Jagadish; Yengo, Christopher M.; Choong, Karen; Istomin, Andrei Y.; Livesay, Dennis R.; Jacobs, Donald J.; Swerdloff, Ronald S.; Miksovska, Jaroslava; Larsen, Randy W.; Bhasin, Shalender
Kinetic and Thermodynamic Characterization of Dihydrotestosterone-Induced Conformational Perturbations in Androgen Receptor Ligand-Binding Domain
MOLECULAR ENDOCRINOLOGY, 23:1231-1241, AUG 2009
abstract, full text, DOI:10.1210/me.2008-0304

Sogaard, Rikke; Alsterfjord, Magnus; MacAulay, Nanna; Zeuthen, Thomas
Ammonium ion transport by the AMT/Rh homolog TaAMT1;1 is stimulated by acidic pH
PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY, 458:733-743, AUG 2009
abstract, full text, DOI:10.1007/s00424-009-0665-z

Gong, Linchen; Zhou, Xin
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations
PHYSICAL REVIEW E, 80 Art. No. 026707, AUG 2009
abstract, full text, DOI:10.1103/PhysRevE.80.026707

Dixit, Anshuman; Verkhivker, Gennady M.
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000487, AUG 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000487

Zhu, Hui; Roeder, Beate; May, Volkhard
Time and frequency resolved spontaneous emission from supramolecular pheophorbide-a complexes: A mixed quantum classical computation
CHEMICAL PHYSICS, 362:19-26, JUL 30 2009
abstract, full text, DOI:10.1016/j.chemphys.2009.05.022

Brooks, B. R.; Brooks, C. L., I.I.I.; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M.
CHARMM: The Biomolecular Simulation Program
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1545-1614, JUL 30 2009
abstract, full text, DOI:10.1002/jcc.21287

Krishnan, Marimuthu; Smith, Jeremy C.
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:10083-10091, JUL 29 2009
abstract, full text, DOI:10.1021/ja901276n

Wei, Chenyu; Pohorille, Andrew
Permeation of Membranes by Ribose and Its Diastereomers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:10237-10245, JUL 29 2009
abstract, full text, DOI:10.1021/ja902531k

Li Jilai; Geng Caiyun; Bu Yuxiang; Zhang Liang; Zhang Laibin; Huang Xuri; Sun Chiachung
Decoupling Interactions between EF-hands of Recoverin and Ca2+: Steered Molecular Dynamics Simulation
ACTA CHIMICA SINICA, 67:1597-1602, JUL 28 2009
abstract, full text

Varga, Andrea; Lionne, Corinne; Lallemand, Perrine; Szabo, Judit; Adamek, Nancy; Valentin, Christian; Vas, Maria; Barman, Tom; Chaloin, Laurent
Direct Kinetic Evidence That Lysine 215 Is Involved in the Phospho-Transfer Step of Human 3-Phosphoglycerate Kinase
BIOCHEMISTRY, 48:6998-7008, JUL 28 2009
abstract, full text, DOI:10.1021/bi900396h

Mehboob, Shahila; Guo, Liang; Fu, Wentao; Mittal, Anuradha; Yau, Tiffany; Truong, Kent; Johlfs, Mary; Long, Fei; Fung, Leslie W. -M.; Johnson, Michael E.
Glutamate Racemase Dimerization Inhibits Dynamic Conformational Flexibility and Reduces Catalytic Rates
BIOCHEMISTRY, 48:7045-7055, JUL 28 2009
abstract, full text, DOI:10.1021/bi9005072

Bucher, Denis; Kuyucak, Serdar
Importance of water polarization for ion permeation in narrow pores
CHEMICAL PHYSICS LETTERS, 477:207-210, JUL 28 2009
abstract, full text, DOI:10.1016/j.cplett.2009.06.069

Yang, Lei; Song, Guang; Jernigan, Robert L.
Protein elastic network models and the ranges of cooperativity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:12347-12352, JUL 28 2009
abstract, full text, DOI:10.1073/pnas.0902159106

Zhuang, Shulin; Peng, Qing; Cao, Yi; Li, Hongbin
Modulating the Mechanical Stability of Extracellular Matrix Protein Tenascin-C in a Controlled and Reversible Fashion
JOURNAL OF MOLECULAR BIOLOGY, 390:820-829, JUL 24 2009
abstract, full text, DOI:10.1016/j.jmb.2009.05.057

Fratev, Filip F.; Jonsdottir, Svava Osk
An in silico study of the molecular basis of B-RAF activation and conformational stability
BMC STRUCTURAL BIOLOGY, 9 Art. No. 47, JUL 22 2009
abstract, full text, DOI:10.1186/1472-6807-9-47

DeMille, Robert C.; Molinero, Valeria
Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 034107, JUL 21 2009
abstract, full text, DOI:10.1063/1.3170982

Chennamsetty, Naresh; Voynov, Vladimir; Kayser, Veysel; Helk, Bernhard; Trout, Bernhardt L.
Design of therapeutic proteins with enhanced stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11937-11942, JUL 21 2009
abstract, full text, DOI:10.1073/pnas.0904191106

Schoen, Philipp A. E.; Michel, Bruno; Curioni, Alessandro; Poulikakos, Dimos
Hydrogen-bond enhanced thermal energy transport at functionalized, hydrophobic and hydrophilic silica-water interfaces
CHEMICAL PHYSICS LETTERS, 476:271-276, JUL 16 2009
abstract, full text, DOI:10.1016/j.cplett.2009.06.052

Talavera, Ariel; Friemann, Rosmarie; Gomez-Puerta, Silvia; Martinez-Fleites, Carlos; Garrido, Greta; Rabasa, Ailem; Lopez-Requena, Alejandro; Pupo, Amaury; Johansen, Rune F.; Sanchez, Oliberto; Krengel, Ute; Moreno, Ernesto
Nimotuzumab, an Antitumor Antibody that Targets the Epidermal Growth Factor Receptor, Blocks Ligand Binding while Permitting the Active Receptor Conformation
CANCER RESEARCH, 69:5851-5859, JUL 15 2009
abstract, full text, DOI:10.1158/0008-5472.CAN-08-4518

Iori, F.; Di Felice, R.; Molinari, E.; Corni, S.
GoIP: An Atomistic Force-Field to Describe the Interaction of Proteins With Au(111) Surfaces in Water
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1465-1476, JUL 15 2009
abstract, full text, DOI:10.1002/jcc.21165

Sun, Ting Guang; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin
A novel back-door pathway for glutamine release from GlnBP revealed by steered molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 905:51-58, JUL 15 2009
abstract, full text, DOI:10.1016/j.theochem.2009.03.012

Hodak, Miroslav; Chisnell, Robin; Lu, Wenchang; Bernholc, J.
Functional implications of multistage copper binding to the prion protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11576-11581, JUL 14 2009
abstract, full text, DOI:10.1073/pnas.0903807106

Halling-Brown, Mark D.; Moss, David S.; Sansom, Clare E.; Shepherd, Adrian J.
A computational Grid framework for immunological applications
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 367:2705-2716, JUL 13 2009
abstract, full text, DOI:10.1098/rsta.2009.0046

Zhang, Xiaofei; Bursulaya, Badry; Lee, Christian C.; Chen, Bihan; Pivaroff, Kendra; Jegla, Timothy
Divalent Cations Slow Activation of EAG Family K+ Channels through Direct Binding to S4
BIOPHYSICAL JOURNAL, 97:110-120, JUL 8 2009
abstract, full text, DOI:10.1016/j.bpj.2009.04.032

Hsin, Jen; Gumbart, James; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus
Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting
BIOPHYSICAL JOURNAL, 97:321-329, JUL 8 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.04.031

Chen, Qu; Wang, Qi; Liu, Ying-Chun; Wu, Tao; Kang, Yu; Moore, Joshua D.; Gubbins, Keith E.
Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 015101, JUL 7 2009
abstract, full text, DOI:10.1063/1.3148025

Silva, Jonathan R.; Pan, Hua; Wu, Dick; Nekouzadeh, Ali; Decker, Keith F.; Cui, Jianmin; Baker, Nathan A.; Sept, David; Rudy, Yoram
A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11102-11106, JUL 7 2009
abstract, full text, DOI:10.1073/pnas.0904505106

Politi, Regina; Sapir, Liel; Harries, Daniel
The Impact of Polyols on Water Structure in Solution: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY A, 113:7548-7555, JUL 2 2009
abstract, full text, DOI:10.1021/jp9010026

Song, Chen; Corry, Ben
Role of acetylcholine receptor domains in ion selectivity
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1466-1473, JUL 2009
abstract, full text, DOI:10.1016/j.bbamem.2009.04.015

Ahn, Kwang H.; Pellegrini, Maria; Tsomaia, Natia; Yatawara, Achani K.; Kendall, Debra A.; Mierke, Dale F.
Structural Analysis of the Human Cannabinoid Receptor One Carboxyl-Terminus Identifies Two Amphipathic Helices
BIOPOLYMERS, 91:565-573, JUL 2009
abstract, full text, DOI:10.1002/bip.21179

Wells, Gordon A.; Mueller, Ingrid B.; Wrenger, Carsten; Louw, Abraham I.
The activity of Plasmodium falciparum arginase is mediated by a novel inter-monomer salt-bridge between Glu295-Arg404
FEBS JOURNAL, 276:3517-3530, JUL 2009
abstract, full text, DOI:10.1111/j.1742-4658.2009.07073.x

Cai, Bin; Ding, Zhi-Chun; Zhang, Qi; Ni, Feng-Yun; Wang, Hui; Zheng, Qi; Wang, Yang; Zhou, Guo-Ming; Wang, Ke-Qiang; Sun, Hong-Zhe; Wu, Hou-Ming; Huang, Zhong-Xian
The structural and biological significance of the EAAEAE insert in the alpha-domain of human neuronal growth inhibitory factor
FEBS JOURNAL, 276:3547-3558, JUL 2009
abstract, full text, DOI:10.1111/j.1742-4658.2009.07075.x

Beckham, Simone A.; Piedrafita, David; Phillips, Carolyn I.; Samarawickrema, Nirma; Law, Ruby H. P.; Smooker, Peter M.; Quinsey, Noelene S.; Irving, James A.; Greenwood, Deanne; Verhelst, Steven H. L.; Bogyo, Matthew; Turk, Boris; Coetzer, Theresa H.; Wijeyewickrema, Lakshmi C.; Spithill, Terry W.; Pike, Robert N.
A major cathepsin B protease from the liver fluke Fasciola hepatica has atypical active site features and a potential role in the digestive tract of newly excysted juvenile parasites
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 41:1601-1612, JUL 2009
abstract, full text, DOI:10.1016/j.biocel.2009.02.003

Guixe, Victoria; Merino, Felipe
The ADP-dependent Sugar Kinase Family: Kinetic and Evolutionary Aspects
IUBMB LIFE, 61:753-761, JUL 2009
abstract, full text, DOI:10.1002/iub.217

Zanuy, David; Ballano, Gema; Jimenez, Ana I.; Casanovas, Jordi; Haspel, Nurit; Cativiela, Carlos; Curco, David; Nussinov, Ruth; Aleman, Carlos
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1623-1629, JUL 2009
full text, DOI:10.1021/ci9001487

Pearce, Bradley C.; Langley, David R.; Kang, Jia; Huang, Hongwei; Kulkarni, Amit
E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1797-1809, JUL 2009
abstract, full text, DOI:10.1021/ci900073k

Hixson, Christopher Adam; Wheeler, Ralph A.
Pressure Annealing as a Complement to Temperature Annealing To Find Low-Energy Structures of Oligomeric Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1883-1894, JUL 2009
abstract, full text, DOI:10.1021/ct800451c

Drikakis, Dimitris; Lechuga, Javier; Pal, Sandip
Effects of Shock Waves on Biological Membranes: A Molecular Dynamics Study
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:1437-1442, JUL 2009
abstract, full text, DOI:10.1166/jctn.2009.1190

Prince-Carter, Alison; Pfaffinger, Paul J.
Multiple intermediate states precede pore block during N-type inactivation of a voltage-gated potassium channel
JOURNAL OF GENERAL PHYSIOLOGY, 134:15-34, JUL 2009
abstract, full text, DOI:10.1085/jgp.200910219

Katti, Dinesh R.; Matar, Mohamed I.; Katti, Kalpana S.; Amarasinghe, Priyanthi M.
Multiscale modeling of swelling clays: A computational and experimental approach
KSCE JOURNAL OF CIVIL ENGINEERING, 13:243-255, JUL 2009
abstract, full text, DOI:10.1007/s12205-009-0243-0

Dorvel, B.; Sigalov, G.; Zhao, Q.; Comer, J.; Dimitrov, V.; Mirsaidov, U.; Aksimentiev, A.; Timp, G.
Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore
NUCLEIC ACIDS RESEARCH, 37:4170-4179, JUL 2009
abstract, full text, DOI:10.1093/nar/gkp317

Pan, Yongping; Nussinov, Ruth
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000448, JUL 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000448

Micluta, Marius A.; Petrescu, Andrei-Jose
PARALLEL COMPUTING IN MOLECULAR SIMULATION AND PROTEIN MODELING
Romanian Journal of Biochemistry, 46:129-148, JUL-DEC 2009
abstract, full text

Luckow, Andre; Jha, Shantenu; Kim, Joohyun; Merzky, Andre; Schnor, Bettina
Adaptive distributed replica-exchange simulations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 367:2595-2606, JUN 28 2009
abstract, full text, DOI:10.1098/rsta.2009.0051

Tralau, Tewes; Lafite, Pierre; Levy, Colin; Combe, John P.; Scrutton, Nigel S.; Leys, David
An Internal Reaction Chamber in Dimethylglycine Oxidase Provides Efficient Protection from Exposure to Toxic Formaldehyde
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:17826-17834, JUN 26 2009
abstract, full text, DOI:10.1074/jbc.M109.006262

Traaseth, Nathaniel J.; Shi, Lei; Verardi, Raffaello; Mullen, Daniel G.; Barany, George; Veglia, Gianluigi
Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:10165-10170, JUN 23 2009
abstract, full text, DOI:10.1073/pnas.0904290106

Saldias, Cesar; Gargallo, Ligia; Sandoval, Claudia; Leiva, Angel; Radic, Deodato; Caballero, Julio; Saavedra, Mario; Gonzalez-Nilo, Fernando D.
Inclusion complexes containing poly(epsilon-caprolactone)diol and cyclodextrins. Experimental and theoretical studies
POLYMER, 50:2926-2932, JUN 19 2009
abstract, full text, DOI:10.1016/j.polymer.2009.04.044

Rodriguez-Ropero, Francisco; Preat, Julien; Zanuy, David; Torras, Juan; Aleman, Carlos
Sensing Mechanism of Calix[4]arene-Substituted Poly(thiophene) Ion Receptor: Effects of the Selectivity on the Molecular Rigidity
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8284-8287, JUN 18 2009
abstract, full text, DOI:10.1021/jp902149r

Bagchi, Sayan; Charnley, Adam K.; Smith, Amos B., I.I.I.; Hochstrasser, Robin M.
Equilibrium Exchange Processes of the Aqueous Tryptophan Dipeptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8412-8417, JUN 18 2009
abstract, full text, DOI:10.1021/jp811168x

Maffeo, Christopher; Aksimentiev, Aleksei
Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer
BIOPHYSICAL JOURNAL, 96:4853-4865, JUN 17 2009
abstract, full text, DOI:10.1016/j.bpj.2009.03.053

Burke, John E.; Babakhani, Arneh; Gorfe, Alemayehu A.; Kokotos, George; Li, Sheng; Woods, Virgil L., Jr.; McCammon, J. Andrew; Dennis, Edward A.
Location of Inhibitors Bound to Group IVA Phospholipase A(2) Determined by Molecular Dynamics and Deuterium Exchange Mass Spectrometry
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:8083-8091, JUN 17 2009
abstract, full text, DOI:10.1021/ja900098y

Tsai, M. Y.; Morozov, A. N.; Chu, K. Y.; Lin, S. H.
Molecular Dynamics insight into the role of tertiary (foldon) interactions on unfolding in Cytochrome c
CHEMICAL PHYSICS LETTERS, 475:111-115, JUN 16 2009
abstract, full text, DOI:10.1016/j.cplett.2009.05.027

McDonald, Sarah M.; Aguayo, Daniel; Gonzalez-Nilo, Fernando D.; Patton, John T.
Shared and Group-Specific Features of the Rotavirus RNA Polymerase Reveal Potential Determinants of Gene Reassortment Restriction
JOURNAL OF VIROLOGY, 83:6135-6148, JUN 15 2009
abstract, full text, DOI:10.1128/JVI.00409-09

Domene, Carmen; Furini, Simone
Dynamics, Energetics, and Selectivity of the Low-K+ KcsA Channel Structure
JOURNAL OF MOLECULAR BIOLOGY, 389:637-645, JUN 12 2009
abstract, full text, DOI:10.1016/j.jmb.2009.04.038

Sen, Kakali; Hackett, John C.
Molecular Oxygen Activation and Proton Transfer Mechanisms in Lanosterol 14 alpha-Demethylase Catalysis
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8170-8182, JUN 11 2009
abstract, full text, DOI:10.1021/jp902932p

Yin, Ying; Arkhipov, Anton; Schulten, Klaus
Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains
STRUCTURE, 17:882-892, JUN 10 2009
abstract, full text, TCBG publications, DOI:10.1016/j.str.2009.03.016

Bennett, Melissa J.; Chik, John. K.; Slysz, Gordon W.; Luchko, Tyler; Tuszynski, Jack; Sackett, Dan L.; Schriemer, David C.
Structural Mass Spectrometry of the alpha beta-Tubulin Dimer Supports a Revised Model of Microtubule Assembly
BIOCHEMISTRY, 48:4858-4870, JUN 9 2009
abstract, full text, DOI:10.1021/bi900200q

Choe, Seungho; Grabe, Michael
Conformational dynamics of the inner pore helix of voltage-gated potassium channels
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 215103, JUN 7 2009
abstract, full text, DOI:10.1063/1.3138906

Cai, Wensheng; Sun, Tingting; Liu, Peng; Chipot, Christophe; Shao, Xueguang
Inclusion Mechanism of Steroid Drugs into beta-Cyclodextrins. Insights from Free Energy Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7836-7843, JUN 4 2009
abstract, full text, DOI:10.1021/jp901825w

Zanuy, David; Flores-Ortega, Alejandra; Jimenez, Ana I.; Calaza, M. Isabel; Cativiela, Carlos; Nussinov, Ruth; Ruoslahti, Erkki; Aleman, Carlos
In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7879-7889, JUN 4 2009
abstract, full text, DOI:10.1021/jp9006119

Cheng, Xiaolin; Ivanov, Ivaylo; Wang, Hailong; Sine, Steven M.; McCammon, J. Andrew
Molecular-Dynamics Simulations of ELIC-a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor
BIOPHYSICAL JOURNAL, 96:4502-4513, JUN 3 2009
abstract, full text, DOI:10.1016/j.bpj.2009.03.018

Rivera, Eva; Straub, John; Thirumalai, D.
Sequence and Crowding Effects in the Aggregation of a 10-Residue Fragment Derived from Islet Amyloid Polypeptide
BIOPHYSICAL JOURNAL, 96:4552-4560, JUN 3 2009
abstract, full text, DOI:10.1016/j.bpj.2009.03.039

Hammoudeh, Dalia I.; Follis, Ariele Viacava; Prochownik, Edward V.; Metallo, Stevan J.
Multiple Independent Binding Sites for Small-Molecule Inhibitors on the Oncoprotein c-Myc
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:7390-7401, JUN 3 2009
abstract, full text, DOI:10.1021/ja900616b

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin
Adsorption of Insulin Peptide on Charged Single-Walled Carbon Nanotubes: Significant Role of Ordered Water Molecules
CHEMPHYSCHEM, 10:1260-1269, JUN 2 2009
abstract, full text, DOI:10.1002/cphc.200800836

Prezhdo, Oleg V.; Pereverzev, Yuriy V.
Theoretical Aspects of the Biological Catch Bond
ACCOUNTS OF CHEMICAL RESEARCH, 42:693-703, JUN 2009
abstract, full text, DOI:10.1021/ar800202z

Maldonado, E.; Roth, M. W.; Gray, Paul A.
Fully Atomistic Molecular Dynamics Simulations of the Behavior of a Simple Model of Crude Oil Confined between Graphene Planes
ACS APPLIED MATERIALS & INTERFACES, 1:1211-1217, JUN 2009
abstract, full text, DOI:10.1021/am900086u

Zhang, Guodong; Chen, Jian An; Tanaka, Takuji
Deregulation of allosteric response of Lactococcus lactis prolidase and its effects on enzyme activity
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1794:968-975, JUN 2009
abstract, full text, DOI:10.1016/j.bbapap.2009.01.008

Mustafa, Morad; Henderson, Douglas J.; Busath, David D.
Computational studies of gramicidin permeation: An entryway sulfonate enhances cation occupancy at entry sites
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1404-1412, JUN 2009
abstract, full text, DOI:10.1016/j.bbamem.2009.03.021

Weidemueller, Christian; Hauser, Karin
Ion transport and energy transduction of P-type ATPases: Implications from electrostatic calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1787:721-729, JUN 2009
abstract, full text, DOI:10.1016/j.bbabio.2009.02.015

Buggert, Matthias; Cadena, Cesar; Mokrushina, Liudmila; Smirnova, Irina; Maginn, Edward J.; Arlt, Wolfgang
COSMO-RS Calculations of Partition Coefficients: Different Tools for Conformational Search
CHEMICAL ENGINEERING & TECHNOLOGY, 32:977-986, JUN 2009
abstract, full text, DOI:10.1002/ceat.200800654

Vistoli, Giulio; Orioli, Marica; Pedretti, Alessandro; Regazzoni, Luca; Canevotti, Renato; Negrisoli, Gianpaolo; Carini, Marina; Aldini, Giancarlo
Design, Synthesis, and Evaluation of Carnosine Derivatives as Selective and Efficient Sequestering Agents of Cytotoxic Reactive Carbonyl Species
CHEMMEDCHEM, 4:967-975, JUN 2009
abstract, full text, DOI:10.1002/cmdc.200800433

Meirovitch, Hagai; Cheluvaraja, Srinath; White, Ronald P.
Methods for Calculating the Entropy and Free Energy and their Application to Problems Involving Protein Flexibility and Ligand Binding
CURRENT PROTEIN & PEPTIDE SCIENCE, 10:229-243, JUN 2009
abstract, full text

Mustafa, Morad; Busath, DavidD.
The Gramicidin Channel Ion Permeation Free-Energy Profile: Direct and Indirect Effects of CHARMM Force Field Improvements
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 1:113-127, JUN 2009
abstract, full text, DOI:10.1007/s12539-009-0025-3

Tatsis, Vasileios A.; Tsoulos, Ioannis G.; Krinas, Christos S.; Alexopoulos, Charalampos; Stavrakoudis, Athanassios
Insights into the structure of the PmrD protein with molecular dynamics simulations
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 44:393-399, JUN 1 2009
abstract, full text, DOI:10.1016/j.ijbiomac.2009.02.006

Bruno, Agostino; Entrena Guadix, Antonio; Costantino, Gabriele
Molecular Dynamics Simulation of the Heterodimeric mGluR2/5HT(2A) Complex. An Atomistic Resolution Study of a Potential New Target in Psychiatric Conditions
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1602-1616, JUN 2009
abstract, full text, DOI:10.1021/ci900067g

Harvey, M. J.; Giupponi, G.; De Fabritiis, G.
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1632-1639, JUN 2009
abstract, full text, DOI:10.1021/ct9000685

Ho, Ming-Hsun; De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.
Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1657-1666, JUN 2009
abstract, full text, DOI:10.1021/ct8004722

Watanabe, Toshio; Inadomi, Yuichi; Umeda, Hiroaki; Fukuzawa, Kaori; Tanaka, Shigenori; Nakano, Tatsuya; Nagashima, Umpei
Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:1328-1337, JUN 2009
abstract, full text, DOI:10.1166/jctn.2009.1182

Schweiker, Stephanie S.; Loughlin, Wendy A.; Brown, Christopher L.; Pierens, Gregory K.
Synthesis of new modified truncated peptides and inhibition of glycogen phosphorylase
JOURNAL OF PEPTIDE SCIENCE, 15:442-450, JUN 2009
abstract, full text, DOI:10.1002/psc.1140

Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
PHYSICAL REVIEW E, 79 Art. No. 060901, JUN 2009
abstract, full text, DOI:10.1103/PhysRevE.79.060901

Bhardwaj, Nitin; Gerstein, Mark
Relating protein conformational changes to packing efficiency and disorder
PROTEIN SCIENCE, 18:1230-1240, JUN 2009
abstract, full text, DOI:10.1002/pro.132

Le Nours, Jerome; De Maria, Leonardo; Welner, Ditte; Jorgensen, Christel T.; Christensen, Lars L. H.; Borchert, Torben V.; Larsen, Sine; Lo Leggio, Leila
Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:977-989, JUN 2009
abstract, full text, DOI:10.1002/prot.22310

Kumar, Dinesh; Misra, Jyoti Ranjan; Kumar, Ashutosh; Chugh, Jeetender; Sharma, Shilpy; Hosur, Ramakrishna V.
NMR-derived solution structure of SUMO from Drosophila melanogaster [dSmt3]
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:1046-1050, JUN 2009
full text

Lee, Tai-Sung; Potts, Steven J.; Albitar, Maher
Basis for Resistance to Imatinib in 16 BCR-ABL Mutants as Determined Using Molecular Dynamics
RECENT PATENTS ON ANTI-CANCER DRUG DISCOVERY, 4:164-173, JUN 2009
abstract, full text

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Yang, Jian
Hydrogen bonding analysis of glycerol aqueous solutions: A molecular dynamics simulation study
JOURNAL OF MOLECULAR LIQUIDS, 146:23-28, MAY 31 2009
abstract, full text, DOI:10.1016/j.molliq.2009.01.009

Docquier, Jean-Denis; Calderone, Vito; De Luca, Filomena; Benvenuti, Manuela; Giuliani, Francesco; Bellucci, Luca; Tafi, Andrea; Nordmann, Patrice; Botta, Maurizio; Rossolini, Gian Maria; Mangani, Stefano
Crystal Structure of the OXA-48 beta-Lactamase Reveals Mechanistic Diversity among Class D Carbapenemases
CHEMISTRY & BIOLOGY, 16:540-547, MAY 29 2009
abstract, full text, DOI:10.1016/j.chembiol.2009.04.010

Song, Chen; Corry, Ben
Intrinsic Ion Selectivity of Narrow Hydrophobic Pores
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7642-7649, MAY 28 2009
abstract, full text, DOI:10.1021/jp810102u

Frydenvang, Karla; Lash, L. Leanne; Naur, Peter; Postila, Pekka A.; Pickering, Darryl S.; Smith, Caleb M.; Gajhede, Michael; Sasaki, Makoto; Sakai, Ryuichi; Pentikainen, Olli T.; Swanson, Geoffrey T.; Kastrup, Jette S.
Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:14219-14229, MAY 22 2009
abstract, full text, DOI:10.1074/jbc.M808547200

Logothetit, Georgia-Evangelia; Ramos, Javier; Economou, Ioannis G.
Molecular Modeling of Imidazolium-Based [Tf2N-] Ionic Liquids: Microscopic Structure, Thermodynamic and Dynamic Properties, and Segmental Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7211-7224, MAY 21 2009
abstract, full text, DOI:10.1021/jp806999y

Walch, Stephen P.; Komadina, Jason D.; Prinz, Fritz B.
A Computational Comparison of Electron Transfer from Reduced Ferredoxin to Flavin Adenine Dinucleotide and a Gold Electrode
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7298-7307, MAY 21 2009
abstract, full text, DOI:10.1021/jp8051104

Bastug, Turgut; Kuyucak, Serdar
Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels
BIOPHYSICAL JOURNAL, 96:4006-4012, MAY 20 2009
abstract, full text, DOI:10.1016/j.bpj.2009.02.041

Zou, Hongling; Liu, Jing; Blasie, J. Kent
Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a Cyanophenylalanine Spectroscopic Probe
BIOPHYSICAL JOURNAL, 96:4188-4199, MAY 20 2009
abstract, full text, DOI:10.1016/j.bpj.2009.01.054

Tian, Jianhui; Garcia, Angel E.
An Alpha-Helical Peptide in AOT Micelles Prefers to be Localized at the Water/Headgroup Interface
BIOPHYSICAL JOURNAL, 96:L57-L59, MAY 20 2009
abstract, full text, DOI:10.1016/j.bpj.2009.03.014

Dubey, Devendra K.; Tomar, Vikas
The effect of tensile and compressive loading on the hierarchical strength of idealized tropocollagen-hydroxyapatite biomaterials as a function of the chemical environment
JOURNAL OF PHYSICS-CONDENSED MATTER, 21 Art. No. 205103, MAY 20 2009
abstract, full text, DOI:10.1088/0953-8984/21/20/205103

Burress, Jacob; Kraus, Michael; Beckner, Matt; Cepel, Raina; Suppes, Galen; Wexler, Carlos; Pfeifer, Peter
Hydrogen storage in engineered carbon nanospaces
NANOTECHNOLOGY, 20 Art. No. 204026, MAY 20 2009
abstract, full text, DOI:10.1088/0957-4484/20/20/204026

Liu, Peng; Marzahn, Melissa R.; Robbins, Arthur H.; Gutierrez-de-Teran, Hugo; Rodriguez, David; McClung, Scott H.; Stevens, Stanley M., Jr.; Yowell, Charles A.; Dame, John B.; McKenna, Robert; Dunn, Ben M.
Recombinant Plasmepsin 1 from the Human Malaria Parasite Plasmodium falciparum: Enzymatic Characterization, Active Site Inhibitor Design, and Structural Analysis
BIOCHEMISTRY, 48:4086-4099, MAY 19 2009
abstract, full text, DOI:10.1021/bi802059r

Peters, Gunther H.
The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein SpoOF studied by molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:648-658, MAY 15 2009
abstract, full text, DOI:10.1002/prot.22276

Chen Cong; Li Weizhong
The Relation between the Ratio of Hydrogen Bonding Acceptor Number to Donor Number and Solute Concentration
ACTA CHIMICA SINICA, 67:883-887, MAY 14 2009
abstract, full text

Dittmer, Jens; Thogersen, Lea; Underhaug, Jarl; Bertelsen, Kresten; Vosegaard, Thomas; Pedersen, Jan M.; Schiott, Birgit; Tajkhorshid, Emad; Skrydstrup, Troels; Nielsen, Niels Chr.
Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6928-6937, MAY 14 2009
abstract, full text, DOI:10.1021/jp811494p

Henin, Jerome; Shinoda, Wataru; Klein, Michael L.
Models for Phosphatidylglycerol Lipids Put to a Structural Test
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6958-6963, MAY 14 2009
abstract, full text, DOI:10.1021/jp900645z

Cheng, Mary H.; Xu, Yan; Tang, Pei
Anionic Lipid and Cholesterol Interactions with alpha 4 beta 2 nAChR: Insights from MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6964-6970, MAY 14 2009
abstract, full text, DOI:10.1021/jp900714b

Paul, Amit; Bezer, Silvia; Venkatramani, Ravindra; Kocsis, Laura; Wierzbinski, Emil; Balaeff, Alexander; Keinan, Shahar; Beratan, David N.; Achim, Catalina; Waldeck, David H.
Role of Nucleobase Energetics and Nucleobase Interactions in Single-Stranded Peptide Nucleic Acid Charge Transfer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:6498-6507, MAY 13 2009
abstract, full text, DOI:10.1021/ja9000163

Wang, Hai-Long; Toghraee, Reza; Papke, David; Cheng, Xiao-Lin; McCammon, J. Andrew; Ravaioli, Umberto; Sine, Steven M.
Single-Channel Current Through Nicotinic Receptor Produced by Closure of Binding Site C-Loop
BIOPHYSICAL JOURNAL, 96:3582-3590, MAY 6 2009
abstract, full text, DOI:10.1016/j.bpj.2009.02.020

Freddolino, Peter L.; Park, Sanghyun; Roux, Benoit; Schulten, Klaus
Force Field Bias in Protein Folding Simulations
BIOPHYSICAL JOURNAL, 96:3772-3780, MAY 6 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2009.02.033

Pedretti, Alessandro; Marconi, Cristina; Bettinelli, Ilaria; Vistoli, Giulio
Comparative modeling of the quaternary structure for the human TRPM8 channel and analysis of its binding features
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:973-982, MAY 2009
abstract, full text, DOI:10.1016/j.bbamem.2009.02.007

Shen, Rong; Guo, Wanlin
Ion binding properties and structure stability of the NaK channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1024-1032, MAY 2009
abstract, full text, DOI:10.1016/j.bbamem.2009.01.008

Kang, Yu; Liu, Ying-Chun; Wang, Qi; Shen, Jia-Wei; Wu, Tao; Guan, Wen-Jun
On the spontaneous encapsulation of proteins in carbon nanotubes
BIOMATERIALS, 30:2807-2815, MAY 2009
abstract, full text, DOI:10.1016/j.biomaterials.2009.01.024

Singh, Narender; Duenas-Gonzalez, Alfonso; Lyko, Frank; Medina-Franco, Jose L.
Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1
CHEMMEDCHEM, 4:792-799, MAY 2009
abstract, full text, DOI:10.1002/cmdc.200900017

Tanrikulu, Yusuf; Proschak, Ewgenij; Werner, Tim; Geppert, Tim; Todoroff, Nickolay; Klenner, Alexander; Kottke, Tim; Sander, Kerstin; Schneider, Erich; Seifert, Roland; Stark, Holger; Clark, Timothy; Schneider, Gisbert
Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H-4 Receptor
CHEMMEDCHEM, 4:820-827, MAY 2009
abstract, full text, DOI:10.1002/cmdc.200800443

Lin, Ying Wu; Ying, Tian Lei; Liao, Li Fu
Dynamic consequences of mutating the typical HPGG motif of apocytochrome b(5) revealed by computer simulation
CHINESE CHEMICAL LETTERS, 20:631-634, MAY 2009
abstract, full text, DOI:10.1016/j.celet.2009.01.037

Pitera, Jed W.
Current developments in and importance of high-performance computing in drug discovery
CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT, 12:388-396, MAY 2009
abstract, full text

Blomberg, L. Mattias; Mangold, Martina; Mitchell, John B. O.; Blumberger, Jochen
Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1284-1294, MAY 2009
abstract, full text, DOI:10.1021/et800480d

Wan, Shunzhou; Coveney, Peter V.
A Comparative Study of the COX-1 and COX-2 Isozymes Bound to Lipid Membranes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1038-1050, MAY 2009
abstract, full text, DOI:10.1002/jcc.21130

Bhowmik, Rahul; Katti, Kalpana S.; Katti, Dinesh R.
Mechanisms of Load-Deformation Behavior of Molecular Collagen in Hydroxyapatite-Tropocollagen Molecular System: Steered Molecular Dynamics Study
JOURNAL OF ENGINEERING MECHANICS, 135:413-421, MAY 2009
abstract, full text, DOI:10.1061/(ASCE)0733-9399(2009)135:5(413)

Fadouloglou, Vasiliki E.; Bastaki, Marina N.; Ashcroft, Alison E.; Phillips, Simon E. V.; Panopoulos, Nicholas J.; Glykos, Nicholas M.; Kokkinidis, Michael
On the quaternary association of the type III secretion system HrcQ(B)-C protein: Experimental evidence differentiates among the various oligomerization models
JOURNAL OF STRUCTURAL BIOLOGY, 166:214-225, MAY 2009
abstract, full text, DOI:10.1016/j.jsb.2009.01.008

Golji, Javad; Collins, Robert; Mofrad, Mohammad R. K.
Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000389, MAY 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000389

Xu, Jiancong; Crowley, Michael F.; Smith, Jeremy C.
Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation
PROTEIN SCIENCE, 18:949-959, MAY 2009
abstract, full text, DOI:10.1002/pro.105

Ekonomiuk, Dariusz; Caflisch, Amedeo
Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism
PROTEIN SCIENCE, 18:1003-1011, MAY 2009
abstract, full text, DOI:10.1002/pro.110

Joshi, Manali; Ebalunode, Jerry Osagie; Briggs, James M.
Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:323-335, MAY 1 2009
abstract, full text, DOI:10.1002/prot.22241

Jones, Peter M.; George, Anthony M.
Opening of the ADP-bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:387-396, MAY 1 2009
abstract, full text, DOI:10.1002/prot.22250

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, Jose N.
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:430-441, MAY 1 2009
abstract, full text, DOI:10.1002/prot.22253

Singh, Rishi P.; Brooks, Bernard R.; Klauda, Jeffery B.
Binding and release of cholesterol in the Osh4 protein of yeast
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:468-477, MAY 1 2009
abstract, full text, DOI:10.1002/prot.22263

GUTIÉRREZ, Pablo A.; ROJANO, Benjamín A.
DOCKING DE CICLOARTANOS INHIBIDORES DE TIROSINASA
Vitae, 16:237-244, 2009-05
abstract, full text

Gutierrez, Pablo A.; Rojano, Benjamin A.
DOCKING OF TYROSINASE CICLOARTANE INHIBITORS
VITAE-REVISTA DE LA FACULTAD DE QUIMICA FARMACEUTICA, 16:245-251, MAY-AUG 2009
abstract, full text

Matsumoto, Fumiko; Maeda, Kayo; Chatake, Toshiyuki; Maeda, Yuichiro; Fujiwara, Satoru
Functional aberration of myofibrils by cardiomyopathy-causing mutations in the coiled-coil region of the troponin-core domain
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 382:205-209, APR 24 2009
abstract, full text, DOI:10.1016/j.bbrc.2009.03.009

Lee, Tai-Sung; Giambasu, George M.; Sosa, Carlos P.; Martick, Monika; Scott, William G.; York, Darrin M.
Threshold Occupancy and Specific Cation Binding Modes in the Hammerhead Ribozyme Active Site are Required for Active Conformation
JOURNAL OF MOLECULAR BIOLOGY, 388:195-206, APR 24 2009
abstract, full text, DOI:10.1016/j.jmb.2009.02.054

Mandal, Pijus K.; Limbrick, Donald; Coleman, David R.; Dyer, Garrett A.; Ren, Zhiyong; Birtwistle, J. Sanderson; Xiong, Chiyi; Chen, Xiaomin; Briggs, James M.; McMurray, John S.
Conformationally Constrained Peptidomimetic Inhibitors of Signal Transducer and Activator of Transcription 3: Evaluation and Molecular Modeling
JOURNAL OF MEDICINAL CHEMISTRY, 52:2429-2442, APR 23 2009
abstract, full text, DOI:10.1021/jm801491w

Long, Hai; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon
Hydrogenase/Ferredoxin Charge-Transfer Complexes: Effect of Hydrogenase Mutations on the Complex Association
JOURNAL OF PHYSICAL CHEMISTRY A, 113:4060-4067, APR 23 2009
abstract, full text, DOI:10.1021/jp810409z

Maruthamuthu, Venkat; Schulten, Klaus; Leckband, Deborah
Elasticity and Rupture of a Multi-Domain Neural Cell Adhesion Molecule Complex
BIOPHYSICAL JOURNAL, 96:3005-3014, APR 22 2009
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2008.12.3936

Schulz, Robert; Kleinekathoefer, Ulrich
Transitions between Closed and Open Conformations of ToIC: The Effects of Ions in Simulations
BIOPHYSICAL JOURNAL, 96:3116-3125, APR 22 2009
abstract, full text, DOI:10.1016/j.bpj.2009.01.021

Shim, Joong-Youn
Transmembrane Helical Domain of the Cannabinoid CB1 Receptor
BIOPHYSICAL JOURNAL, 96:3251-3262, APR 22 2009
abstract, full text, DOI:10.1016/j.bpj.2008.12.3934

Gulla, Stefano V.; Sharma, Gaurav; Borbat, Peter; Freed, Jack H.; Ghimire, Harishchandra; Benedikt, Monica R.; Holt, Natasha L.; Lorigan, Gary A.; Rege, Kaushal; Mavroidis, Constantinos; Budil, David E.
Molecular-Scale Force Measurement in a Coiled-Coil Peptide Dimer by Electron Spin Resonance
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:5374-+, APR 22 2009
abstract, full text, DOI:10.1021/ja900230w

Dittrich, Birger; Warren, John E.; Fabbiani, Francesca P. A.; Morgenroth, Wolfgang; Corry, Ben
Temperature dependence of rotational disorder in a non-standard amino acid from X-ray crystallography and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:2601-2609, APR 21 2009
abstract, full text, DOI:10.1039/b819157c

Sethi, Anurag; Eargle, John; Black, Alexis A.; Luthey-Schulten, Zaida
Dynamical networks in tRNA: protein complexes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:6620-6625, APR 21 2009
abstract, full text, DOI:10.1073/pnas.0810961106

Karayiannis, Nikos Ch.; Laso, Manuel; Kroeger, Martin
Detailed Atomistic Molecular Dynamics Simulations of alpha-Conotoxin AuIB in Water
JOURNAL OF PHYSICAL CHEMISTRY B, 113:5016-5024, APR 16 2009
abstract, full text, DOI:10.1021/jp806734c

Khandelia, Himanshu; Jensen, Morten O.; Mouritsen, Ole G.
To Gate or Not To Gate: Using Molecular Dynamics Simulations To Morph Gated Plant Aquaporins into Constitutively Open Conformations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:5239-5244, APR 16 2009
abstract, full text, DOI:10.1021/jp809152c

Lee, Tai-Sung; Ma, Wanlong; Zhang, Xi; Giles, Francis; Kantarjian, Hagop; Albitar, Maher
Mechanisms of Constitutive Activation of Janus Kinase 2-V617F Revealed at the Atomic Level Through Molecular Dynamics Simulations
CANCER, 115:1692-1700, APR 15 2009
abstract, full text, DOI:10.1002/cncr.24183

Swift, Robert V.; McCammon, J. Andrew
Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:5126-5133, APR 15 2009
abstract, full text, DOI:10.1021/ja808064g

Bellesia, Giovanni; Shea, Joan-Emma
Effect of beta-sheet propensity on peptide aggregation
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 145103, APR 14 2009
abstract, full text, DOI:10.1063/1.3108461

Calderon, Christopher P.; Janosi, Lorant; Kosztin, Ioan
Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 144908, APR 14 2009
abstract, full text, DOI:10.1063/1.3106225

Roberts, Benjamin P.; Scanlon, Martin J.; Krippner, Guy Y.; Chalmers, David K.
Molecular Dynamics of Poly(L-lysine) Dendrimers with Naphthalene Disulfonate Caps
MACROMOLECULES, 42:2775-2783, APR 14 2009
abstract, full text, DOI:10.1021/ma802154e

Roberts, Benjamin P.; Krippner, Guy Y.; Scanlon, Martin J.; Chalmers, David K.
Molecular Dynamics of Variegated Polyamide Dendrimers
MACROMOLECULES, 42:2784-2794, APR 14 2009
abstract, full text, DOI:10.1021/ma8021579

Masetti, Matteo; Cavalli, Andrea; Recanatini, Maurizio; Gervasio, Francesco Luigi
Exploring Complex Protein-Ligand Recognition Mechanisms with Coarse Metadynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:4807-4816, APR 9 2009
abstract, full text, DOI:10.1021/jp803936q

Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Dynamics of the Internal Water Molecules in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 96:2572-2576, APR 8 2009
abstract, full text, DOI:10.1016/j.bpj.2008.12.3927

Chen, Po-chia; Kuyucak, Serdar
Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 96:2577-2588, APR 8 2009
abstract, full text, DOI:10.1016/j.bpj.2008.12.3952

Khandelia, Himanshu; Mouritsen, Ole G.
Lipid Gymnastics: Evidence of Complete Acyl Chain Reversal in Oxidized Phospholipids from Molecular Simulations
BIOPHYSICAL JOURNAL, 96:2734-2743, APR 8 2009
abstract, full text, DOI:10.1016/j.bpj.2009.01.007

Cheng, Yuan; Pei, Qing Xiang; Gao, Huajian
Molecular-dynamics studies of competitive replacement in peptide-nanotube assembly for control of drug release
NANOTECHNOLOGY, 20 Art. No. 145101, APR 8 2009
abstract, full text, DOI:10.1088/0957-4484/20/14/145101

Park, Sanghyun; Bardhan, Jaydeep P.; Roux, Benoit; Makowski, Lee
Simulated x-ray scattering of protein solutions using explicit-solvent models
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 134114, APR 7 2009
abstract, full text, DOI:10.1063/1.3099611

Quick, Matthias; Winther, Anne-Marie Lund; Shi, Lei; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A.
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:5563-5568, APR 7 2009
abstract, full text, DOI:10.1073/pnas.0811322106

Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong
Cold Adaptation of Zinc Metalloproteases in the Thermolysin Family from Deep Sea and Arctic Sea Ice Bacteria Revealed by Catalytic and Structural Properties and Molecular Dynamics NEW INSIGHTS INTO RELATIONSHIP BETWEEN CONFORMATIONAL FLEXIBILITY AND HYDROGEN BONDING
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:9257-9269, APR 3 2009
abstract, full text, DOI:10.1074/jbc.M808421200

Nyblom, Maria; Frick, Anna; Wang, Yi; Ekvall, Mikael; Hallgren, Karin; Hedfalk, Kristina; Neutze, Richard; Tajkhorshid, Emad; Tornroth-Horsefield, Susanna
Structural and Functional Analysis of SoPIP2;1 Mutants Adds Insight into Plant Aquaporin Gating
JOURNAL OF MOLECULAR BIOLOGY, 387:653-668, APR 3 2009
abstract, full text, DOI:10.1016/j.jmb.2009.01.065

Szori, Milan; Tobias, Douglas J.; Roeselova, Martina
Microscopic Wetting of Mixed Self-assembled Monolayers: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 113:4161-4169, APR 2 2009
abstract, full text, DOI:10.1021/jp8074139

Cai Kai-Cong; Wang Jian-Ping
Molecular Dynamical Structures of Glycolaldehyde
ACTA PHYSICO-CHIMICA SINICA, 25:677-683, APR 2009
abstract, full text, DOI:10.3866/PKU.WHXB200904021

Upadhayaya, Ram Shankar; Vandavasi, Jaya Kishore; Vasireddy, Nageswara Rao; Sharma, Vivek; Dixit, Shailesh S.; Chattopadhyaya, Jyoti
Design, synthesis, biological evaluation and molecular modelling studies of novel quinoline derivatives against Mycobacterium tuberculosis
BIOORGANIC & MEDICINAL CHEMISTRY, 17:2830-2841, APR 1 2009
abstract, full text, DOI:10.1016/j.bmc.2009.02.026

Czub, Jacek; Neumann, Anna; Borowski, Edward; Baginski, Maciej
Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 141:105-116, APR 2009
abstract, full text, DOI:10.1016/j.bpc.2009.01.001

Klepeis, John L.; Lindorff-Larsen, Kresten; Dror, Ron O.; Shaw, David E.
Long-timescale molecular dynamics simulations of protein structure and function
CURRENT OPINION IN STRUCTURAL BIOLOGY, 19:120-127, APR 2009
abstract, full text, DOI:10.1016/j.sbi.2009.03.004

Su, Zhi-Yuan; Wang, Yeng-Tseng
A Molecular Dynamics Simulation of the Human Lysozyme Camelid VHH HL6 Antibody System
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 10:1719-1727, APR 2009
abstract, full text, DOI:10.3390/ijms10041719

Sharma, Gaurav; Mavroidis, Constantinos; Rege, Kaushal; Yarmush, Martin L.; Budil, David
Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH, 28:421-435, APR 2009
abstract, full text, DOI:10.1177/0278364908100278

Wiley, Adrian P.; Williams, Sarah L.; Essex, Jonathan W.
Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1117-1128, APR 2009
abstract, full text, DOI:10.1021/ct800152d

Chang, Christopher H.; Kim, Kwiseon
Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1137-1145, APR 2009
abstract, full text, DOI:10.1021/ct800342w

Carvajal-Diaz, Jennifer A.; Liu, Lijun; Cagin, Tahir
Structure and Dynamics of Water Within Single Wall Carbon Nanotubes and Self-Assembled Cyclic Peptide Nanotubes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:894-902, APR 2009
abstract, full text, DOI:10.1166/jctn.2009.1123

Jetton, Neal; Rothberg, Karen G.; Hubbard, James G.; Wise, John; Li, Yan; Ball, Haydn L.; Ruben, Larry
The cell cycle as a therapeutic target against Trypanosoma brucei: Hesperadin inhibits Aurora kinase-1 and blocks mitotic progression in bloodstream forms
MOLECULAR MICROBIOLOGY, 72:442-458, APR 2009
abstract, full text, DOI:10.1111/j.1365-2958.2009.06657.x

Liu, Bo; Li, Xiaoyi; Li, Baolei; Xu, Bingqian; Zhao, Yuliang
Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation
NANO LETTERS, 9:1386-1394, APR 2009
abstract, full text, DOI:10.1021/nl8030339

Kang, Youn K.; Lee, One-Sun; Deria, Pravas; Kim, Sang Hoon; Park, Tae-Hong; Bonnell, Dawn A.; Saven, Jeffery G.; Therien, Michael J.
Helical Wrapping of Single-Walled Carbon Nanotubes by Water Soluble Poly(p-phenyleneethynylene)
NANO LETTERS, 9:1414-1418, APR 2009
abstract, full text, DOI:10.1021/nl8032334

Khalfa, A.; Treptow, W.; Maigret, B.; Tarek, M.
Self assembly of peptides near or within membranes using coarse grained MD simulations
CHEMICAL PHYSICS, 358:161-170, MAR 30 2009
abstract, full text, DOI:10.1016/j.chemphys.2009.01.012

Skjaerven, Lars; Hollup, Siv M.; Reuter, Nathalie
Normal mode analysis for proteins
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 898:42-48, MAR 30 2009
abstract, full text, DOI:10.1016/j.theochem.2008.09.024

Lin, Ying-Wu; Ni, Feng-Yun; Ying, Tian-Lei
Early events in thermal unfolding of apocytochrome b(562) and its double-cysteine mutant as revealed by molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 898:82-89, MAR 30 2009
abstract, full text, DOI:10.1016/j.theochem.2008.07.006

Matsunaga, Yasuhiro; Fuchigami, Sotaro; Kidera, Akinori
Multivariate frequency domain analysis of protein dynamics
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 124104, MAR 28 2009
abstract, full text, DOI:10.1063/1.3090812

Xu, Dong; Newhouse, E. Irene; Amaro, Rommie E.; Pao, Hsing C.; Cheng, Lily S.; Markwick, Phineus R. L.; McCammon, J. Andrew; Li, Wilfred W.; Arzberger, Peter W.
Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective
JOURNAL OF MOLECULAR BIOLOGY, 387:465-491, MAR 27 2009
abstract, full text, DOI:10.1016/j.jmb.2009.01.040

Vakhrushev, A. V.; Suyetin, M. V.
Methane storage in bottle-like nanocapsules
NANOTECHNOLOGY, 20 Art. No. 125602, MAR 25 2009
abstract, full text, DOI:10.1088/0957-4484/20/12/125602

Coskuner, Orkid; Bergeron, Denis E.; Rincon, Luis; Hudgens, Jeffrey W.; Gonzalez, Carlos A.
Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2491-2499, MAR 19 2009
abstract, full text, DOI:10.1021/jp805747f

Dixit, Purushottam D.; Merchant, Safir; Asthagiri, D.
Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site
BIOPHYSICAL JOURNAL, 96:2138-2145, MAR 18 2009
abstract, full text, DOI:10.1016/j.bpj.2008.12.3917

Telesco, Shannon E.; Radhakrishnan, Ravi
Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 96:2321-2334, MAR 18 2009
abstract, full text, DOI:10.1016/j.bpj.2008.12.3912

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai
Bounding the electrostatic free energies associated with linear continuum models of molecular solvation
JOURNAL OF CHEMICAL PHYSICS, 130 Art. No. 104108, MAR 14 2009
abstract, full text, DOI:10.1063/1.3081148

Peng, Qing; Zhuang, Shulin; Wang, Meijia; Cao, Yi; Khor, Yuanai; Li, Hongbin
Mechanical Design of the Third FnIII Domain of Tenascin-C
JOURNAL OF MOLECULAR BIOLOGY, 386:1327-1342, MAR 13 2009
abstract, full text, DOI:10.1016/j.jmb.2009.01.019

Ridge, Clark D.; Shaka, A. J.
"Ersatz" and "Hybrid" NMR Spectral Estimates Using the Filter Diagonalization Method
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2036-2052, MAR 12 2009
abstract, full text, DOI:10.1021/jp808666f

Moussa, Samar G.; McIntire, Theresa M.; Szori, Milan; Roeselova, Martina; Tobias, Douglas J.; Grimm, Ronald L.; Hemminger, John C.; Finlayson-Pitts, Barbara J.
Experimental and Theoretical Characterization of Adsorbed Water on Self-Assembled Monolayers: Understanding the Interaction of Water with Atmospherically Relevant Surfaces
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2060-2069, MAR 12 2009
abstract, full text, DOI:10.1021/jp808710n

Bondar, Ana-Nicoleta; del Val, Coral; White, Stephen H.
Rhomboid Protease Dynamics and Lipid Interactions
STRUCTURE, 17:395-405, MAR 11 2009
abstract, full text, DOI:10.1016/j.str.2008.12.017

Miao, Lingling; Schulten, Klaus
Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics
STRUCTURE, 17:449-459, MAR 11 2009
abstract, full text, TCBG publications, DOI:10.1016/j.str.2008.12.021

Yang, Sichun; Banavali, Nilesh K.; Roux, Benoit
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:3776-3781, MAR 10 2009
abstract, full text, DOI:10.1073/pnas.0808261106

Xia, Zhen; Zhu, Zhihong; Zhu, Jun; Zhou, Ruhong
Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 96:1761-1769, MAR 4 2009
abstract, full text, DOI:10.1016/j.bpj.2008.11.047

Chen Cong; Li Wei-Zhong
Molecular Dynamics Simulation of Hydrogen Bonding Characteristics in Aqueous Glycerol Solutions
ACTA PHYSICO-CHIMICA SINICA, 25:507-512, MAR 2009
abstract, full text, DOI:10.3866/PKU.WHXB20090318

Taylor, Justine; Whiteford, Nava E.; Bradley, Geoff; Watson, Graeme W.
Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:638-649, MAR 2009
abstract, full text, DOI:10.1016/j.bbamem.2008.10.013

Chen, Wei; Lou, Jizhong; Zhu, Cheng
Molecular Dynamics Simulated Unfolding of von Willebrand Factor A Domains by Force
CELLULAR AND MOLECULAR BIOENGINEERING, 2:75-86, MAR 2009
abstract, full text, DOI:10.1007/s12195-009-0051-0

Slater, Gary W.; Holm, Christian; Chubynsky, Mykyta V.; de Haan, Hendrick W.; Dube, Antoine; Grass, Kai; Hickey, Owen A.; Kingsburry, Christine; Sean, David; Shendruk, Tyler N.; Nhan, Lixin
Modeling the separation of macromolecules: A review of current computer simulation methods
ELECTROPHORESIS, 30:792-818, MAR 2009
abstract, full text, DOI:10.1002/elps.200800673

Cideciyan, Artur V.; Swider, Malgorzata; Aleman, Tomas S.; Tsybovsky, Yaroslav; Schwartz, Sharon B.; Windsor, Elizabeth A. M.; Roman, Alejandro J.; Sumaroka, Alexander; Steinberg, Janet D.; Jacobson, Samuel G.; Stone, Edwin M.; Palczewski, Krzysztof
ABCA4 disease progression and a proposed strategy for gene therapy
HUMAN MOLECULAR GENETICS, 18:931-941, MAR 1 2009
abstract, full text, DOI:10.1093/hmg/ddn421

Tatsis, Vasileios A.; Tsoulos, Ioannis G.; Stavrakoudis, Athanassios
Molecular Dynamics Simulations of the TSSPSAD Peptide Antigen in Free and Bound with CAMPATH-1H Fab Antibody States: The Importance of the beta-Turn Conformation
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:1-9, MAR 2009
abstract, full text, DOI:10.1007/s10989-008-9155-y

Nandi, Tapas K.; Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Sekar, K.; Sukul, Dipankar; Bera, Asim K.
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease
JOURNAL OF BIOSCIENCES, 34:27-34, MAR 2009
abstract, full text

Panek, Jaroslaw J.; Ward, Thomas R.; Jezierska, Aneta; Novic, Marjana
Effects of tryptophan residue fluorination on streptavidin stability and biotin-streptavidin interactions via molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 15:257-266, MAR 2009
abstract, full text, DOI:10.1007/s00894-008-0382-0

Mascayano, Carolina; Caroli Rezende, Marcos; Mendez, Carolina; Nunez, Gabriel; Chiang, Valeska
Solute-Solvent Interactions in Solutions of Solvatochromic Phenoxides: A Dynamics Simulation Study
JOURNAL OF SOLUTION CHEMISTRY, 38:363-371, MAR 2009
abstract, full text, DOI:10.1007/s10953-009-9369-4

Djajamuliadi, Jhonsen; Kagawa, Todd F.; Ohgo, Kosuke; Kumashiro, Kristin K.
Insights into a putative hinge region in elastin using molecular dynamics simulations
MATRIX BIOLOGY, 28:92-100, MAR 2009
abstract, full text, DOI:10.1016/j.matbio.2008.12.001

Hashem, Yaser; Auffinger, Pascal
A short guide for molecular dynamics simulations of RNA systems
METHODS, 47:187-197, MAR 2009
abstract, full text, DOI:10.1016/j.ymeth.2008.09.020

Guptaroy, Bipasha; Zhang, Minjia; Bowton, Erica; Binda, Francesca; Shi, Lei; Weinstein, Harel; Galli, Aurelio; Javitch, Jonathan A.; Neubig, Richard R.; Gnegy, Margaret E.
A Juxtamembrane Mutation in the N Terminus of the Dopamine Transporter Induces Preference for an Inward-Facing Conformation
MOLECULAR PHARMACOLOGY, 75:514-524, MAR 2009
abstract, full text, DOI:10.1124/mol.108.048744

Hardy, David J.; Stone, John E.; Schulten, Klaus
Multilevel summation of electrostatic potentials using graphics processing units
PARALLEL COMPUTING, 35:164-177, MAR 2009
abstract, full text, TCBG publications, DOI:10.1016/j.parco.2008.12.005

Leone, Vanessa; Lattanzi, Gianluca; Molteni, Carla; Carloni, Paolo
Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 5 Art. No. e1000309, MAR 2009
abstract, full text, DOI:10.1371/journal.pcbi.1000309

Salcedo, Ernesto; Farrell, David M.; Zheng, Lijun; Phistry, Meridee; Bagg, Eve E.; Britt, Steven G.
The Green-absorbing Drosophila Rh6 Visual Pigment Contains a Blue-shifting Amino Acid Substitution That Is Conserved in Vertebrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:5717-5722, FEB 27 2009
abstract, full text, DOI:10.1074/jbc.M807368200

Kagawa, Todd F.; O'Connell, Maurice R.; Mouat, Pania; Paoli, Max; O'Toole, Paul W.; Cooney, Jakki C.
Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 angstrom Crystal Structure of the Active Form of ScpA
JOURNAL OF MOLECULAR BIOLOGY, 386:754-772, FEB 27 2009
abstract, full text, DOI:10.1016/j.jmb.2008.12.074

Cabeca, Luis F.; Pickholz, Monica; de Paula, Eneida; Marsaioli, Anita J.
Liposome-Prilocaine Interaction Mapping Evaluated through STD NMR and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:2365-2370, FEB 26 2009
abstract, full text, DOI:10.1021/jp8069496

Sener, Melih; Hsin, Jen; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus
Structural model and excitonic properties of the dimeric RC-LH1-Pufx complex from Rhodobacter sphaeroides
CHEMICAL PHYSICS, 357:188-197, FEB 23 2009
abstract, full text, TCBG publications, DOI:10.1016/j.chemphys.2009.01.003

Gunnerson, Kim N.; Pereverzev, Yuriy V.; Prezhdo, Oleg V.
Atomistic Simulation Combined with Analytic Theory To Study the Response of the P-Selectin/PSGL-1 Complex to an External Force
JOURNAL OF PHYSICAL CHEMISTRY B, 113:2090-2100, FEB 19 2009
abstract, full text, DOI:10.1021/jp803955u

Szep, Szilvia; Park, Sheldon; Boder, Eric T.; Van Duyne, Gregory D.; Saven, Jeffery G.
Structural coupling between FKBP12 and buried water
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:603-611, FEB 15 2009
abstract, full text, DOI:10.1002/prot.22176

Skjot, Michael; De Maria, Leonardo; Chatterjee, Robin; Svendsen, Allan; Patkar, Sharnkant A.; Ostergaard, Peter R.; Brask, Jesper
Understanding the Plasticity of the alpha/beta Hydrolase Fold: Lid Swapping on the Candida antarctica Lipase B Results in Chimeras with Interesting Biocatalytic Properties
CHEMBIOCHEM, 10:520-527, FEB 13 2009
abstract, full text, DOI:10.1002/cbic.200800668

Scarselli, Maria; Cantini, Francesca; Santini, Laura; Veggi, Daniele; Dragonetti, Sara; Donati, Claudio; Savino, Silvana; Giuliani, Marzia M.; Comanducci, Maurizio; Di Marcello, Federica; Romagnoli, Giacomo; Pizza, Mariagrazia; Banci, Lucia; Rappuoli, Rino
Epitope Mapping of a Bactericidal Monoclonal Antibody against the Factor H Binding Protein of Neisseria meningitidis
JOURNAL OF MOLECULAR BIOLOGY, 386:97-108, FEB 13 2009
abstract, full text, DOI:10.1016/j.jmb.2008.12.005

Radi, Marco; Maga, Giovanni; Alongi, Maddalena; Angeli, Lucilla; Samuele, Alberta; Zanoli, Samantha; Bellucci, Luca; Tafi, Andrea; Casaluce, Gianni; Giorgi, Gianluca; Armand-Ugon, Mercedes; Gonzalez, Emmanuel; Este, Jose A.; Baltzinger, Mireille; Bec, Guillaume; Dumas, Philippe; Ennifar, Eric; Botta, Maurizio
Discovery of Chiral Cyclopropyl Dihydro-Alkylthio-Benzyl-Oxopyrimidine (S-DABO) Derivatives as Potent HIV-1 Reverse Transcriptase Inhibitors with High Activity Against Clinically Relevant Mutants
JOURNAL OF MEDICINAL CHEMISTRY, 52:840-851, FEB 12 2009
abstract, full text, DOI:10.1021/jm801330n

Cai, Kaicong; Wang, Jianping
Multiple Anharmonic Vibrational Probes of Sugar Structure and Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1681-1692, FEB 12 2009
abstract, full text, DOI:10.1021/jp8070025

Lee, One-Sun; Schatz, George C.
Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY C, 113:2316-2321, FEB 12 2009
abstract, full text, DOI:10.1021/jp8094165

Khavrutskii, Ilja V.; Gorfe, Alemayehu A.; Lu, Benzhuo; McCammon, J. Andrew
Free Energy for the Permeation of Na+ and Cl- Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:1706-1716, FEB 11 2009
abstract, full text, DOI:10.1021/ja8081704

Rodriguez, Javier; Semino, Rocio; Laria, Daniel
Building up Nanotubes: Docking of "Janus" Cyclodextrins in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1241-1244, FEB 5 2009
abstract, full text, DOI:10.1021/jp8106815

Poghosyan, Armen H.; Arsenyan, Levon H.; Gharabekyan, Hrant H.; Koetz, Joachim; Shahinyan, Aram A.
Molecular Dynamics Study of Poly(diallyldimethylammonium chloride) (PDADMAC)/Sodium Dodecyl Sulfate (SDS)/Decanol/Water Systems
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1303-1310, FEB 5 2009
abstract, full text, DOI:10.1021/jp806289c

Rodriguez, Javier; Elola, M. Dolores
Encapsulation of Small Ionic Molecules within alpha-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1423-1428, FEB 5 2009
abstract, full text, DOI:10.1021/jp808947m

Cruz-Chu, Eduardo R.; Aksimentiev, Aleksei; Schulten, Klaus
Ionic Current Rectification through Silica Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 113:1850-1862, FEB 5 2009
abstract, full text, TCBG publications, DOI:10.1021/jp804724p

Dixit, Anshuman; Torkamani, Ali; Schork, Nicholas J.; Verkhivker, Gennady
Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability
BIOPHYSICAL JOURNAL, 96:858-874, FEB 4 2009
abstract, full text, DOI:10.1016/j.bpj.2008.10.041

Bellesia, Giovanni; Shea, Joan-Emma
What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?
BIOPHYSICAL JOURNAL, 96:875-886, FEB 4 2009
abstract, full text, DOI:10.1016/j.bpj.2008.10.040

Fuson, Kerry L.; Ma, Liang; Sutton, R. Bryan; Oberhauser, Andres F.
The C2 Domains of Human Synaptotagmin 1 Have Distinct Mechanical Properties
BIOPHYSICAL JOURNAL, 96:1083-1090, FEB 4 2009
abstract, full text, DOI:10.1016/j.bpj.2008.10.025

Michel Espinoza-Fonseca, L.
Leucine-rich hydrophobic clusters promote folding of the N-terminus of the intrinsically disordered transactivation domain of p53
FEBS LETTERS, 583:556-560, FEB 4 2009
abstract, full text, DOI:10.1016/j.febslet.2008.12.060

Swift, Robert V.; Durrant, Jacob; Amaro, Rommie E.; McCammont, J. Andrew
Toward Understanding the Conformational Dynamics of RNA Ligation
BIOCHEMISTRY, 48:709-719, FEB 3 2009
abstract, full text, DOI:10.1021/bi8018114

Yu, Xiang; Wang, Qiuming; Yang, Jui-Chen; Buch, Idit; Tsai, Chung-Jung; Ma, Buyong; Cheng, Stephen Z. D.; Nussinov, Ruth; Zheng, Jie
Mutational Analysis and Allosteric Effects in the HIV-1 Capsid Protein Carboxyl-Terminal Dimerization Domain
BIOMACROMOLECULES, 10:390-399, FEB 2009
abstract, full text, DOI:10.1021/bm801151r

Poghosyan, Armen H.; Shahinyan, Aram A.
A new parameter for validation molecular dynamics simulation (MD) data
COMPUTER PHYSICS COMMUNICATIONS, 180:238-240, FEB 2009
abstract, full text, DOI:10.1016/j.cpc.2008.09.013

Russel, Daniel; Lasker, Keren; Phillips, Jeremy; Schneidman-Duhovny, Dina; Velazquez-Muriel, Javier A.; Sali, Andrej
The structural dynamics of macromolecular processes
CURRENT OPINION IN CELL BIOLOGY, 21:97-108, FEB 2009
abstract, full text, DOI:10.1016/j.ceb.2009.01.022

Verdone, Giuliana; Corazza, Alessandra; Colebrooke, Simon A.; Cicero, Daniel; Eliseo, Tommaso; Boyd, Jonathan; Doliana, Roberto; Fogolari, Federico; Viglino, Paolo; Colombatti, Alfonso; Campbell, Iain D.; Esposito, Gennaro
NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1
JOURNAL OF BIOMOLECULAR NMR, 43:79-96, FEB 2009
abstract, full text, DOI:10.1007/s10858-008-9290-y

Bairagya, Hridoy R.; Mukhopadhyay, Bishnu P.; Sekarz, K.
Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 26:497-507, FEB 2009
abstract, full text

Williams, Sarah L.; Essex, Jonathan W.
Study of the Conformational Dynamics of the Catalytic Loop of WT and G140A/G149A HIV-1 Integrase Core Domain Using Reversible Digitally Filtered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:411-421, FEB 2009
abstract, full text, DOI:10.1021/ct800162v

Wong, Sergio; Amaro, Rommie E.; McCammon, J. Andrew
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:422-429, FEB 2009
abstract, full text, DOI:10.1021/ct8003707

Miao, Yinglong; Ortoleva, Peter J.
Molecular Dynamics/Order Parameter Extrapolation for Bionanosystem Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:423-437, FEB 2009
abstract, full text, DOI:10.1002/jcc.21071

Petridis, Loukas; Smith, Jeremy C.
A Molecular Mechanics Force Field for Lignin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:457-467, FEB 2009
abstract, full text, DOI:10.1002/jcc.21075

Sharma, Monika; Khanna, Smriti; Bulusu, Gopalakrishnan; Mitra, Abhijit
Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: A multifunctional target for antischistosomal therapy
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:665-675, FEB 2009
abstract, full text, DOI:10.1016/j.jmgm.2008.10.009

Stavrakoudis, Athanassios
A disulfide linked model of the complement protein C8 gamma complexed with C8 alpha indel peptide
JOURNAL OF MOLECULAR MODELING, 15:165-171, FEB 2009
abstract, full text, DOI:10.1007/s00894-008-0412-y

Pagadala, Nataraj Sekhar; Arha, Manish; Reddy, P. S.; Kumar, Ranadheer; Sirisha, V. L.; Prashant, S.; Reddy, K. Janardhan; Khan, Bashir; Rawal, S. K.; Kishor, P. B. Kavi
Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl-CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala)
JOURNAL OF MOLECULAR MODELING, 15:203-221, FEB 2009
abstract, full text, DOI:10.1007/s00894-008-0395-8

Ines Barria, Maria; Gonzalez, Angel; Vera-Otarola, Jorge; Leon, Ursula; Vollrath, Valeska; Marsac, Delphine; Monasterio, Octavio; Perez-Acle, Tomas; Soza, Alejandro; Lopez-Lastra, Marcelo
Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation
NUCLEIC ACIDS RESEARCH, 37:957-971, FEB 2009
abstract, full text, DOI:10.1093/nar/gkn1022

Clark, Louis A.; Boriack-Sjodin, P. Ann; Day, Eric; Eldredge, John; Fitch, Christopher; Jarpe, Matt; Miller, Stephan; Li, You; Simon, Ken; van Vlijmen, Herman W. T.
An antibody loop replacement design feasibility study and a loop-swapped dimer structure
PROTEIN ENGINEERING DESIGN & SELECTION, 22:93-101, FEB 2009
abstract, full text, DOI:10.1093/protein/gzn072

Huang, Qiang; Korte, Thomas; Rachakonda, P. Sivaramakrishna; Knapp, Ernst-Walter; Herrmann, Andreas
Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:291-303, FEB 1 2009
abstract, full text, DOI:10.1002/prot.22157

Banavali, Nilesh K.; Roux, Benoit
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:378-389, FEB 1 2009
abstract, full text, DOI:10.1002/prot.22133

Furini, Simone; Beckstein, Oliver; Domene, Carmen
Permeation of water through the KcsA K+ channel
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:437-448, FEB 1 2009
abstract, full text, DOI:10.1002/prot.22163

Kaminski, Steve; Daminelli, Grazia; Mroginski, Maria Andrea
Molecular Dynamics Simulations of the Chromophore Binding Site of Deinococcus radiodurans Bacteriophytochrome Using New Force Field Parameters for the Phytochromobilin Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 113:945-958, JAN 29 2009
abstract, full text, DOI:10.1021/jp8047532

Reddy, Govardhan; Straub, John E.; Thirumalai, D.
Influence of Preformed Asp23-Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of A beta Peptides with Implications for Rates of Fibril Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1162-1172, JAN 29 2009
abstract, full text, DOI:10.1021/jp808914c

Khurana, Ekta; Dal Peraro, Matteo; DeVane, Russell; Vemparala, Satyavani; DeGrado, William F.; Klein, Michael L.
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:1069-1074, JAN 27 2009
abstract, full text, DOI:10.1073/pnas.0811720106

Zhu, Yudan; Wei, Mingjie; Shao, Qing; Lu, Linghong; Lu, Xiaohua; Shen, Wenfeng
Molecular Dynamics Study of Pore Inner Wall Modification Effect in Structure of Water Molecules Confined in Single-Walled Carbon Nanotubes
Journal of Physical Chemistry C, 113:882-889, JAN 22 2009
abstract, full text, DOI:10.1021/jp8089006

Jones, Martin K.; Catte, Andrea; Patterson, James C.; Gu, Feifei; Chen, Jianguo; Li, Ling; Segrest, Jere P.
Thermal Stability of Apolipoprotein A-I in High-Density Lipoproteins by Molecular Dynamics
BIOPHYSICAL JOURNAL, 96:354-371, JAN 21 2009
abstract, full text, DOI:10.1016/j.bpj.2008.09.041

Tayefeh, Sascha; Kloss, Thomas; Kreim, Michael; Gebhardt, Manuela; Baumeister, Dirk; Hertel, Brigitte; Richter, Christian; Schwalbe, Harald; Moroni, Anna; Thiel, Gerhard; Kast, Stefan M.
Model Development for the Viral Kcv Potassium Channel
BIOPHYSICAL JOURNAL, 96:485-498, JAN 21 2009
abstract, full text, DOI:10.1016/j.bpj.2008.09.050

Comer, Jeffrey; Dimitrov, Valentin; Zhao, Qian; Timp, Gregory; Aksimentiev, Aleksei
Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores
BIOPHYSICAL JOURNAL, 96:593-608, JAN 21 2009
abstract, full text, DOI:10.1016/j.bpj.2008.09.023

Chen, Yong; Chen, Chongguang; Kotsikorou, Evangelia; Lynch, Diane L.; Reggio, Patricia H.; Liu-Chen, Lee-Yuan
GEC1-kappa Opioid Receptor Binding Involves Hydrophobic Interactions
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:1673-1685, JAN 16 2009
abstract, full text, DOI:10.1074/jbc.M808303200

Berteotti, Anna; Cavalli, Andrea; Branduardi, Davide; Gervasio, Francesco Luigi; Recanatini, Maurizio; Parrinello, Michele
Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:244-250, JAN 14 2009
abstract, full text, DOI:10.1021/ja806846q

Tiberio, Giustiniano; Muccioli, Luca; Berardi, Roberto; Zannoni, Claudio
Towards in Silico Liquid Crystals. Realistic Transition Temperatures and Physical Properties for n-Cyanobiphenyls via Molecular Dynamics Simulations
CHEMPHYSCHEM, 10:125-136, JAN 12 2009
abstract, full text, DOI:10.1002/cphc.200800231

Ju, Pengchu; Pages, Guilhem; Riek, R. Peter; Chen, Po-chia; Torres, Allan M.; Bansal, Paramjit S.; Kuyucak, Serdar; Kuchel, Philip W.; Vandenberg, Jamie I.
The Pore Domain Outer Helix Contributes to Both Activation and Inactivation of the hERG K+ Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:1000-1008, JAN 9 2009
abstract, full text, DOI:10.1074/jbc.M806400200

Peters, Guenther H.; Hansen, Flemming Y.; Moller, Martin S.; Westh, Peter
Effects of Fatty Acid Inclusion in a DMPC Bilayer Membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 113:92-102, JAN 8 2009
abstract, full text, DOI:10.1021/jp806205m

Calderon, Christopher P.; Harris, Nolan C.; Kiang, Ching-Hwa; Cox, Dennis D.
Quantifying Multiscale Noise Sources in Single-Molecule Time Series
JOURNAL OF PHYSICAL CHEMISTRY B, 113:138-148, JAN 8 2009
abstract, full text, DOI:10.1021/jp807908c

Toschi, Francesca; Lugli, Francesca; Biscarini, Fabio; Zerbetto, Francesco
Effects of Electric Field Stress on a beta-Amyloid Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:369-376, JAN 8 2009
abstract, full text, DOI:10.1021/jp807896g

Sinicropi, Adalgisa; Bernini, Caterina; Basosi, Riccardo; Olivucci, Massimo
A novel biomimetic photochemical switch at work: design of a photomodulable peptide
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 8:1639-1649, 2009
abstract, full text, DOI:10.1039/b906271h

Dooley, Isaac; Lee, Chee Wai; Kale, Laxmikant V.
Continuous Performance Monitoring for Large-Scale Parallel Applications
16TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING (HIPC), PROCEEDINGS, 445-452, 2009
abstract, full text

Liu, Ming; Li, Ping; Cong, Xiao-Jing; Tan, Jian-Jun; Chen, Wei-Zu; Wang, Cun-Xin
Study on the Resistance and the Binding Mode of HIV-1 Integrase to NSC158393
2009 3RD INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1-11, 720-723, 2009
abstract, full text

Tan, Jian Jun; Li, Ming; Yi, Zhang Xiao; Chen, Wei Zu; Wang, Cun Xin
Analysis of the Interactions between the N-terminal Peptide of gp41 and T20 Using Molecular Dynamics and Free Energy Calculations
2009 3RD INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1-11, 724-727, 2009
abstract, full text

Wang, Li; Wan, Huagen; Peng, Qunsheng; Chen, Xin; Wu, Tao; Wang, Junhui
Volumetric Visualization and Analysis of Molecular Interaction Field
2009 3RD INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1-11, 852-855, 2009
abstract, full text

Romo, Tod D.; Grossfield, Alan
LOOS: An Extensible Platform for the Structural Analysis of Simulations
2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20, 2332-2335, 2009
abstract, full text, DOI:10.1109/IEMBS.2009.5335065

Ye, Xue-song; Wang, Peng; Zhou, Tao; Liu, Jun; Liu, Feng
Molecular Mechanism for Conformation Mobility of the Active Center of Glucose Oxidase Adsorbed on Single Wall Carbon Nanotubes
2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20, 2739-2743, 2009
abstract, full text

Wang, Cun Xin; Liu, Ming; Li, Ping; Cong, Xiao Jing; Tan, Jian Jun; Chen, Wei Zu
Study on the Binding Mode of the Integrase with DNA via Steered Molecular Dynamics Simulation
2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20, 4894-4897, 2009
abstract, full text, DOI:10.1109/IEMBS.2009.5332821

Li, Yaohang; Wardell, Douglas; Freeh, Vincent
A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications
2009 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-5, 1578-1585, 2009
abstract, full text

Alam, Sadaf R.; Barrett, Richard F.; Kuehn, Jeffery A.; Poole, Steve W.
Performance Analysis and Projections for Petascale Applications on Cray XT Series Systems
2009 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-5, 2089-2096, 2009
abstract, full text

Guo, He; Su, Lili; Wang, Yuxin; Long, Zhu
FPGA-Accelerated Molecular Dynamics Simulations System
2009 INTERNATIONAL CONFERENCE ON SCALABLE COMPUTING AND COMMUNICATIONS & EIGHTH INTERNATIONAL CONFERENCE ON EMBEDDED COMPUTING, 360-365, 2009
abstract, full text, DOI:10.1109/EmbeddedCom-ScalCom.2009.71

Fernandes, Elisabeth; Jorge, Alipio M.; Silva, Candida G.; Brito, Rui M. M.
A Knowledge Discovery Method for the Characterization of Protein Unfolding Processes
2ND INTERNATIONAL WORKSHOP ON PRACTICAL APPLICATIONS OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (IWPACBB 2008), 49:180-188, 2009
abstract, full text

Ma, Anguo; Cai, Jing; Cheng, Yu; Ni, Xiaoqiang; Tang, Yuxing; Xing, Zuocheng
Performance Optimization Strategies of High Performance Computing on GPU
ADVANCED PARALLEL PROCESSING TECHNOLOGIES, PROCEEDINGS, 5737:150-164, 2009
abstract, full text

Zhuang, Wei; Hayashi, Tomoyuki; Mukamel, Shaul
Coherent Multidimensional Vibrational Spectroscopy of Biomolecules: Concepts, Simulations, and Challenges
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 48:3750-3781, 2009
full text, DOI:10.1002/anie.200802644

Vitalis, Andreas; Pappu, Rohit V.
Methods for Monte Carlo Simulations of Biomacromolecules
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 5, 5:49-76, 2009
abstract, full text, DOI:10.1016/S1574-1400(09)00503-9

Iacono, Salvatore
Numerical Simulation of Capillary Flows Through Molecular Dynamics
APPLIED AND INDUSTRIAL MATHEMATICS IN ITALY III, 82:389-400, 2009
abstract, full text

Davis, Joseph E.; Ozsoy, Adnan; Patel, Sandeep; Taufer, Michela
Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors
BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, PROCEEDINGS, 5462:176-186, 2009
abstract, full text

Tzamali, Eleftheria; Poirazi, Panayiota; Reczko, Martin
Methods for Dynamical Inference in Intracellular Networks
Bioinformatics for Systems Biology, 541-561, 2009
abstract, full text, DOI:10.1007/978-1-59745-440-7_28

Zanuy, David; Curco, David; Nussinov, Ruth; Aleman, Carlos
Influence of the Dye Presence on the Conformational Preferences of CREKA, a Tumor Homing Linear Pentapeptide
BIOPOLYMERS, 92:83-93, 2009
abstract, full text, DOI:10.1002/bip.21122

Stavrakoudis, Athanassios; Tsoulos, Ioannis G.; Shenkarev, Zakhar O.; Ovchinnikova, Tatiana V.
Molecular Dynamics Simulation of Antimicrobial Peptide Arenicin-2: beta-Hairpin Stabilization by Noncovalent Interactions
BIOPOLYMERS, 92:143-155, 2009
abstract, full text, DOI:10.1002/bip.21149

Chiu, Chi-cheng; Dieckmann, Gregg R.; Nielsen, Steven O.
Role of Peptide-Peptide Interactions in Stabilizing Peptide-Wrapped Single-Walled Carbon Nanotubes: A Molecular Dynamics Study
BIOPOLYMERS, 92:156-163, 2009
abstract, full text, DOI:10.1002/bip.21159

Williams, Sarah L.; Andrew McCammon, J.
Conformational Dynamics of the Flexible Catalytic Loop in Mycobacterium tuberculosis 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase
CHEMICAL BIOLOGY & DRUG DESIGN, 73:26-38, JAN 2009
abstract, full text, DOI:10.1111/j.1747-0285.2008.00749.x

Monti, Maria Chiara; Casapullo, Agostino; Cavasotto, Claudio N.; Tosco, Alessandra; Dal Piaz, Fabrizio; Ziemys, Arturas; Margarucci, Luigi; Riccio, Raffaele
The Binding Mode of Petrosaspongiolide M to the Human Group HA Phospholipase A(2): Exploring the Role of Covalent and Noncovalent Interactions in the Inhibition Process
CHEMISTRY-A EUROPEAN JOURNAL, 15:1155-1163, 2009
abstract, full text, DOI:10.1002/chem.200801512

Casanovas, Jordi; Preat, Julien; Zanuy, David; Aleman, Carlos
Sensing Abilities of Crown Ether Functionalized Polythiophenes
CHEMISTRY-A EUROPEAN JOURNAL, 15:4676-4684, 2009
abstract, full text, DOI:10.1002/chem.200802006

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Bolchi, Cristiano; Testa, Bernard
Influence of Ionization State on the Activation of Temocapril by hCES1: A Molecular-Dynamics Study
CHEMISTRY & BIODIVERSITY, 6:2092-2100, 2009
abstract, full text

Vaidehi, Nagarajan; Pease, James E.; Horuk, Richard
MODELING SMALL MOLECULE-COMPOUND BINDING To G-PROTEIN-COUPLED RECEPTORS
CHEMOKINES, PT A, 460:263-+, 2009
abstract, full text, DOI:10.1016/S0076-6879(09)05213-6

Noid, W. G.; Ayton, Gary S.; Izvekov, Sergei; Voth, Gregory A.
The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse-Graining
Coarse-Graining of Condensed Phase and Biomolecular Systems, 21-39, 2009
full text

Freddolino, Peter L.; Shih, Amy Y.; Arkhipov, Anton; Ying, Ying; Chen, Zhongzhou; Schulten, Klaus
Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations
Coarse-Graining of Condensed Phase and Biomolecular Systems, 299-315, 2009
full text, TCBG publications

Wang, Jihua; Cao, Zanxia; Li, Shuqiang
Molecular Dynamics Simulations of Intrinsically Disordered Proteins in Human Diseases
CURRENT COMPUTER-AIDED DRUG DESIGN, 5:280-287, 2009
abstract, full text

Vasilyeva, Aksana; Clodfelter, Jill E.; Rector, Brian; Hollis, Thomas; Scarpinato, Karin D.; Salsbury, Freddie R., Jr.
Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death
DNA REPAIR, 8:103-113, JAN 1 2009
abstract, full text, DOI:10.1016/j.dnarep.2008.09.008

Zhu, Hui; May, Volkhard
Mixed Quantum Classical Simulations of Electronic Excitation Energy Transfer and Related Optical Spectra: Supramolecular Pheophorbide-a Complexes in Solution
ENERGY TRANSFER DYNAMICS IN BIOMATERIAL SYSTEMS, 93:35-71, 2009
abstract, full text, DOI:10.1007/978-3-642-02306-4_2

Yakubovich, A. V.; Solov'yov, I. A.; Solov'yov, A. V.; Greiner, W.
Phase transitions in polypeptides: analysis of energy fluctuations
EUROPEAN PHYSICAL JOURNAL D, 51:25-32, JAN 2009
abstract, full text, DOI:10.1140/epjd/e2008-00126-y

Cruz-Chu, Eduardo R.; Ritz, Thorsten; Siwy, Zuzanna S.; Schulten, Klaus
Molecular control of ionic conduction in polymer nanopores
FARADAY DISCUSSIONS, 143:47-62, 2009
abstract, full text, TCBG publications, DOI:10.1039/b906279n

Tobias, Douglas J.; Sengupta, Neelanjana; Tarek, Nlounir
Hydration dynamics of purple membranes
FARADAY DISCUSSIONS, 141:99-116, 2009
abstract, full text, DOI:10.1039/b809371g

Awad, Mariette
FPGA SUPERCOMPUTING PLATFORMS: A SURVEY
FPL: 2009 INTERNATIONAL CONFERENCE ON FIELD PROGRAMMABLE LOGIC AND APPLICATIONS, 564-568, 2009
abstract, full text

Zhmakin, Alexander I.
Fundamentals of Cryobiology Physical Phenomena and Mathematical Models Introduction
FUNDAMENTALS OF CRYOBIOLOGY: PHYSICAL PHENOMENA AND MATHEMATICAL MODELS, 1-+, 2009
full text

Saint, Nathalie; Montserret, Roland; Chipot, Christophe; Penin, Francois
Structural and Functional Analysis of the HCV p7 Protein
Hepatitis C: Methods and Protocols, Second Edition, 510:125-143, 2009
abstract, full text, DOI:10.1007/978-1-59745-394-3_10

Priyadarzini, T. R. K.; Selvin, J. Fermin Angelo; Veluraja, K.
Molecular Dynamics Simulation Studies on Sialic acid and its Acetylated Derivatives and their Interaction with Vibrio Cholerae Neuraminidase
IACSIT-SC 2009: INTERNATIONAL ASSOCIATION OF COMPUTER SCIENCE AND INFORMATION TECHNOLOGY - SPRING CONFERENCE, 562-566, 2009
abstract, full text, DOI:10.1109/IACSIT-SC.2009.62

Bhatele, Abhinav; Kale, Laxmikant V.; Kumar, Sameer
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications
ICS'09: PROCEEDINGS OF THE 2009 ACM SIGARCH INTERNATIONAL CONFERENCE ON SUPERCOMPUTING, 110-116, 2009
abstract, full text

Bhowmik, Rahul; Katti, Kalpana S.; Katti, Dinesh R.
Molecular interactions of degradable and non-degradable polymers with hydroxyapatite influence mechanics of polymer-hydroxyapatite nanocomposite biomaterials
INTERNATIONAL JOURNAL OF NANOTECHNOLOGY, 6:511-529, 2009
abstract, full text

Alizadeh, Ali; Parsafar, Golam Abbas; Ejtehadi, Mohammad Reza
Mechanism of water permeation through modified carbon nanotubes as a model for peptide nanotube channels
INTERNATIONAL JOURNAL OF NANOTECHNOLOGY, 6:926-941, 2009
abstract, full text

Yakubovich, Alexander; Solov'yov, Andrey V.; Greiner, Walter
Statistical Mechanics Model for Protein Folding
ISACC 2009: FOURTH INTERNATIONAL SYMPOSIUM ON ATOMIC CLUSTER COLLISIONS: STRUCTURE AND DYNAMICS FROM THE NUCLEAR TO THE BIOLOGICAL SCALE, 1197:186-200, 2009
abstract, full text, DOI:10.1063/1.3275681

Lundberg, Marcus; Kawatsu, Tsutomu; Vreven, Thom; Frisch, Michael J.; Morokuma, Keiji
Transition States in a Protein Environment - ONIOM QM:MM Modeling of Isopenicillin N Synthesis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:222-234, JAN 2009
abstract, full text, DOI:10.1021/ct800457g

Artali, Roberto; Beretta, Giangiacomo; Morazzoni, Paolo; Bombardelli, Ezio; Meneghetti, Fiorella
Green tea catechins in chemoprevention of cancer: A molecular docking investigation into their interaction with glutathione S-transferase (GST P1-1)
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 24:287-295, 2009
abstract, full text, DOI:10.1080/14756360802177282

Suter, James L.; Anderson, Richard L.; Greenwell, H. Christopher; Coveney, Peter V.
Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals
JOURNAL OF MATERIALS CHEMISTRY, 19:2482-2493, 2009
abstract, full text, DOI:10.1039/b820445d

Jia, Lingling; Nguyen, Dat; Halley, J. W.; Pham, Phat; Lamanna, William; Hamrock, Steven
Proton Transport in HTFSI-TFSI-EMI Mixtures: Experiment and Theory
JOURNAL OF THE ELECTROCHEMICAL SOCIETY, 156:B136-B151, 2009
abstract, full text, DOI:10.1149/1.2975195

Piotto, S.; Concilio, S.; Mavelli, F.; Iannelli, P.
Computer Simulations of Natural and Synthetic Polymers in Confined Systems
MACROMOLECULAR SYMPOSIA, 286:25-33, 2009
abstract, full text, DOI:10.1002/masy.200951203

Gargallo, L.; Vargas, D.; Becerra, N.; Sandoval, C.; Saldias, C.; Leiva, A.; Radic, D.
Supramolecular Structures, Organization and Surface Behavior at Interfaces
MACROMOLECULAR SYMPOSIA, 278:80-88, 2009
abstract, full text, DOI:10.1002/masy.200950410

Tarasov, Denis Stanislavovich; Izotova, Ekaterina Dmitrievna; Alisheva, Diana Airatovna; Akberova, Natal'ya Ivanovna
GPAMM - software package for molecular dynamics on graphical processing units
Mathematical Models and Computer Simulations, 21:31-40, 2009
full text

Bosnacki, Dragan; Edelkamp, Stefan; Sulewski, Damian
Efficient Probabilistic Model Checking on General Purpose Graphics Processors
MODEL CHECKING SOFTWARE, 5578:32-49, 2009
abstract, full text

Allen, Michael P.
Molecular simulation methods for soft matter
MODELING AND SIMULATION OF NEW MATERIALS, 1091:1-43, 2009
abstract, full text

Rikvold, P. A.; Abou Hamad, I.; Juwono, T.; Robb, D. T.; Novotny, M. A.
Applications of Computer Simulations and Statistical Mechanics in Surface Electrochemistry
MODERN ASPECTS OF ELECTROCHEMISTRY, NO 44: MODELLING AND NUMERICAL SIMULATIONS II, Issue 44, 131-149, 2009
abstract, full text, DOI:10.1007/978-0-387-49586-6_4

Broeer, Angelika; Balkrishna, Sarojini; Kottra, Gabor; Davis, Sarah; Oakley, Aaron; Broeer, Stefan
Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20)
MOLECULAR MEMBRANE BIOLOGY, 26:333-346, 2009
abstract, full text, DOI:10.1080/09687680903150027

Fratev, Filip; Jonsdottir, Svava Osk; Mihaylova, Elina; Pajeva, Ilza
Molecular Basis of Inactive B-RAF(WT) and B-RAF(V600E) Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study
MOLECULAR PHARMACEUTICS, 6:144-157, JAN-FEB 2009
abstract, full text, DOI:10.1021/mp8001107

Chen, Cong; Li, Weizhong; Song, Yongchen; Yang, Jian
Molecular dynamics simulation studies of cryoprotective agent solutions: the relation between melting temperature and the ratio of hydrogen bonding acceptor to donor number
MOLECULAR PHYSICS, 107:673-684, 2009
abstract, full text, DOI:10.1080/00268970902852632

Cruzeiro, Leonor; Lopes, Paulo A.
Are the native states of proteins kinetic traps?
MOLECULAR PHYSICS, 107:1485-1493, 2009
abstract, full text, DOI:10.1080/00268970902950386

Nevidimov, Alexander V.; Razumov, Vladimir F.
Molecular dynamics simulations of AOT reverse micelles' self-assembly
MOLECULAR PHYSICS, 107:2169-2180, 2009
abstract, full text, DOI:10.1080/00268970903203736

Garate, J. -A.; English, N. J.; MacElroy, J. M. D.
Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields
MOLECULAR SIMULATION, 35:3-12, 2009
abstract, full text, DOI:10.1080/08927020802353491

Gallo, Marco T.; Grant, Barry J.; Teodoro, Miguel L.; Melton, Julia; Cieplak, Piotr; Phillips, George N., Jr.; Stec, Boguslaw
Novel procedure for thermal equilibration in molecular dynamics simulation
MOLECULAR SIMULATION, 35:349-357, 2009
abstract, full text, DOI:10.1080/08927020802647272

Choi, H. J.; Kim, J. Y.; Hong, S. D.; Ha, M. Y.; Jang, J.
Molecular simulation of the nanoscale water confined between an atomic force microscope tip and a surface
MOLECULAR SIMULATION, 35:466-472, 2009
abstract, full text, DOI:10.1080/08927020802635129

Mulheran, Paul; Kubiak, Karina
Protein adsorption mechanisms on solid surfaces: lysozyme-on-mica
MOLECULAR SIMULATION, 35:561-566, 2009
abstract, full text, DOI:10.1080/08927020802610288

Zhao, Xiongce
Motions of ions in a nanoscale Paul trap from molecular dynamics
MOLECULAR SIMULATION, 35:812-821, 2009
abstract, full text, DOI:10.1080/08927020902801555

Hong, S. D.; Choi, H. J.; Ha, M. Y.; Jang, J.
Dynamic change in water meniscus arising from tapping of an AFM tip
NANOTECH CONFERENCE & EXPO 2009, VOL 3, TECHNICAL PROCEEDINGS: NANOTECHNOLOGY 2009: BIOFUELS, RENEWABLE ENERGY, COATINGS FLUIDICS AND COMPACT MODELING, 296-299, 2009
abstract, full text

Gajdanowicz, Pawel; Garcia-Mata, Carlos; Gonzalez, Wendy; Elias Morales-Navarro, Samuel; Sharma, Tripti; Danilo Gonzalez-Nilo, Fernando; Gutowicz, Jan; Mueller-Roeber, Bernd; Blatt, Michael R.; Dreyer, Ingo
Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity
NEW PHYTOLOGIST, 182:380-391, 2009
abstract, full text, DOI:10.1111/j.1469-8137.2008.02749.x

Olsson, Johan D. M.; Landstrom, Jens; Ronnols, Jerk; Oscarson, Stefan; Widmalm, Goeran
Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis
ORGANIC & BIOMOLECULAR CHEMISTRY, 7:1612-1618, 2009
abstract, full text, DOI:10.1039/b823428k

Goldsmith, Jacob; Martens, Craig C.
Pressure-induced water flow through model nanopores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:528-533, 2009
abstract, full text, DOI:10.1039/b807823h

Murtola, Teemu; Bunker, Alex; Vattulainen, Ilpo; Deserno, Markus; Karttunen, Mikko
Multiscale modeling of emergent materials: biological and soft matter
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:1869-1892, 2009
abstract, full text, DOI:10.1039/b818051b

Zegarra, Fabio C.; Peralta, Gian N.; Coronado, Alberto M.; Gao, Yi Qin
Free energies and forces in helix-coil transition of homopolypeptides under stretching
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:4019-4024, 2009
abstract, full text, DOI:10.1039/b820021a

Sezer, Deniz; Prandolini, M. J.; Prisner, Thomas F.
Dynamic nuclear polarization coupling factors calculated from molecular dynamics simulations of a nitroxide radical in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:6626-6637, 2009
abstract, full text, DOI:10.1039/b905709a

Sezer, Deniz; Gafurov, Marat; Prandolini, M. J.; Denysenkov, Vasyl P.; Prisner, Thomas F.
Dynamic nuclear polarization of water by a nitroxide radical: rigorous treatment of the electron spin saturation and comparison with experiments at 9.2 Tesla
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:6638-6653, 2009
abstract, full text, DOI:10.1039/b906719c

Cai, Kaicong; Han, Chen; Wang, Jianping
Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:9149-9159, 2009
abstract, full text, DOI:10.1039/b910269h

Ponomarev, Sergei Y.; Putkaradze, Vakhtang; Bishop, Thomas C.
Relaxation dynamics of nucleosomal DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:10633-10643, 2009
abstract, full text, DOI:10.1039/b910937b

Zakrzewska, Krystyna; Bouvier, Benjamin; Michon, Alexis; Blanchet, Christophe; Lavery, Richard
Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:10712-10721, 2009
abstract, full text, DOI:10.1039/b910888m

Flenner, Elijah; Das, Jhuma; Rheinstadter, Maikel C.; Kosztin, Ioan
Subdiffusion and lateral diffusion coefficient of lipid atoms and molecules in phospholipid bilayers
PHYSICAL REVIEW E, 79 Art. No. 011907, JAN 2009
abstract, full text, DOI:10.1103/PhysRevE.79.011907

Calleja, Veronique; Laguerre, Michel; Parker, Peter J.; Larijani, Banafshe
Role of a Novel PH-Kinase Domain Interface in PKB/Akt Regulation: Structural Mechanism for Allosteric Inhibition
PLOS BIOLOGY, 7:189-200, JAN 2009
abstract, full text, DOI:10.1371/journal.pbio.1000017

Katti, D. R.; Katti, K. S.; Amarasinghe, P.; Pradhan, S.
Interlayer Fluid Flow and the Role of Clay-Fluid Molecular Interactions on the Swelling Behavior of Montmorillonite Clays
PORO-MECHANICS IV, 836-841, 2009
abstract, full text

Bourne, Jonathan W.; Torzilli, Peter A.
COLLAGEN MOLECULAR CONFORMATION EXHIBITS STRAIN-RATE DEPENDENT RESPONSE TO AXIAL DEFORMATION IN SILICO
PROCEEDINGS OF THE ASME SUMMER BIOENGINEERING CONFERENCE - 2009, PT A AND B, 995-996, 2009
full text

Chen, Wei; Lou, Jizhong; Hsin, Jen; Schulten, Klaus; Zhu, Cheng
IN SILICO FORCE-INDUCED UNBENDING OF alpha(v)beta(3) INTEGRIN
PROCEEDINGS OF THE ASME SUMMER BIOENGINEERING CONFERENCE - 2009, PT A AND B, 1029-1030, 2009
full text, TCBG publications

Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; Mackenzie, Kenneth M.; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, Kevin J.; Chow, Edmond; Eastwood, Michael P.; Ierardi, Douglas J.; Klepeis, John L.; Kuskin, Jeffrey S.; Larson, Richard H.; Lindorff-Larsen, Kresten; Maragakis, Paul; Moraes, Mark A.; Piana, Stefano; Shan, Yibing; Towles, Brian
Millisecond-Scale Molecular Dynamics Simulations on Anton
PROCEEDINGS OF THE CONFERENCE ON HIGH PERFORMANCE COMPUTING NETWORKING, STORAGE AND ANALYSIS, , 2009
abstract, full text

Shaw, David E.; Dror, Ron O.; Salmon, John K.; Grossman, J. P.; Mackenzie, Kenneth M.; Bank, Joseph A.; Young, Cliff; Deneroff, Martin M.; Batson, Brannon; Bowers, Kevin J.; Chow, Edmond; Eastwood, Michael P.; Ierardi, Douglas J.; Klepeis, John L.; Kuskin, Jeffrey S.; Larson, Richard H.; Lindorff-Larsen, Kresten; Maragakis, Paul; Moraes, Mark A.; Piana, Stefano; Shan, Yibing; Towles, Brian
Millisecond-Scale Molecular Dynamics Simulations on Anton
PROCEEDINGS OF THE CONFERENCE ON HIGH PERFORMANCE COMPUTING NETWORKING, STORAGE AND ANALYSIS, , 2009
abstract, full text

Yang, Qian; Du, Lupei; Tsai, Keng-Chang; Wang, Xiaojian; Li, Minyong; You, Qidong
Pharmacophore Mapping for Kv1.5 Potassium Channel Blockers
QSAR & COMBINATORIAL SCIENCE, 28:59-71, JAN 2009
abstract, full text, DOI:10.1002/qsar.200810050

Maginn, Edward J.
Atomistic Simulation of Ionic Liquids
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 26, 26:421-493, 2009
full text

Baskin, I. I.; Palyulin, V. A.; Zefirov, N. S.
Molecular modelling of receptors of physiologically active compounds for medicinal chemistry purposes
RUSSIAN CHEMICAL REVIEWS, 78:495-511, 2009
abstract, full text, DOI:10.1070/RC2009v078n06ABEH004032

Tsigelny, I. F.; Sharikov, Y.; Miller, M. A.; Masliah, E.
Molecular mechanism of pore creation in bacterial membranes by amyloid proteins
SCIDAC 2009: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING, 180 Art. No. UNSP 012026, 2009
abstract, full text, DOI:10.1088/1742-6596/180/1/012026

Shi, Guochun; Kindratenko, Volodymyr V.; Ufimtsev, Ivan S.; Martinez, Todd J.; Phillips, James C.; Gottlieb, Steven A.
Implementation of scientific computing applications on the Cell Broadband Engine
SCIENTIFIC PROGRAMMING, 17:135-151, 2009
abstract, full text, DOI:10.3233/SPR-2009-0273

Mernea, M.; Leca, A.; Calborean, O.; Dinca, M. P.; Dascalu, T.; Mihailescu, D.
3D protein structure determination by THz Spectroscopy and molecular modelling: case study on Bovine Serum Albumin
TERAHERTZ AND MID INFRARED RADIATION: BASIC RESEARCH AND PRACTICAL APPLICATIONS, WORKSHOP PROCEEDINGS, 49-50, 2009
abstract, full text

Marchese, Francis T.
Interactive Molecular Visualization at the Interface
TRENDS IN INTERACTIVE VISUALIZATION: STATE-OF-THE-ART SURVEY, 251-267, 2009
abstract, full text, DOI:10.1007/978-1-84800-269-2_11

Benitez, Benedetta A. Sampoli; Arora, Karunesh; Balistreri, Lisa; Schlick, Tamar
Mismatched Base-Pair Simulations for ASFV Pol x/DNA Complexes Help Interpret Frequent G.G Misincorporation
JOURNAL OF MOLECULAR BIOLOGY, 384:1086-1097, DEC 31 2008
abstract, full text, DOI:10.1016/j.jmb.2008.10.025

Pomata, Matias H. H.; Laria, Daniel; Skaf, Munir S.; Elola, M. Dolores
Molecular dynamics simulations of AOT-water/formamide reverse micelles: Structural and dynamical properties
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 244503, DEC 28 2008
abstract, full text, DOI:10.1063/1.3042275

Zhu, Jianghai; Luo, Bing-Hao; Xiao, Tsan; Zhang, Chengzhong; Nishida, Noritaka; Springer, Timothy A.
Structure of a Complete Integrin Ectodomain in a Physiologic Resting State and Activation and Deactivation by Applied Forces
MOLECULAR CELL, 32:849-861, DEC 26 2008
abstract, full text, DOI:10.1016/j.molcel.2008.11.018

Chiu, Chi-cheng; Dieckmann, Gregg R.; Nielsen, Steven O.
Molecular Dynamics Study of a Nanotube-Binding Amphiphilic Helical Peptide at Different Water/Hydrophobic Interfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 112:16326-16333, DEC 25 2008
abstract, full text, DOI:10.1021/jp805313p

Peters, Baron; Zimmermann, Nils E. R.; Beckham, Gregg T.; Tester, Jefferson W.; Trout, Bernhardt L.
Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:17342-17350, DEC 24 2008
abstract, full text, DOI:10.1021/ja802014m

Rodriguez, Yoel; Mezei, Mihaly; Osman, Roman
The PT1-Ca(2+) Gla Domain Binds to a Membrane through Two Dipalmitoylphosphatidylserines. A Computational Study
BIOCHEMISTRY, 47:13267-13278, DEC 16 2008
abstract, full text, DOI:10.1021/bi801199v

Wu, Sangwook; Zhuravlev, Pavel I.; Papoian, Garegin A.
High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics
BIOPHYSICAL JOURNAL, 95:5524-5532, DEC 15 2008
abstract, full text, DOI:10.1529/biophysj.108.136697

Peplowski, L.; Kubiak, K.; Nowak, W.
Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095
CHEMICAL PHYSICS LETTERS, 467:144-149, DEC 15 2008
abstract, full text, DOI:10.1016/j.cplett.2008.10.072

Rheinstaedter, Maikel C.; Das, Jhuma; Flenner, Elijah J.; Bruening, Beate; Seydel, Tilo; Kosztin, Ioan
Motional Coherence in Fluid Phospholipid Membranes
PHYSICAL REVIEW LETTERS, 101 Art. No. 248106, DEC 12 2008
abstract, full text, DOI:10.1103/PhysRevLett.101.248106

Sint, Kyaw; Wang, Boyang; Kral, Petr
Selective Ion Passage through Functionalized Graphene Nanopores
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:16448-+, DEC 10 2008
abstract, full text, DOI:10.1021/ja804409f

van der Kamp, Marc W.; Shaw, Katherine E.; Woods, Christopher J.; Mulholland, Adrian J.
Biomolecular simulation and modelling: status, progress and prospects
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 5:S173-S190, DEC 6 2008
abstract, full text, DOI:10.1098/rsif.2008.0105.focus

Kelkar, Manish S.; Shi, Wei; Maginn, Edward J.
Determining the Accuracy of Classical Force Fields for Ionic Liquids: Atomistic Simulation of the Thermodynamic and Transport Properties of 1-Ethyl-3-methylimidazolium Ethylsulfate ([emim][EtSO(4)]) and Its Mixtures with Water
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 47:9115-9126, DEC 3 2008
abstract, full text, DOI:10.1021/ie800843u

Heo, Jiyoung; Ja, William W.; Benzer, Seymour; Goddard, William A., I.I.I.
The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster
BIOCHEMISTRY, 47:12740-12749, DEC 2 2008
abstract, full text, DOI:10.1021/bi801335p

Giupponi, G.; Harvey, M. J.; De Fabritiis, G.
The impact of accelerator processors for high-throughput molecular modeling and simulation
DRUG DISCOVERY TODAY, 13:1052-1058, DEC 2008
abstract, full text, DOI:10.1016/j.drudis.2008.08.001

Raimondo, Domenico; Giorgetti, Alejandro; Bernassola, Francesca; Melino, Gerry; Tramontano, Anna
Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7
BIOCHEMICAL PHARMACOLOGY, 76:1620-1627, DEC 1 2008
abstract, full text, DOI:10.1016/j.bcp.2008.08.026

Grigorenko, B. L.; Shadrina, M. S.; Topol, I. A.; Collins, J. R.; Nemukhin, A. V.
Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1784:1908-1917, DEC 2008
abstract, full text, DOI:10.1016/j.bbapap.2008.08.003

Fowler, Philip W.; Tai, Kaihsu; Sansom, Mark S. P.
The Selectivity of K+ Ion Channels: Testing the Hypotheses
BIOPHYSICAL JOURNAL, 95:5062-5072, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.132035

Zhang, Zhiyong; Lu, Lanyuan; Noid, Will G.; Krishna, Vinod; Pfaendtner, Jim; Voth, Gregory A.
A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules
BIOPHYSICAL JOURNAL, 95:5073-5083, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.139626

Wen, Po-Chao; Tajkhorshid, Emad
Dimer Opening of the Nucleotide Binding Domains of ABC Transporters after ATP Hydrolysis
BIOPHYSICAL JOURNAL, 95:5100-5110, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.139444

Shaikh, Saher Afshan; Tajkhorshid, Emad
Potential Cation and H+ Binding Sites in Acid Sensing Ion Channel-1
BIOPHYSICAL JOURNAL, 95:5153-5164, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.141606

Sengupta, Neelanjana; Jaud, Simon; Tobias, Douglas J.
Hydration Dynamics in a Partially Denatured Ensemble of the Globular Protein Human alpha-Lactalbumin Investigated with Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 95:5257-5267, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.136531

Pfaendtner, Jim; Voth, Gregory A.
Molecular Dynamics Simulation and Coarse-Grained Analysis of the Arp2/3 Complex
BIOPHYSICAL JOURNAL, 95:5324-5333, DEC 1 2008
abstract, full text, DOI:10.1529/biophysj.108.143313

Singh, Narender; Briggs, James M.
Molecular Dynamics Simulations of Factor Xa: Insight into Conformational Transition of Its Binding Subsites
BIOPOLYMERS, 89:1104-1113, DEC 2008
abstract, full text, DOI:10.1002/bip.21062

Orlowski, Slawomir; Nowak, Wieslaw
Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin
BIOSYSTEMS, 94:263-266, DEC 2008
abstract, full text, DOI:10.1016/j.biosystems.2008.04.016

Alexiadis, Alessio; Kassinos, Stavros
Molecular Simulation of Water in Carbon Nanotubes
CHEMICAL REVIEWS, 108:5014-5034, DEC 2008
full text, DOI:10.1021/cr078140f

Pedretti, Alessandro; De Luca, Laura; Marconi, Cristina; Negrisoli, Gianpaolo; Aldini, Giancarlo; Vistoli, Giulio
Modeling of the Intestinal Peptide Transporter hPepT1 and Analysis of Its Transport Capacities by Docking and Pharmacophore Mapping
CHEMMEDCHEM, 3:1913-1921, DEC 2008
abstract, full text, DOI:10.1002/cmdc.200800184

Colizzi, Francesco; Recanatini, Maurizio; Cavalli, Andrea
Mechanical Features of Plasmodium falciparum Acyl Carrier Protein in the Delivery of Substrates
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2289-2293, DEC 2008
abstract, full text, DOI:10.1021/ci800297v

Verstraelen, Toon; Van Houteghem, Marc; Van Speybroeck, Veronique; Waroquier, Michel
MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2414-2424, DEC 2008
abstract, full text, DOI:10.1021/ci800233y

Emperador, Agusti; Meyer, Tim; Orozco, Modesto
United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:2001-2010, DEC 2008
abstract, full text, DOI:10.1021/ct8003832

Chipot, Christophe
Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:2150-2159, DEC 2008
abstract, full text, DOI:10.1021/ct800313k

Labro, Alain J.; Raes, Adam L.; Grottesi, Alessandro; Van Hoorick, Diane; Sansom, Mark S. P.; Snyders, Dirk J.
Kv Channel Gating Requires a Compatible S4-S5 Linker and Bottom Part of S6, Constrained by Non-interacting Residues
JOURNAL OF GENERAL PHYSIOLOGY, 132:667-680, DEC 2008
abstract, full text, DOI:10.1085/jgp.200810048

Gumbart, James; Schulten, Klaus
The Roles of Pore Ring and Plug in the SecY Protein-conducting Channel
JOURNAL OF GENERAL PHYSIOLOGY, 132:709-719, DEC 2008
abstract, full text, TCBG publications, DOI:10.1085/jgp.200810062

Shen, Hongbo; Xu, Feng; Hu, Hairong; Wang, Feifei; Wu, Qi; Huang, Qiang; Wang, Honghai
Coevolving residues of (beta/alpha)(8)-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 164:281-292, DEC 2008
abstract, full text, DOI:10.1016/j.jsb.2008.09.003

Lee, Tai-Sung; Ma, Wanlong; Zhang, Xi; Giles, Francis; Cortes, Jorge; Kantarjian, Hagop; Albitar, Maher
BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations
MOLECULAR CANCER THERAPEUTICS, 7:3834-3841, DEC 2008
abstract, full text, DOI:10.1158/1535-7163.MCT-08-0482

Kim, Sang N.; Kuang, Zhifeng; Grote, James G.; Farmer, Barry L.; Naik, Rajesh R.
Enrichment of (6,5) Single Wall Carbon Nanotubes Using Genomic DNA
NANO LETTERS, 8:4415-4420, DEC 2008
abstract, full text, DOI:10.1021/nl802332v

Tsigelny, Igor F.; Sharikov, Yuriy; Miller, Mark A.; Masliah, Eliezer
Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE, 4:350-357, DEC 2008
abstract, full text, DOI:10.1016/j.nano.2008.05.005

Laio, Alessandro; Gervasio, Francesco L.
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
REPORTS ON PROGRESS IN PHYSICS, 71 Art. No. 126601, DEC 2008
abstract, full text, DOI:10.1088/0034-4885/71/12/126601

Liu, Feng; Ye, Xue-song; Wu, Tao; Wang, Chang-Tao; Shen, Jia-wei; Kang, Yu
Conformational Mobility of GOx Coenzyme Complex on Single-Wall Carbon Nanotubes
SENSORS, 8:8453-8462, DEC 2008
abstract, full text, DOI:10.3390/s8128453

Feng, Jiu-Ju; Murgida, Daniel H.; Kuhlmann, Uwe; Utesch, Tillmann; Mroginski, Maria Andrea; Hildebrandt, Peter; Weidinger, Inez M.
Gated Electron Transfer of Yeast Iso-1 Cytochrome c on Self-Assembled Monolayer-Coated Electrodes
JOURNAL OF PHYSICAL CHEMISTRY B, 112:15202-15211, NOV 27 2008
abstract, full text, DOI:10.1021/jp8062383

Romanowska, Julia; Setny, Piotr; Trylska, Joanna
Molecular Dynamics Study of the Ribosomal A-Site
JOURNAL OF PHYSICAL CHEMISTRY B, 112:15227-15243, NOV 27 2008
abstract, full text, DOI:10.1021/jp806814s

Wedberg, Rasmus; Peters, Gunther H.; Abildskov, Jens
Total correlation function integrals and isothermal compressibilities from molecular simulations
FLUID PHASE EQUILIBRIA, 273:1-10, NOV 25 2008
abstract, full text, DOI:10.1016/j.fluid.2008.07.011

Vladimirov, Egor; Ivanova, Anela; Roesch, Notker
Effect of solvent polarization on the reorganization energy of electron transfer from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 194515, NOV 21 2008
abstract, full text, DOI:10.1063/1.3013456

Vaitheeswaran, S.; Thirumalai, D.
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:17636-17641, NOV 18 2008
abstract, full text, DOI:10.1073/pnas.0803990105

Jang, Hyunbum; Ma, Buyong; Lal, Ratnesh; Nussinov, Ruth
Models of Toxic beta-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer beta-Amyloid Ion Channels
BIOPHYSICAL JOURNAL, 95:4631-4642, NOV 15 2008
abstract, full text, DOI:10.1529/biophysj.108.134551

Hogberg, Carl-Johan; Nikitin, Alexei M.; Lyubartsev, Alexander P.
Modification of the CHARMM force field for DMPC lipid bilayer
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:2359-2369, NOV 15 2008
abstract, full text, DOI:10.1002/jcc.20974

Haddadian, Esmael J.; Cheng, Mary Hongying; Coalson, Rob D.; Xu, Yan; Tang, Pei
In Silico Models for the Human alpha 4 beta 2 Nicotinic Acetylcholine Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 112:13981-13990, NOV 6 2008
abstract, full text, DOI:10.1021/jp804868s

Pickholz, Monica; Fraceto, Leonardo Fernandes; de Paula, Eneida
Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 108:2386-2391, NOV 5 2008
abstract, full text, DOI:10.1002/qua.21767

Gutowski, Keith E.; Maginn, Edward J.
Amine-Functionalized Task-Specific Ionic Liquids: A Mechanistic Explanation for the Dramatic Increase in Viscosity upon Complexation with CO2 from Molecular Simulation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:14690-14704, NOV 5 2008
abstract, full text, DOI:10.1021/ja804654b

Firlej, L.; Kuchta, B.; Roth, M. W.; Connolly, M. J.; Wexler, Carlos
Structural and Phase Properties of Tetracosane (C24H50) Monolayers Adsorbed on Graphite: An Explicit Hydrogen Molecular Dynamics Study
LANGMUIR, 24:12392-12397, NOV 4 2008
abstract, full text, DOI:10.1021/la802071a

Hua, Lan; Zhou, Ruhong; Thirumalai, D.; Berne, B. J.
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:16928-16933, NOV 4 2008
abstract, full text, DOI:10.1073/pnas.0808427105

McDaniel, Allison; Fuchs, Erica; Liu, Ying; Ford, Clark
Directed evolution of Aspergillus niger glucoamylase to increase thermostability
MICROBIAL BIOTECHNOLOGY, 1:523-531, NOV 2008
abstract, full text, DOI:10.1111/j.1751-7915.2008.00055.x

Trzaskowski, Bartosz; Leonarski, Filip; Les, Andrzej; Adamowicz, Ludwik
Altering the Orientation of Proteins on Self-Assembled Monolayers: A Computational Study
BIOMACROMOLECULES, 9:3239-3245, NOV 2008
abstract, full text, DOI:10.1021/bm800806n

Liu, Ming; Su, Ji Guo; Kong, Ren; Sun, Ting Guang; Tan, Jian Jun; Chen, Wei Zu; Wang, Cun Xin
Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT
BIOPHYSICAL CHEMISTRY, 138:42-49, NOV 2008
abstract, full text, DOI:10.1016/j.bpc.2008.09.001

Lyman, Edward; Pfaendtner, Jim; Voth, Gregory A.
Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins
BIOPHYSICAL JOURNAL, 95:4183-4192, NOV 1 2008
abstract, full text, DOI:10.1529/biophysj.108.139733

Vashisth, Harish; Abrams, Cameron F.
Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex
BIOPHYSICAL JOURNAL, 95:4193-4204, NOV 1 2008
abstract, full text, DOI:10.1529/biophysj.108.139675

Thogersen, Lea; Schiott, Birgit; Vosegaard, Thomas; Nielsen, Niels Chr.; Tajkhorshid, Emad
Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 95:4337-4347, NOV 1 2008
abstract, full text, DOI:10.1529/biophysj.108.133330

Harding, John H.; Duffy, Dorothy M.; Sushko, Maria L.; Rodger, P. Mark; Quigley, David; Elliott, James A.
Computational Techniques at the Organic-Inorganic Interface in Biomineralization
CHEMICAL REVIEWS, 108:4823-4854, NOV 2008
full text, DOI:10.1021/cr078278y

Miguel, Virginia; Monti, Mariela R.; Argarana, Carlos E.
The role of MutS oligomers on Pseudomonas aeruginosa Mismatch Repair System activity
DNA REPAIR, 7:1799-1808, NOV 1 2008
abstract, full text, DOI:10.1016/j.dnarep.2008.07.005

Chimerel, Catalin; Movileanu, Liviu; Pezeshki, Soroosh; Winterhalter, Mathias; Kleinekathoefer, Ulrich
Transport at the nanoscale: temperature dependence of ion conductance
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 38:121-125, NOV 2008
abstract, full text, DOI:10.1007/s00249-008-0366-0

Tintori, Cristina; Corradi, Valentina; Magnani, Matteo; Manetti, Fabrizio; Botta, Maurizio
Targets Looking for Drugs: A Multistep Computational Protocol for the Development of Structure-Based Pharmacophores and Their Applications for Hit Discovery
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2166-2179, NOV 2008
abstract, full text, DOI:10.1021/ci800105p

Wang, Liguo; Ounjai, Puey; Sigworth, Fred J.
Streptavidin crystals as nanostructured supports and image-calibration references for cryo-EM data collection
JOURNAL OF STRUCTURAL BIOLOGY, 164:190-198, NOV 2008
abstract, full text, DOI:10.1016/j.jsb.2008.07.008

Alam, Sadaf R.; Agarwal, Pratul K.; Vetter, Jeffrey S.
Performance characteristics of biomolecular simulations on high-end systems with multi-core processors
PARALLEL COMPUTING, 34:640-651, NOV 2008
abstract, full text, DOI:10.1016/j.parco.2008.05.003

Forney, Michael W.; Janosi, Lorant; Kosztin, Ioan
Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes
PHYSICAL REVIEW E, 78 Art. No. 051913, NOV 2008
abstract, full text, DOI:10.1103/PhysRevE.78.051913

Buehler, Markus J.; Keten, Sinan; Ackbarow, Theodor
Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture
PROGRESS IN MATERIALS SCIENCE, 53:1101-1241, NOV 2008
abstract, full text, DOI:10.1016/j.pmatsci.2008.06.002

Wang, Boyang; Vukovic, Lela; Kral, Petr
Nanoscale Rotary Motors Driven by Electron Tunneling
PHYSICAL REVIEW LETTERS, 101 Art. No. 186808, OCT 31 2008
abstract, full text, DOI:10.1103/PhysRevLett.101.186808

Cooke, Ben; Schmidler, Scott C.
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 164112, OCT 28 2008
abstract, full text, DOI:10.1063/1.2989802

Halverson, Jonathan D.; Maldarelli, Charles; Couzis, Alexander; Koplik, Joel
A molecular dynamics study of the motion of a nanodroplet of pure liquid on a wetting gradient
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 164708, OCT 28 2008
abstract, full text, DOI:10.1063/1.2996503

Cozzini, Pietro; Kellogg, Glen E.; Spyrakis, Francesca; Abraham, Donald J.; Costantino, Gabriele; Emerson, Andrew; Fanelli, Francesca; Gohlke, Holger; Kuhn, Leslie A.; Morris, Garrett M.; Orozco, Modesto; Pertinhez, Thelma A.; Rizzi, Menico; Sotriffer, Christoph A.
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
JOURNAL OF MEDICINAL CHEMISTRY, 51:6237-6255, OCT 23 2008
full text, DOI:10.1021/jm800562d

Bonomi, Massimiliano; Branduardi, Davide; Gervasio, Francesco L.; Parrinello, Michele
The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:13938-13944, OCT 22 2008
abstract, full text, DOI:10.1021/ja803652f

Huber, Thomas; Menon, Santosh; Sakmar, Thomas P.
Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery
BIOCHEMISTRY, 47:11013-11023, OCT 21 2008
abstract, full text, DOI:10.1021/bi800891r

Rodinger, Tomas; Howell, P. Lynne; Pomes, Regis
Calculation of absolute protein-ligand binding free energy using distributed replica sampling
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 155102, OCT 21 2008
abstract, full text, DOI:10.1063/1.2989800

Joshi, Mohan Chandra; Sharma, Animesh; Kant, Sashi; Birah, Ajanta; Gupta, Gorakh Prasad; Khan, Sharik R.; Bhatnagar, Rakesh; Banerjee, Nirupama
An insecticidal GroEL protein with chitin binding activity from Xenorhabdus nematophila
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:28287-28296, OCT 17 2008
abstract, full text, DOI:10.1074/jbc.M804416200

Ballano, Gema; Zanuy, David; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Aleman, Carlos
Structural Analysis of a beta-Helical Protein Motif Stabilized by Targeted Replacements with Conformationally Constrained Amino Acids
JOURNAL OF PHYSICAL CHEMISTRY B, 112:13101-13115, OCT 16 2008
abstract, full text, DOI:10.1021/jp8032116

Tsukazaki, Tomoya; Mori, Hiroyuki; Fukai, Shuya; Ishitani, Ryuichiro; Mori, Takaharu; Dohmae, Naoshi; Perederina, Anna; Sugita, Yuji; Vassylyev, Dmitry G.; Ito, Koreaki; Nureki, Osamu
Conformational transition of Sec machinery inferred from bacterial SecYE structures
NATURE, 455:988-U72, OCT 16 2008
abstract, full text, DOI:10.1038/nature07421

Zeiger, A. S.; Layton, Bradley Edward
Molecular Modeling of the Axial and Circumferential Elastic Moduli of Tubulin
BIOPHYSICAL JOURNAL, 95:3606-3618, OCT 15 2008
abstract, full text, DOI:10.1529/biophysj.108.131359

Tuncel, Aytug; Kavakli, Ibrahim Halil; Keskin, Ozlem
Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase
BIOPHYSICAL JOURNAL, 95:3628-3639, OCT 15 2008
abstract, full text, DOI:10.1529/biophysj.107.123042

Long, Hai; Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon
Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii
BIOPHYSICAL JOURNAL, 95:3753-3766, OCT 15 2008
abstract, full text, DOI:10.1529/biophysj.107.127548

Sharma, Deepak; Feng, Gang; Khor, Dingyue; Genchev, Georgi Z.; Lu, Hui; Li, Hongbin
Stabilization provided by neighboring strands is critical for the mechanical stability of proteins
BIOPHYSICAL JOURNAL, 95:3935-3942, OCT 15 2008
abstract, full text, DOI:10.1529/biophysj.108.134072

Zhong, Wenyu; Guo, Wanlin; Ma, Shaojie
Intrinsic aqueduct orifices facilitate K+ channel gating
FEBS LETTERS, 582:3320-3324, OCT 15 2008
abstract, full text, DOI:10.1016/j.febslet.2008.08.020

Herrera, Fernando E.; Chesi, Alessandra; Paleologou, Katerina E.; Schmid, Adrian; Munoz, Adriana; Vendruscolo, Michele; Gustincich, Stefano; Lashuel, Hilal A.; Carloni, Paolo
Inhibition of alpha-Synuclein Fibrillization by Dopamine Is Mediated by Interactions with Five C-Terminal Residues and with E83 in the NAC Region
PLOS ONE, 3 Art. No. e3394, OCT 14 2008
abstract, full text, DOI:10.1371/journal.pone.0003394

Chen, L. Y.
Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 144113, OCT 14 2008
abstract, full text, DOI:10.1063/1.2992153

Park, Sanghyun; Lau, Albert Y.; Roux, Benoit
Computing conformational free energy by deactivated morphing
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 134102, OCT 7 2008
abstract, full text, DOI:10.1063/1.2982170

Ishitani, Ryuichiro; Sugita, Yuji; Dohmae, Naoshi; Furuya, Noritaka; Hattori, Motoyuki; Nureki, Osamu
Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:15393-15398, OCT 7 2008
abstract, full text, DOI:10.1073/pnas.0802991105

Karachevtsev, Victor A.; Gladchenko, Galyna O.; Karachevtsev, Maksym V.; Valeev, Vladimir A.; Leontiev, Victor S.; Lytvyn, Oksana S.
Adsorption of poly(rA) on the carbon nanotube surface and its hybridization with poly(rU)
CHEMPHYSCHEM, 9:2010-2018, OCT 6 2008
abstract, full text, DOI:10.1002/cphc.200800182

Bhattacharya, Supriyo; Hall, Spencer E.; Vaidehi, Nagarajan
Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors
JOURNAL OF MOLECULAR BIOLOGY, 382:539-555, OCT 3 2008
abstract, full text, DOI:10.1016/j.jmb.2008.06.084

Falvo, Cyril; Hayashi, Tomoyuki; Zhuang, Wei; Mukamel, Shaul
Coherent two dimensional infrared spectroscopy of a cyclic decapeptide Antamanide. A simulation study of the amide-I and A bands
JOURNAL OF PHYSICAL CHEMISTRY B, 112:12479-12490, OCT 2 2008
abstract, full text, DOI:10.1021/jp801493y

Levoin, Nicolas; Calmels, Thierry; Poupardin-Olivier, Olivia; Labeeuw, Olivier; Danvy, Denis; Robert, Philippe; Berrebi-Bertrand, Isabelle; Ganellin, C. Robin; Schunack, Walter; Stark, Holger; Capet, Marc
Refined Docking as a Valuable Tool for Lead Optimization: Application to Histamine H-3 Receptor Antagonists
ARCHIV DER PHARMAZIE, 341:610-623, OCT 2008
abstract, full text, DOI:10.1002/ardp.200800042

Floquet, Nicolas; Dedieu, Stephane; Martiny, Laurent; Dallchez, Manuel; Perahia, David
Human thrombospondin's (TSP-1) C-terminal domain opens to interact with the CD-47 receptor: A molecular modeling study
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 478:103-109, OCT 1 2008
abstract, full text, DOI:10.1016/j.abb.2008.07.015

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu
Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces
BIOMATERIALS, 29:3847-3855, OCT 2008
abstract, full text, DOI:10.1016/j.biomaterials.2008.06.013

Mitra, Arpita; Sept, David
Taxol allosterically alters the dynamics of the tubulin dimer and increases the flexibility of microtubules
BIOPHYSICAL JOURNAL, 95:3252-3258, OCT 1 2008
abstract, full text, DOI:10.1529/biophysj.108.133884

Gorfe, Alemayehu A.; Baron, Riccardo; McCammon, J. Andrew
Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven hydrophobic effect
BIOPHYSICAL JOURNAL, 95:3269-3277, OCT 1 2008
abstract, full text, DOI:10.1529/biophysj.108.136481

Damjanovic, Ana; Miller, Benjamin T.; Wenaus, Torre J.; Maksimovic, Petar; Garcia-Moreno E, Bertrand; Brooks, Bernard R.
Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2021-2029, OCT 2008
abstract, full text, DOI:10.1021/ci800263c

Streiff, John H.; Jones, Keith A.
Volatile Anesthetic Binding to Proteins Is Influenced by Solvent and Aliphatic Residues
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2066-2073, OCT 2008
abstract, full text, DOI:10.1021/6800206a

Cerutti, David S.; Duke, Robert; Freddolino, Peter L.; Fan, Hao; Lybrand, Terry P.
A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:1669-1680, OCT 2008
abstract, full text, DOI:10.1021/ct8002173

Hong, Rolando; Magistrato, Alessandra; Carloni, Paolo
Anthrax Lethal Factor Investigated by Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:1745-1756, OCT 2008
abstract, full text, DOI:10.1021/ct8001877

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Tomoda, Shuji; Ueda, Hiroki R.
Perturbational formulation of principal component analysis in molecular dynamics simulation
PHYSICAL REVIEW E, 78 Art. No. 046702, OCT 2008
abstract, full text, DOI:10.1103/PhysRevE.78.046702

De Fabritiis, G.; Coveney, P. V.; Villa-Freixa, J.
Energetics of K(+) permeability through Gramicidin A by forward-reverse steered molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 73:185-194, OCT 2008
abstract, full text, DOI:10.1002/prot.22036

Liu, Ming S.; Todd, B. D.; Yao, Shenggen; Feng, Zhi-Ping; Norton, Raymond S.; Sadus, Richard J.
Coarse-grained dynamics of the receiver domain of NtrC: Fluctuations, correlations and implications for allosteric cooperativity
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 73:218-227, OCT 2008
abstract, full text, DOI:10.1002/prot.22056

Pei, Q. X.; Lim, C. G.; Cheng, Y.; Gao, Huajian
Molecular dynamics study on DNA oligonucleotide translocation through carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 125101, SEP 28 2008
abstract, full text, DOI:10.1063/1.2981798

Zlatev, Ivan; Dutartre, Helene; Barvik, Ivan; Neyts, Johan; Canard, Bruno; Vasseur, Jean-Jacques; Alvarez, Karine; Morvan, Francois
Phosphoramidate dinucleosides as hepatitis C virus polymerase inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 51:5745-5757, SEP 25 2008
abstract, full text, DOI:10.1021/jm800617c

Xiao, Bailong; Dubin, Adrienne E.; Bursulaya, Badry; Viswanath, Veena; Jegla, Timothy J.; Patapoutian, Ardem
Identification of transmembrane domain 5 as a critical molecular determinant of menthol sensitivity in mammalian TRPA1 channels
JOURNAL OF NEUROSCIENCE, 28:9640-9651, SEP 24 2008
abstract, full text, DOI:10.1523/JNEUROSCI.2772-08.2008

Dehez, Francois; Pebay-Peyroula, Eva; Chipot, Christophe
Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:12725-12733, SEP 24 2008
abstract, full text, DOI:10.1021/ja8033087

Brannigan, Grace; Henin, Jerome; Law, Richard; Eckenhoff, Roderic; Klein, Michael L.
Embedded cholesterol in the nicotinic acetylcholine receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:14418-14423, SEP 23 2008
abstract, full text, DOI:10.1073/pnas.0803029105

Manna, Debasis; Bhardwaj, Nitin; Vora, Mohsin S.; Stahelin, Robert V.; Lu, Hui; Cho, Wonhwa
Differential roles of phosphatidylserine, PtdIns(4,5)P-2, and PtdIns(3,4,5)P-3 in plasma membrane targeting of C2 domains - Molecular dynamics simulation, membrane binding, and cell translocation studies of the PKC alpha C2 domain
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:26047-26058, SEP 19 2008
abstract, full text, DOI:10.1074/jbc.M802617200

Glosser, Christopher J.; Hill, Roger C.
Dielectric screening in a spherical cavity
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 41 Art. No. 375402, SEP 19 2008
abstract, full text, DOI:10.1088/1751-8113/41/37/375402

Espinoza-Fonseca, L. Michel; Kast, David; Thomas, David D.
Thermodynamic and structural basis of phosphorylation-induced disorder-to-order transition in the regulatory light chain of smooth muscle myosin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:12208-+, SEP 17 2008
abstract, full text, DOI:10.1021/ja803143g

Lou, Jizhong; Zhu, Cheng
Flow induces loop-to-beta-hairpin transition on the beta-switch of platelet glycoprotein Ib alpha
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:13847-13852, SEP 16 2008
abstract, full text, DOI:10.1073/pnas.0801965105

Roberts, Elijah; Sethi, Anurag; Montoya, Jonathan; Woese, Carl R.; Luthey-Schulten, Zaida
Molecular signatures of ribosomal evolution
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:13953-13958, SEP 16 2008
abstract, full text, DOI:10.1073/pnas.0804861105

Stancanelli, Rosanna; Crupi, Vincenza; De Luca, Laura; Ficarra, Paola; Ficarra, Rita; Gitto, Rosaria; Guardo, Marta; Iraci, Nunzio; Majolino, Domenico; Tommasini, Silvana; Venuti, Valentina
Improvement of water solubility of non-competitive AMPA receptor antagonists by complexation with beta-cyclodextrin
BIOORGANIC & MEDICINAL CHEMISTRY, 16:8706-8712, SEP 15 2008
abstract, full text, DOI:10.1016/j.bmc.2008.07.085

Corry, Ben; Jayatilaka, Dylan
Simulation of structure, orientation, and energy transfer between AlexaFluor molecules attached to MscL
BIOPHYSICAL JOURNAL, 95:2711-2721, SEP 15 2008
abstract, full text, DOI:10.1529/biophysj.107.126243

Law, Richard J.; Munson, Keith; Sachs, George; Lightstone, Felice C.
An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations
BIOPHYSICAL JOURNAL, 95:2739-2749, SEP 15 2008
abstract, full text, DOI:10.1529/biophysj.107.128025

Arkhipov, Anton; Yin, Ying; Schulten, Klaus
Four-scale description of membrane sculpting by BAR domains
BIOPHYSICAL JOURNAL, 95:2806-2821, SEP 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.108.132563

Chandler, Danielle E.; Hsin, Jen; Harrison, Christopher B.; Gumbart, James; Schulten, Klaus
Intrinsic curvature properties of photosynthetic proteins in chromatophores
BIOPHYSICAL JOURNAL, 95:2822-2836, SEP 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.108.132852

Luan, Binquan; Aksimentiev, Aleksei
Strain softening in stretched DNA
PHYSICAL REVIEW LETTERS, 101 Art. No. 118101, SEP 12 2008
abstract, full text, DOI:10.1103/PhysRevLett.101.118101

Neres, Joao; Labello, Nicholas P.; Somu, Ravindranadh V.; Boshoff, Helena I.; Wilson, Daniel J.; Vannada, Jagadeshwar; Chen, Liqiang; Barry, Clifton E., I.I.I.; Bennett, Eric M.; Aldrich, Courtney C.
Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: Structure-activity relationships of the nucleobase domain of 5 '-O-[N-(salicyl)sulfamoyl]adenosine
JOURNAL OF MEDICINAL CHEMISTRY, 51:5349-5370, SEP 11 2008
abstract, full text, DOI:10.1021/jm800567v

McAllister, Karen A.; Zou, Hongling; Cochran, Frank V.; Bender, Gretchen M.; Senes, Alessandro; Fry, H. Christopher; Nanda, Vikas; Keenan, Patricia A.; Lear, James D.; Saven, Jeffery G.; Therien, Michael J.; Blasie, J. Kent; DeGrado, William F.
Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:11921-11927, SEP 10 2008
abstract, full text, DOI:10.1021/ja800697g

Tsigelny, Igor F.; Crews, Leslie; Desplats, Paula; Shaked, Gideon M.; Sharikov, Yuriy; Mizuno, Hideya; Spencer, Brian; Rockenstein, Edward; Trejo, Margarita; Platoshyn, Oleksandr; Yuan, Jason X. -J.; Masliah, Eliezer
Mechanisms of Hybrid Oligomer Formation in the Pathogenesis of Combined Alzheimer's and Parkinson's Diseases
PLOS ONE, 3 Art. No. e3135, SEP 4 2008
abstract, full text, DOI:10.1371/journal.pone.0003135

Emperador, Agusti; Carrillo, Oliver; Rueda, Manuel; Orozco, Modesto
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
BIOPHYSICAL JOURNAL, 95:2127-2138, SEP 1 2008
abstract, full text, DOI:10.1529/biophysj.107.119115

Priya, M. Hamsa; Shah, J. K.; Asthagiri, D.; Paulaitis, M. E.
Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces
BIOPHYSICAL JOURNAL, 95:2219-2225, SEP 1 2008
abstract, full text, DOI:10.1529/biophysj.108.133553

Furini, Simone; Domene, Carmen; Rossi, Michele; Tartagni, Marco; Cavalcanti, Silvio
Model-based prediction of the alpha-hemolysin structure in the hexameric state
BIOPHYSICAL JOURNAL, 95:2265-2274, SEP 1 2008
abstract, full text, DOI:10.1529/biophysj.107.127019

Huang, Zhijian; Tajkhorshid, Emad
Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter
BIOPHYSICAL JOURNAL, 95:2292-2300, SEP 1 2008
abstract, full text, DOI:10.1529/biophysj.108.133421

Tantar, Alexandru-Adrian; Conilleau, Sebastien; Parent, Benjamin; Melab, Nouredine; Brillet, Lorraine; Roy, Sylvaine; Talbi, El-Ghazali; Horvath, Dragos
Docking and biomolecular simulations on computer grids: Status and trends
CURRENT COMPUTER-AIDED DRUG DESIGN, 4:235-249, SEP 2008
abstract, full text, DOI:10.2174/157340908785747438

Sadiq, S. Kashif; Wright, David; Watson, Sirrion J.; Zasada, Stefan J.; Stoica, Ileana; Coveney, Peter V.
Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1909-1919, SEP 2008
abstract, full text, DOI:10.1021/ci8000937

Miller, Benjamin T.; Singh, Rishi P.; Klauda, Jeffery B.; Hodoscek, Milan; Brooks, Bernard R.; Woodcock, H. Lee, I.I.I.
CHARMMing: A new, flexible web portal for CHARMM
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1920-1929, SEP 2008
abstract, full text, DOI:10.1021/ci800133b

Yago, Tadayuki; Lou, Jizhong; Wu, Tao; Yang, Jun; Miner, Jonathan J.; Coburn, Leslie; Lopez, Josd A.; Cruz, Miguel A.; Dong, Jing-Fei; McIntire, Larry V.; McEver, Rodger P.; Zhu, Cheng
Platelet glycoprotein lb alpha forms catch bonds with human WT vWF but not with type 2B von Willebrand disease vWF
JOURNAL OF CLINICAL INVESTIGATION, 118:3195-3207, SEP 2008
abstract, full text, DOI:10.1172/JCI35754

Amaro, Rommie E.; Baron, Riccardo; McCammon, J. Andrew
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 22:693-705, SEP 2008
abstract, full text, DOI:10.1007/s10822-007-9159-2

Yang, Qian; Du, Lupei; Wang, Xiaojian; Li, Minyong; You, Qidong
Modeling the binding modes of Kv1.5 potassium channel and blockers
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:178-187, SEP 2008
abstract, full text, DOI:10.1016/j.jmgm.2008.04.002

Mura, Cameron; McCammon, J. Andrew
Molecular dynamics of a kappa B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation
NUCLEIC ACIDS RESEARCH, 36:4941-4955, SEP 2008
abstract, full text, DOI:10.1093/nar/gkn473

De Fabritiis, Gianni; Geroult, Sebastien; Coveney, Peter V.; Waksman, Gabriel
Insights from the energetics binding at the domain-ligand of the Src SH2 domain of water interface
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:1290-1297, SEP 2008
abstract, full text, DOI:10.1002/prot.22027

Snyder, Stacy E.; Rotkin, Slava V.
Optical identification of a DNA-wrapped carbon nanotube: Signs of helically broken symmetry
SMALL, 4:1284-1286, SEP 2008
full text, DOI:10.1002/smll.200800114

Martinez, Leandro; Polikarpov, Igor; Skaf, Munir S.
Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach
JOURNAL OF PHYSICAL CHEMISTRY B, 112:10741-10751, AUG 28 2008
abstract, full text, DOI:10.1021/jp803403c

Guzman, Dora L.; Roland, Jason T.; Keer, Harindar; Kong, Yen Peng; Ritz, Thorsten; Yee, Albert; Guan, Zhibin
Using steered molecular dynamics simulations and single-molecule force spectroscopy to guide the rational design of biomimetic modular polymeric materials
POLYMER, 49:3892-3901, AUG 26 2008
abstract, full text, DOI:10.1016/j.polymer.2008.06.047

Caballero, Julio; Zamora, Claudia; Aguayo, Daniel; Yanez, Claudia; Gonzalez-Nilo, Fernando D.
Study of the interaction between progesterone and beta-cyclodextrin by electrochemical techniques and steered molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 112:10194-10201, AUG 21 2008
abstract, full text, DOI:10.1021/jp8006766

Stavrakoudis, Athanassios
Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit water
CHEMICAL PHYSICS LETTERS, 461:294-299, AUG 20 2008
abstract, full text, DOI:10.1016/j.cplett.2008.07.007

De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.
Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:10955-10962, AUG 20 2008
abstract, full text, DOI:10.1021/ja8005786

Homouz, Dirar; Perham, Michael; Samiotakis, Antonios; Cheung, Margaret S.; Wittung-Stafshede, Pernilla
Crowded, cell-like environment induces shape changes in aspherical protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:11754-11759, AUG 19 2008
abstract, full text, DOI:10.1073/pnas.0803672105

Dynowski, Marek; Schaaf, Gabriel; Loque, Dominique; Moran, Oscar; Ludewig, Uwe
Plant plasma membrane water channels conduct the signalling molecule H2O2
BIOCHEMICAL JOURNAL, 414:53-61, AUG 15 2008
abstract, full text, DOI:10.1042/BJ20080287

Moritsugu, Kei; Smith, Jeremy C.
REACH coarse-grained biomolecular simulation: Transferability between different protein structural classes
BIOPHYSICAL JOURNAL, 95:1639-1648, AUG 15 2008
abstract, full text, DOI:10.1529/biophysj.108.131714

Blood, Philip D.; Swenson, Richard D.; Voth, Gregory A.
Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations
BIOPHYSICAL JOURNAL, 95:1866-1876, AUG 15 2008
abstract, full text, DOI:10.1529/biophysj.107.121160

Vanacore, Roberto M.; Ham, Amy-Joan L.; Cartailler, Jean-Philippe; Sundaramoorthy, Munirathinam; Todd, Parvin; Pedchenko, Vadim; Sado, Yoshikazu; Borza, Dorin-Bogdan; Hudson, Billy G.
A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen - Structural basis for the crypticity of B cell epitopes
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:22737-22748, AUG 15 2008
abstract, full text, DOI:10.1074/jbc.M803451200

Beautrait, Alexandre; Karaboga, Arnaud S.; Souchet, Michel; Maigret, Bernard
Induced fit in liver X receptor beta: A molecular dynamics-based investigation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:873-882, AUG 15 2008
abstract, full text, DOI:10.1002/prot.21977

Coluci, V. R.; Sato, F.; Braga, S. F.; Skaf, M. S.; Galvao, D. S.
Rotational dynamics and polymerization of C(60) in C(60)-cubane crystals: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 064506, AUG 14 2008
abstract, full text, DOI:10.1063/1.2965885

Anzini, Maurizio; Braile, Carlo; Valenti, Salvatore; Cappelli, Andrea; Vomero, Salvatore; Marinelli, Luciana; Limongelli, Vittorio; Novellino, Ettore; Betti, Laura; Giannaccini, Gino; Lucacchini, Antonio; Ghelardini, Carla; Norcini, Monica; Makovec, Francesco; Giorgi, Gianluca; Fryer, R. Ian
Ethyl 8-fluoro-6-(3-nitrophenyl)-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carbox ylate as novel, highly potent, and safe antianxiety agent
JOURNAL OF MEDICINAL CHEMISTRY, 51:4730-4743, AUG 14 2008
abstract, full text, DOI:10.1021/jm8002944

Ding, Zhi-Chun; Chen, Dong; Ni, Feng-Yun; Zheng, Qi; Cai, Bin; Yao, Wen-Hua; Wang, Yang; Zhou, Guo-Ming; Huang, Zhong-Xian
Incorporation of a glycine within the conserved TCPCP motif of human neuronal growth inhibitory factor significantly reduces its bioactivity
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 372:779-784, AUG 8 2008
abstract, full text, DOI:10.1016/j.bbrc.2008.05.136

Yao, Yongneng; Harrison, Chris B.; Freddolino, Peter L.; Schulten, Klaus; Mayer, Mark L.
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors
EMBO JOURNAL, 27:2158-2170, AUG 6 2008
abstract, full text, TCBG publications, DOI:10.1038/emboj.2008.140

Murphy, Drew L.; Kosa, Jessica; Jaeger, Joachim; Sweasy, Joann B.
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding
BIOCHEMISTRY, 47:8048-8057, AUG 5 2008
abstract, full text, DOI:10.1021/bi702104y

Materese, Christopher Kroboth; Goldmon, Christa Charisse; Papoian, Garegin A.
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:10659-10664, AUG 5 2008
abstract, full text, DOI:10.1073/pnas.0801850105

Lin, Jianping; Seeman, Nadrian C.; Vaidehi, Nagarajan
Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface
BIOPHYSICAL JOURNAL, 95:1099-1107, AUG 1 2008
abstract, full text, DOI:10.1529/biophysj.107.119230

Chen, Zhongzhou; Lou, Jizhong; Zhu, Cheng; Schulten, Klaus
Flow-induced structural transition in the beta-switch region of glycoprotein Ib
BIOPHYSICAL JOURNAL, 95:1303-1313, AUG 1 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.108.132324

Greene, Dina N.; Garcia, Tzintzuni; Sutton, R. Bryan; Gernert, Kim M.; Benian, Guy M.; Oberhauser, Andres F.
Single-molecule force spectroscopy reveals a stepwise unfolding of Caenorhabditis elegans giant protein kinase domains
BIOPHYSICAL JOURNAL, 95:1360-1370, AUG 1 2008
abstract, full text, DOI:10.1529/biophysj.108.130237

Buku, Angeliki; Keselman, Inna; Lupyan, Dmitry; Mezei, Mihaly; Price, Joseph A.
Effective mast cell degranulating peptide inhibitors of the IgE/Fc epsilon RI receptor interaction
CHEMICAL BIOLOGY & DRUG DESIGN, 72:133-139, AUG 2008
abstract, full text, DOI:10.1111/j.1747-0285.2008.00684.x

Merino, Felipe; Guixe, Victoria
Specificity evolution of the ADP-dependent sugar kinase family - in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii
FEBS JOURNAL, 275:4033-4044, AUG 2008
abstract, full text, DOI:10.1111/j.1742-4658.2008.06544.x

Artigas, Rocio A.; Gonzalez, Angel; Riquelme, Erick; Carvajal, Cristian A.; Cattani, Andreina; Martinez-Aguayo, Alejandro; Kalergis, Alexis M.; Perez-Acle, Tomas; Fardella, Carlos E.
A novel adrenocorticotropin receptor mutation alters its structure and function, causing familial glucocorticoid deficiency
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 93:3097-3105, AUG 2008
abstract, full text, DOI:10.1210/jc.2008-0048

Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G.; Im, Wonpil
Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1859-1865, AUG 2008
abstract, full text, DOI:10.1002/jcc.20945

Bray, Jenelle K.; Goddard, William A., I.I.I.
The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:66-81, AUG 2008
abstract, full text, DOI:10.1016/j.jmgm.2008.02.006

Luan, Binquan; Aksimentiev, Aleksei
Electro-osmotic screening of the DNA charge in a nanopore
PHYSICAL REVIEW E, 78 Art. No. 021912, AUG 2008
abstract, full text, DOI:10.1103/PhysRevE.78.021912

Pedretti, Alessandro; Bocci, Elisabetta; Maggi, Roberto; Vistoli, Giulio
Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations
STEROIDS, 73:708-719, AUG 2008
abstract, full text, DOI:10.1016/j.steroids.2008.02.007

Joung, In Suk; Cheatham, Thomas E., I.I.I.
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:9020-9041, JUL 31 2008
abstract, full text, DOI:10.1021/jp8001614

Alexiadis, Alessio; Kassinos, Stavros
Molecular dynamic simulations of carbon nanotubes in CO2 atmosphere
CHEMICAL PHYSICS LETTERS, 460:512-516, JUL 30 2008
abstract, full text, DOI:10.1016/j.cplett.2008.06.050

Iori, F.; Corni, S.
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1656-1666, JUL 30 2008
abstract, full text, DOI:10.1002/jcc.20928

Coskuner, Orkid; Bergeron, Denis E.; Rincon, Luis; Hudgens, Jeffrey W.; Gonzalez, Carlos A.
Glycosidic linkage conformation of methyl-alpha-mannopyranoside
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 045102, JUL 28 2008
abstract, full text, DOI:10.1063/1.2958916

Hu, Xiaohui; Murata, Lauren B.; Weichsel, Andrzej; Brailey, Jacqueline L.; Roberts, Sue A.; Nighorn, Alan; Montfort, William R.
Allostery in recombinant soluble guanylyl cyclase from Manduca sexta
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:20968-20977, JUL 25 2008
abstract, full text, DOI:10.1074/jbc.M801501200

Wang, Boyang; Kral, Petr
Dragging of polarizable nanodroplets by distantly solvated ions
PHYSICAL REVIEW LETTERS, 101 Art. No. 046103, JUL 25 2008
abstract, full text, DOI:10.1103/PhysRevLett.101.046103

Lugli, Francesca; Zerbetto, Francesco
Atomistic simulation of "drop-on-demand" inkjet dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 112:10616-10621, JUL 24 2008
abstract, full text, DOI:10.1021/jp075482g

Domene, Carmen; Klein, Michael L.; Branduardi, Davide; Gervasio, Francesco L.; Parrinello, Michele
Conformational changes and gating at the selectivity filter of potassium channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:9474-9480, JUL 23 2008
abstract, full text, DOI:10.1021/ja801792g

Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.
Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization
CHEMICAL PHYSICS LETTERS, 460:284-288, JUL 20 2008
abstract, full text, DOI:10.1016/j.cplett.2008.05.060

Mao, Yanli; Tero, Ryugo; Imai, Yosuke; Hoshino, Tyuji; Urisu, Tsuneo
The morphology of GM1(x)/SM(0.6-x)/Chol(0.4) planar bilayers supported on SiO(2) surfaces
CHEMICAL PHYSICS LETTERS, 460:289-294, JUL 20 2008
abstract, full text, DOI:10.1016/j.cplett.2008.05.097

Verkhivker, Gennady; Tiana, Guido; Camilloni, Carlo; Provasi, Davide; Broglia, Ricardo A.
Atomistic simulations of the HIV-1 protease folding inhibition
BIOPHYSICAL JOURNAL, 95:550-562, JUL 15 2008
abstract, full text, DOI:10.1529/biophysj.107.127621

Isin, Basak; Schulten, Klaus; Tajkhorshid, Emad; Bahar, Ivet
Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes
BIOPHYSICAL JOURNAL, 95:789-803, JUL 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.120691

Voltz, Karine; Trylska, Joanna; Tozzini, Valentina; Kurkal-Siebert, Vandana; Langowski, Joerg; Smith, Jeremy
Coarse-grained force field for the nucleosome from self-consistent multiscaling
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1429-1439, JUL 15 2008
abstract, full text, DOI:10.1002/jcc.20902

Wang, Yi; Tajkhorshid, Emad
Electrostatic funneling of substrate in mitochondrial inner membrane carriers
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:9598-9603, JUL 15 2008
abstract, full text, DOI:10.1073/pnas.0801786105

Eshet, Hagai; Bruneval, Fabien; Parrinello, Michele
New Lennard-Jones metastable phase
JOURNAL OF CHEMICAL PHYSICS, 129 Art. No. 026101, JUL 14 2008
full text, DOI:10.1063/1.2953327

Kim, Kyoung-Yun; Nascimento, Alessandro S.; Golubev, Alexander M.; Polikarpov, Igor; Kim, Chung-Sei; Kang, Su-Il; Kim, Su-Il
Catalytic mechanism of inulinase from Arthrobacter sp S37
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 371:600-605, JUL 11 2008
abstract, full text, DOI:10.1016/j.bbrc.2008.03.126

Cheng, Lily S.; Amaro, Romanic E.; Xu, Dong; Li, Wilfred W.; Arzberger, Peter W.; McCammon, J. Andrew
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
JOURNAL OF MEDICINAL CHEMISTRY, 51:3878-3894, JUL 10 2008
abstract, full text, DOI:10.1021/jm8001197

Dynowski, Marek; Mayer, Maria; Moran, Oscar; Ludewig, Uwe
Molecular determinants of ammonia and urea conductance in plant aquaporin homologs
FEBS LETTERS, 582:2458-2462, JUL 9 2008
abstract, full text, DOI:10.1016/j.febslet.2008.06.012

Brazdova, V.; Bowler, D. R.
Automatic data distribution and load balancing with space-filling curves: implementation in CONQUEST
JOURNAL OF PHYSICS-CONDENSED MATTER, 20 Art. No. 275223, JUL 9 2008
abstract, full text, DOI:10.1088/0953-8984/20/27/275223

Zhu, Hui; May, Volkhard; Roeder, Beate
Mixed quantum classical simulations of electronic excitation energy transfer: The pheophorbide-a DAB dendrimer P-4 in solution
CHEMICAL PHYSICS, 351:117-128, JUL 3 2008
abstract, full text, DOI:10.1016/j.chemphys.2008.04.009

Budi, Akin; Legge, F. Sue; Treutlein, Herbert; Yarovsky, Irene
Comparative study of insulin chain-b in isolated and monomeric environments under external stress
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7916-7924, JUL 3 2008
abstract, full text, DOI:10.1021/jp800350v

Andreozzi, Francesco; Formoso, Gloria; Prudente, Sabrina; Hribal, Marta Letizia; Pandolfi, Assunta; Bellacchio, Emanuele; Di Silvestre, Sara; Trischitta, Vincenzo; Consoli, Agostino; Sesti, Giorgio
TRIB3 r84 variant is associated with impaired insulin-mediated nitric oxide production in human endothelial cells
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 28:1355-1360, JUL 2008
abstract, full text, DOI:10.1161/ATVBAHA.108.162883

Diao, Jiankuai; Tajkhorshid, Emad
Indirect role of Ca2+ in the assembly of extracellular matrix proteins
BIOPHYSICAL JOURNAL, 95:120-127, JUL 1 2008
abstract, full text, DOI:10.1529/biophysj.108.129106

Iskandarsyah; Tejo, Bimo A.; Tambunan, Usman S. F.; Verkhivker, Gennady; Siahaan, Teruna J.
Structural modifications of ICAM-1 cyclic peptides to improve the activity to inhibit heterotypic adhesion of T cells
CHEMICAL BIOLOGY & DRUG DESIGN, 72:27-33, JUL 2008
abstract, full text, DOI:10.1111/j.1747-0285.2008.00676.x

Shaw, David E.; Deneroff, Martin M.; Dror, Ron O.; Kuskin, Jeffrey S.; Larson, Richard H.; Salmon, John K.; Young, Cliff; Batson, Brannon; Bowers, Kevin J.; Chao, Jack C.; Eastwood, Michael P.; Gagliardo, Joseph; Grossman, J. P.; Ho, C. Richard; Ierardi, Douglas J.; Kolossvary, Istvan; Klepeis, John L.; Layman, Timothy; Mcleavey, Christine; Moraes, Mark A.; Mueller, Rolf; Priest, Edward C.; Shan, Yibing; Spengler, Jochen; Theobald, Michael; Towles, Brian; Wang, Stanley C.
Anton, a special-purpose machine for molecular dynamics simulation
COMMUNICATIONS OF THE ACM, 51:91-97, JUL 2008
abstract, full text, DOI:10.1145/1364782.1364802

Verstraelen, T.; Van Speybroeck, V.; Waroquier, M.
ZEOBUILDER: A GUI toolkit for the construction of complex molecular structures on the nanoscale with building blocks
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1530-1541, JUL 2008
abstract, full text, DOI:10.1021/ci8000748

Anishkin, Andriy; Kamaraju, Kishore; Sukharev, Sergei
Mechanosensitive channel MscS in the open state: Modeling of the transition, explicit simulations, and experimental measurements of conductance
JOURNAL OF GENERAL PHYSIOLOGY, 132:67-83, JUL 2008
abstract, full text, DOI:10.1085/jgp.200810000

Blanchette, Craig D.; Law, Richard; Benner, W. Henry; Pesavento, Joseph B.; Cappuccio, Jenny A.; Walsworth, Vicki; Kuhn, Edward A.; Corzett, Michele; Chromy, Brett A.; Segelke, Brent W.; Coleman, Matthew A.; Bench, Graham; Hoeprich, Paul D.; Sulchek, Todd A.
Quantifying size distributions of nanolipoprotein particles with single-particle analysis and molecular dynamic simulations
JOURNAL OF LIPID RESEARCH, 49:1420-1430, JUL 2008
abstract, full text, DOI:10.1194/jlr.M700586-JLR200

Cruzeiro, L.
Proteins multi-funnel energy landscape and misfolding diseases
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 21:549-554, JUL-AUG 2008
abstract, full text, DOI:10.1002/poc.1315

Marksteiner, Markus; Haslinger, Philipp; Ulbricht, Hendrik; Sclafani, Michele; Oberhofer, Harald; Dellago, Christoph; Arndt, Markus
Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 19:1021-1026, JUL 2008
abstract, full text, DOI:10.1016/j.jasms.2008.04.028

Sonoda, Milton T.; Martinez, Leandro; Webb, Paul; Skaf, Munir S.; Polikarpov, Igor
Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations
MOLECULAR ENDOCRINOLOGY, 22:1565-1578, JUL 2008
abstract, full text, DOI:10.1210/me.2007-0501

Jo, Sunhwan; Vargyas, Miklos; Vasko-Szedlar, Judit; Roux, Benoit; Im, Wonpil
PBEQ-Solver for online visualization of electrostatic potential of biomolecules
NUCLEIC ACIDS RESEARCH, 36:W270-W275, JUL 2008
abstract, full text, DOI:10.1093/nar/gkn314

Jang, Hyunbum; Michaud-Agrawal, Naveen; Johnston, Jennifer M.; Woolf, Thomas B.
How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:299-312, JUL 2008
abstract, full text, DOI:10.1002/prot.21925

Zou, Jun; Wang, Yi-Dong; Ma, Fan-Xin; Xiang, Ming-Li; Shi, Bing; Wei, Yu-Quan; Yang, Sheng-Yong
Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:323-332, JUL 2008
abstract, full text, DOI:10.1002/prot.21928

Nilsson, Lina M.; Thomas, Wendy E.; Sokurenko, Evgeni V.; Vogel, Viola
Beyond induced-fit receptor-ligand interactions: Structural changes that can significantly extend bond lifetimes
STRUCTURE, 16:1047-1058, JUL 2008
abstract, full text, DOI:10.1016/j.str.2008.03.012

Nalian, Armen; Iakhiaev, Alexei V.
Possible mechanisms contributing to oxidative inactivation of activated protein C: Molecular dynamics study
THROMBOSIS AND HAEMOSTASIS, 100:18-25, JUL 2008
abstract, full text, DOI:10.1160/TH07-12-0750

Noid, W. G.; Chu, Jhih-Wei; Ayton, Gary S.; Krishna, Vinod; Izvekov, Sergei; Voth, Gregory A.; Das, Avisek; Andersen, Hans C.
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 244114, JUN 28 2008
abstract, full text, DOI:10.1063/1.2938860

Beckham, Gregg T.; Peters, Baron; Trout, Bernhardt L.
Evidence for a size dependent nucleation mechanism in solid state polymorph transformations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7460-7466, JUN 26 2008
abstract, full text, DOI:10.1021/jp710192u

Rodriguez, Javier; Hernan Rico, Daniel; Domenianni, Luis; Laria, Daniel
Confinement of polar solvents within beta-cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7522-7529, JUN 26 2008
abstract, full text, DOI:10.1021/jp711609q

Lechuga, Javier; Drikakis, Dimitris; Pal, Sandip
Molecular dynamics study of the interaction of a shock wave with a biological membrane
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 57:677-692, JUN 20 2008
abstract, full text, DOI:10.1002/fld.1588

Kniazeff, Julie; Shi, Lei; Loland, Claus J.; Javitch, Jonathan A.; Weinstein, Harel; Gether, Ulrik
An intracellular interaction network regulates conformational transitions in the dopamine transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:17691-17701, JUN 20 2008
abstract, full text, DOI:10.1074/jbc.M800475200

Shi, Lei; Quick, Matthias; Zhao, Yongfang; Weinstein, Harel; Javitch, Jonathan A.
The mechanism of a neurotransmitter : sodium symporter - Inward release of Na+ and substrate is triggered by substrate in a second binding site
MOLECULAR CELL, 30:667-677, JUN 20 2008
abstract, full text, DOI:10.1016/j.molcel.2008.05.008

Zhao, Xiongce
Interaction of C-60 derivatives and ssDNA from simulations
JOURNAL OF PHYSICAL CHEMISTRY C, 112:8898-8906, JUN 19 2008
abstract, full text, DOI:10.1021/jp801180w

Sotomayor, Marcos; Schulten, Klaus
The allosteric role of the Ca(2+) switch in adhesion and elasticity of C-cadherin
BIOPHYSICAL JOURNAL, 94:4621-4633, JUN 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.125591

Wise, John G.; Vogel, Pia D.
Subunit b-dimer of the Escherichia coli ATP synthase can form left-handed coiled-coils
BIOPHYSICAL JOURNAL, 94:5040-5052, JUN 15 2008
abstract, full text, DOI:10.1529/biophysj.107.121012

Shih, Amy Y.; Sligar, Stephen G.; Schulten, Klaus
Molecular models need to be tested: The case of a solar flares discoidal HDL model
BIOPHYSICAL JOURNAL, 94:L87-L89, JUN 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.108.131581

Krippner-Heidenreich, Anja; Grunwald, Ingo; Zimmermann, Gudrun; Kuehnle, Marie; Gerspach, Jeannette; Sterns, Theobald; Shnyder, Steve D.; Gill, Jason H.; Maennel, Daniela N.; Pfizenmaier, Klaus; Scheurich, Peter
Single-chain TNF, a TNF derivative with enhanced stability and antitumoral activity
JOURNAL OF IMMUNOLOGY, 180:8176-8183, JUN 15 2008
abstract, full text

Prentiss, Michael C. -; Wales, David J.; Wolynes, Peter G.
Protein structure prediction using basin-hopping
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 225106, JUN 14 2008
abstract, full text, DOI:10.1063/1.2929833

Espinoza-Fonseca, L. Michel; Garcia-Machorro, Jazmin
Aromatic-aromatic interactions in the formation of the MDM2-p53 complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 370:547-551, JUN 13 2008
abstract, full text, DOI:10.1016/j.bbrc.2008.03.053

Henin, Jerome; Shinoda, Wataru; Klein, Michael L.
United-atom acyl chains for CHARMM phospholipids
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7008-7015, JUN 12 2008
abstract, full text, DOI:10.1021/jp800687p

Lee, Tai-Sung; York, Darrin M.
Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:7168-+, JUN 11 2008
abstract, full text, DOI:10.1021/ja711242b

Pincus, David L.; Hyeon, Changbong; Thirumalai, D.
Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:7364-7372, JUN 11 2008
abstract, full text, DOI:10.1021/ja078326w

Casanovas, Jordi; Zanuy, David; Aleman, Carlos
Structural and electronic properties of crown ether functionalized oligothiophenes
MACROMOLECULES, 41:3919-3924, JUN 10 2008
abstract, full text, DOI:10.1021/ma800174b

Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Nussinov, Ruth
Annular structures as intermediates in fibril formation of Alzheimer A beta(17-42)
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6856-6865, JUN 5 2008
abstract, full text, DOI:10.1021/jp711335b

Liu, Ming; Sun, TingGuang; Hu, JianPing; Chen, WeiZu; Wang, CunXin
Study on the mechanism of the BtuF periplasmic-binding protein for vitamin B-12
BIOPHYSICAL CHEMISTRY, 135:19-24, JUN 2008
abstract, full text, DOI:10.1016/j.bpc.2008.02.017

Vemparala, Satyavani; Domene, Carmen; Klein, Michael L.
Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis
BIOPHYSICAL JOURNAL, 94:4260-4269, JUN 1 2008
abstract, full text, DOI:10.1529/biophysj.107.119958

Ding, Shi-You; Xu, Qi; Crowley, Michael; Zeng, Yining; Nimlos, Mark; Lamed, Raphael; Bayer, Edward A.; Himmel, Michael E.
A biophysical perspective on the cellulosome: new opportunities for biomass conversion
CURRENT OPINION IN BIOTECHNOLOGY, 19:218-227, JUN 2008
abstract, full text, DOI:10.1016/j.copbio.2008.04.008

DeMarco, Mari L.; Woods, Robert J.
Structural glycobiology: A game of snakes and ladders
GLYCOBIOLOGY, 18:426-440, JUN 2008
abstract, full text, DOI:10.1093/glycob/cwn026

Scrofano, Ronald; Gokhale, Maya B.; Trouw, Frans; Prasanna, Viktor K.
Accelerating molecular dynamics simulations with reconfigurable computers
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 19:764-778, JUN 2008
abstract, full text, DOI:10.1109/TPDS.2007.70777

Di Rocco, Giulia; Battistuzzi, Gianantonio; Borsari, Marco; De Rienzo, Francesca; Ranieri, Antonio; Tutino, Maria Luisa; Sola, Marco
Cloning, expression and physicochemical characterization of a di-heme cytochrome c(4) from the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC 125
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 13:789-799, JUN 2008
abstract, full text, DOI:10.1007/s00775-008-0366-7

Jojart, Balazs; Kiss, Robert; Viskolcz, Bela; Keseru, Gyoergy M.
Activation mechanism of the human histamine H4 receptor - An explicit membrane molecular dynamics simulation study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1199-1210, JUN 2008
abstract, full text, DOI:10.1021/ci700450w

Rodriguez-Ropero, Francisco; Zanuy, David; Aleman, Carlos
Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1233-1241, JUN 2008
abstract, full text, DOI:10.1002/jcc.20882

Fernandez-Ballester, G.; Ferrer-Montiel, A.
Molecular modeling of the full-length human TRPV1 channel in closed and desensitized states
JOURNAL OF MEMBRANE BIOLOGY, 223:161-172, JUN 2008
abstract, full text, DOI:10.1007/s00232-008-9123-7

Kimura, S. Roy; Tebben, Andrew J.; Langley, David R.
Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1919-1929, JUN 2008
abstract, full text, DOI:10.1002/prot.21906

Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma
Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1995-2011, JUN 2008
abstract, full text, DOI:10.1002/prot.21878

Witt, Magdalena; Slusarz, Magdalena J.; Ciarkowski, Jerzy
Molecular modeling of Vasopressin V2 Receptor tetramer in hydrated lipid membrane
QSAR & COMBINATORIAL SCIENCE, 27:684-693, JUN 2008
abstract, full text, DOI:10.1002/qsar.200730082

Gorfe, Alemayehu A.; Grant, Barry J.; McCammon, J. Andrew
Mapping the nucleotide and isoform-dependent structural and dynamical features of ras proteins
STRUCTURE, 16:885-896, JUN 2008
abstract, full text, DOI:10.1016/j.str.2008.03.009

Pan, Yongping; Nussinov, Ruth
P53-induced DNA bending: The interplay between p53-ONA and p53-p53 interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6716-6724, MAY 29 2008
abstract, full text, DOI:10.1021/jp800680w

Chang, Chia-en A.; McLaughlin, William A.; Baron, Riccardo; Wang, Wei; McCammon, J. Andrew
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:7456-7461, MAY 27 2008
abstract, full text, DOI:10.1073/pnas.0800452105

Sikdar, Debashis; Pradhan, Shashindra M.; Katti, Dinesh R.; Katti, Kalpana S.; Mohanty, Bedabibhas
Altered phase model for polymer clay nanocomposites
LANGMUIR, 24:5599-5607, MAY 20 2008
abstract, full text, DOI:10.1021/la800583h

Freddolino, Peter L.; Liu, Feng; Gruebele, Martin; Schulten, Klaus
Ten-microsecond molecular dynamics simulation of a fast-folding WW domain
BIOPHYSICAL JOURNAL, 94:L75-L77, MAY 15 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.108.131565

Minh, David D. L.; McCammon, J. Andrew
Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5892-5897, MAY 15 2008
abstract, full text, DOI:10.1021/jp0733163

Klauda, Jeffery B.; Eldho, Nadukkudy V.; Gawrisch, Klaus; Brooks, Bernard R.; Pastor, Richard W.
Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5924-5929, MAY 15 2008
abstract, full text, DOI:10.1021/jp075641w

Wang, Jianping; Zhuang, Wei; Mukamel, Shaul; Hochstrasser, Robin
Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5930-5937, MAY 15 2008
abstract, full text, DOI:10.1021/jp075683k

Lopez, Carlos F.; Darst, Richard K.; Rossky, Peter J.
Mechanistic elements of protein cold denaturation
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5961-5967, MAY 15 2008
abstract, full text, DOI:10.1021/jp075928t

Oliveira, Leandro C.; Schug, Alexander; Onuchic, Jose N.
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: A detailed investigation of several reduced models
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6131-6136, MAY 15 2008
abstract, full text, DOI:10.1021/jp0769835

Zanuy, David; Aleman, Carlos
Simulation of the self-assembly of poly(alpha-glutamate) and dodecyltrimethylammonium: Diffusive role of the surfactant cations
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 46:917-924, MAY 15 2008
abstract, full text, DOI:10.1002/polb.21426

Lim, Melvin C. G.; Pei, Qx; Zhong, Z. W.
Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 387:3111-3120, MAY 15 2008
abstract, full text, DOI:10.1016/j.physa.2008.01.111

Venkatramani, Ravindra; Radhakrishnan, Ravi
Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermaphilus
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1360-1372, MAY 15 2008
abstract, full text, DOI:10.1002/prot.21824

Krishnan, Arun; Giuliani, Alessandro; Zbilut, Joseph P.; Tomita, Masaru
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
PLOS ONE, 3 Art. No. e2149, MAY 14 2008
abstract, full text, DOI:10.1371/journal.pone.0002149

Zhao, Xiongce; Krstic, Predrag S.
A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap
NANOTECHNOLOGY, 19 Art. No. 195702, MAY 14 2008
abstract, full text, DOI:10.1088/0957-4484/19/19/195702

Bellesia, Giovanni; Fedorov, Maxim V.; Timoshenko, Edward G.
Structural transitions in model beta-sheet tapes
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 195105, MAY 12 2008
abstract, full text, DOI:10.1063/1.2909550

Veluraja, K.; Seethalakshmi, Arunachalam N.
Dynamics of sialyl Lewis(a) in aqueous solution and prediction of the structure of the sialyl Lewis(a)-SelectinE complex
JOURNAL OF THEORETICAL BIOLOGY, 252:15-23, MAY 7 2008
abstract, full text, DOI:10.1016/j.jtbi.2007.12.024

Shushkov, Philip G.; Tzvetanov, Stanislav A.; Ivanova, Anela N.; Tadjer, Alia V.
Dielectric properties tangential to the interface in model insoluble monolayers: Theoretical assessment
LANGMUIR, 24:4615-4624, MAY 6 2008
abstract, full text, DOI:10.1021/la703616c

Fushinobu, Shinya; Mertz, Blake; Hill, Anthony D.; Hidaka, Masafurni; Kitaoka, Motomitsu; Reilly, Peter J.
Computational analyses of the conformational itinerary along the reaction pathway of GH94 cellobiose phosphorylase
CARBOHYDRATE RESEARCH, 343:1023-1033, MAY 5 2008
abstract, full text, DOI:10.1016/j.carres.2008.02.026

Pedretti, Alessandro; Marconi, Cristina; Bolchi, Cristiano; Fumagalli, Laura; Ferrara, Rossana; Pallavicini, Marco; Valoti, Ermanno; Vistoli, Giulio
Modelling of full-length human alpha 4 beta 2 nicotinic receptor by fragmental approach and analysis of its binding modes
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 369:648-653, MAY 2 2008
abstract, full text, DOI:10.1016/j.bbrc.2008.02.080

Canagarajah, Bertram J.; Hummer, Gerhard; Prinz, William A.; Hurley, James H.
Dynamics of cholesterol exchange in the oxysterol binding protein family
JOURNAL OF MOLECULAR BIOLOGY, 378:737-748, MAY 2 2008
abstract, full text, DOI:10.1016/j.jmb.2008.01.075

Chen, Xin; Wu, Tao; Wang, Qi; Shen, Jia-Wei
Shield effect of silicate on adsorption of proteins onto silicon-doped hydroxyapatite (100) surface
BIOMATERIALS, 29:2423-2432, MAY 2008
abstract, full text, DOI:10.1016/j.biomaterials.2008.02.002

Yogurtcu, Osman N.; Erdemli, S. Bora; Nussinov, Ruth; Turkay, Metin; Keskin, Ozlem
Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
BIOPHYSICAL JOURNAL, 94:3475-3485, MAY 1 2008
abstract, full text, DOI:10.1529/biophysj.107.114835

Alexiadis, Alessio; Kassinos, Stavros
Influence of water model and nanotube rigidity on the density of water in carbon nanotubes
CHEMICAL ENGINEERING SCIENCE, 63:2793-2797, MAY 2008
abstract, full text, DOI:10.1016/j.ces.2008.03.004

Bebenek, Katarzyna; Garcia-Diaz, Miguel; Foley, Meredith C.; Pedersen, Lars C.; Schlick, Tamar; Kunkel, Thomas A.
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda
EMBO REPORTS, 9:459-464, MAY 2008
abstract, full text, DOI:10.1038/embor.2008.33

Gentilucci, Luca; Squassabia, Federico; Demarco, Rossella; Artali, Roberto; Cardillo, Giuliana; Tolomelli, Alessandra; Spampinato, Santi; Bedini, Andrea
Investigation of the interaction between the atypical agonist c[YpwFG] and MOR
FEBS JOURNAL, 275:2315-2337, MAY 2008
abstract, full text, DOI:10.1111/j.1742-4658.2008.06386.x

Zheng, Jie; Ma, Buyong; Chang, Yung; Nussinov, Ruth
Molecular dynamics simulations of Alzheimer A beta(40) elongation and lateral association
FRONTIERS IN BIOSCIENCE, 13:3919-3930, MAY 2008
abstract, full text, DOI:10.2741/2980

Bellesia, Giovanni; Shea, Joan-Emma
Structure and stability of amyloid fibrils formed from synthetic beta-peptides
FRONTIERS IN BIOSCIENCE, 13:6957-6965, MAY 2008
abstract, full text, DOI:10.2741/3202

Project, Elad; Nachliel, Esther; Gutman, Menachem
Parameterization of Ca+2-protein interactions for molecular dynamics simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1163-1169, MAY 2008
abstract, full text, DOI:10.1002/jcc.20876

Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A.
General purpose molecular dynamics simulations fully implemented on graphics processing units
JOURNAL OF COMPUTATIONAL PHYSICS, 227:5342-5359, MAY 1 2008
abstract, full text, DOI:10.1016/j.jcp.2008.01.047

Mathew, Damien C.; Luthey-Schulten, Zaida
On the physical basis of the amino acid polar requirement
JOURNAL OF MOLECULAR EVOLUTION, 66:519-528, MAY 2008
abstract, full text, DOI:10.1007/s00239-008-9073-9

Yu, Yanmin; Cai, Wensheng; Chipot, Christophe; Sun, Tingting; Shao, Xueguang
Spatial arrangement of alpha-cyclodextrins in a rotaxane. Insights from free-energy calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5268-5271, MAY 1 2008
abstract, full text, DOI:10.1021/jp711413a

Economou, I. G.; Karakatsani, E. K.; Logotheti, G. -E.; Ramos, J.; Vanin, A. A.
Multi-scale modeling of structure, dynamic and thermodynamic properties of imidazolium-based ionic liquids: Ab initio DFT calculations, molecular simulation and equation of state predictions
OIL & GAS SCIENCE AND TECHNOLOGY-REVUE D IFP ENERGIES NOUVELLES, 63:283-293, MAY-JUN 2008
abstract, full text, DOI:10.2516/ogst:2008007

Gu, Yongfeng; VanCourt, Tom; Herbordt, Martin C.
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
PARALLEL COMPUTING, 34:261-277, MAY 2008
abstract, full text, DOI:10.1016/j.parco.2008.01.007

Owens, John D.; Houston, Mike; Luebke, David; Green, Simon; Stone, John E.; Phillips, James C.
GPU computing
PROCEEDINGS OF THE IEEE, 96:879-899, MAY 2008
abstract, full text, DOI:10.1109/JPROC.2008.917757

Delgado-Buscalioni, R.; Coveney, P. V.; De Fabritiis, G.
Towards multi-scale modelling of complex liquids using hybrid particle-continuum schemes
PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART C-JOURNAL OF MECHANICAL ENGINEERING SCIENCE, 222:769-776, MAY 2008
abstract, full text, DOI:10.1243/09544062JMES746

Harms, Michael J.; Schlessman, Jamie L.; Chimenti, Michael S.; Sue, Gloria R.; Damjanovic, Ana; Garcia-Moreno E, Bertrand
A buried lysine that titrates with a normal pK(a): Role of conformational flexibility at the protein-water interface as a determinant of pK(a)values
PROTEIN SCIENCE, 17:833-845, MAY 2008
abstract, full text, DOI:10.1110/ps.073397708

Wang, Xu; Bansal, Sonal; Jiang, Mei; Prestegard, James H.
RDC-assisted modeling of symmetric protein homo-oligomers
PROTEIN SCIENCE, 17:899-907, MAY 2008
abstract, full text, DOI:10.1110/ps.073395108

Cheng, Mary Hongying; Coalson, Rob D.; Cascio, Michael
Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:972-981, MAY 1 2008
abstract, full text, DOI:10.1002/prot.21784

Trabuco, Leonardo G.; Villa, Elizabeth; Mitra, Kakoli; Frank, Joachim; Schulten, Klaus
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
STRUCTURE, 16:673-683, MAY 2008
abstract, full text, TCBG publications, DOI:10.1016/j.str.2008.03.005

Jacob, Christoph R.; Neugebauer, Johannes; Visscher, Lucas
Software news and update a flexible implementation of frozen-density embedding for use in multilevel Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1011-1018, APR 30 2008
abstract, full text, DOI:10.1002/jcc.20861

Kaila, Ville R. I.; Verkhovsky, Michael I.; Hummer, Gerhard; Wikstrom, Marten
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:6255-6259, APR 29 2008
abstract, full text, DOI:10.1073/pnas.0800770105

Qvist, Johan; Davidovic, Monika; Hamelberg, Donald; Halle, Bertil
A dry ligand-binding cavity in a solvated protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:6296-6301, APR 29 2008
abstract, full text, DOI:10.1073/pnas.0709844105

Zhang Chi; Wu Wei-Bin; Lu Yu-Jing; Gu Lian-Quan; Huang Zhi-Shu
Molecular modeling studies of interactions between quindoline derivatives and G-quadruplex
ACTA CHIMICA SINICA, 66:953-958, APR 28 2008
abstract, full text

Bastug, Turgut; Chen, Po-Chia; Patra, Swarna M.; Kuyucak, Serdar
Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 155104, APR 21 2008
abstract, full text, DOI:10.1063/1.2904461

Zhu, Hui; May, Volkhard; Roeder, Beate; Renger, Thomas
Linear absorbance of the pheophorbide-a butanediamine dendrimer P(4) in solution: Computational studies using a mixed quantum classical methodology
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 154905, APR 21 2008
abstract, full text, DOI:10.1063/1.2890721

Tornatore, Laura; Marasco, Daniela; Dathan, Nina; Vitale, Rosa Maria; Benedetti, Ettore; Papa, Salvatore; Franzoso, Guido; Ruvo, Menotti; Monti, Simona Maria
Gadd45 beta forms a homodimeric complex that binds tightly to MKK7
JOURNAL OF MOLECULAR BIOLOGY, 378:97-111, APR 18 2008
abstract, full text, DOI:10.1016/j.jmb.2008.01.074

Dong, Xiu-Li; Zhou, Hai-Long; Wu, Tao; Wang, Qi
Behavior regulation of adsorbed proteins via hydroxyapatite surface texture control
JOURNAL OF PHYSICAL CHEMISTRY B, 112:4751-4759, APR 17 2008
abstract, full text, DOI:10.1021/jp0768672

Kang, Yu; Wang, Qi; Liu, Ying-Chun; Wu, Tao; Chen, Qu; Guan, Wen-Jun
Dynamic mechanism of collagen-like peptide encapsulated into carbon nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 112:4801-4807, APR 17 2008
abstract, full text, DOI:10.1021/jp711392g

Gonzalez, Angel; Duran, Leonardo Sepulveda; Araya-Secchi, Raul; Garate, Jose A.; Pessoa-Mahana, C. David; Lagos, Carlos F.; Perez-Acle, Tomas
Computational modeling study of functional microdomains in cannabinoid receptor type 1
BIOORGANIC & MEDICINAL CHEMISTRY, 16:4378-4389, APR 15 2008
abstract, full text, DOI:10.1016/j.bmc.2008.02.070

Klauda, Jeffery B.; Roberts, Mary F.; Redfield, Alfred G.; Brooks, Bernard R.; Pastor, Richard W.
Rotation of lipids in membranes: Molecular dynamics simulation, P-31 spin-lattice relaxation, and rigid-body dynamics
BIOPHYSICAL JOURNAL, 94:3074-3083, APR 15 2008
abstract, full text, DOI:10.1529/biophysj.107.121806

Lee, Tai-Sung; Potts, Steven J.; Kantarjian, Hagop; Cortes, Jorge; Giles, Francis; Albitar, Maher
Molecular basis explanation for imatinib resistance of BCR-ABL due to T3151 and P-loop mutations from molecular dynamics simulations
CANCER, 112:1744-1753, APR 15 2008
abstract, full text, DOI:10.1002/cncr.23355

Grohmann, Dina; Corradi, Valentina; Elbasyouny, Mira; Baude, Annika; Horenkamp, Florian; Laufer, Sandra D.; Manetti, Fabrizio; Botta, Maurizio; Restle, Tobias
Small molecule inhibitors targeting HIV-1 reverse transcriptase dimerization
CHEMBIOCHEM, 9:916-922, APR 14 2008
abstract, full text, DOI:10.1002/cbic.200700669

Darve, Eric; Rodriguez-Gomez, David; Pohorille, Andrew
Adaptive biasing force method for scalar and vector free energy calculations
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 144120, APR 14 2008
abstract, full text, DOI:10.1063/1.2829861

Eargle, John; Black, Alexis A.; Sethi, Anurag; Trabuco, Leonardo G.; Luthey-Schulten, Zaida
Dynamics of recognition between tRNA and elongation factor Tu
JOURNAL OF MOLECULAR BIOLOGY, 377:1382-1405, APR 11 2008
abstract, full text, DOI:10.1016/j.jmb.2008.01.073

Castro-Camus, E.; Johnston, M. B.
Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy
CHEMICAL PHYSICS LETTERS, 455:289-292, APR 10 2008
abstract, full text, DOI:10.1016/j.cplett.2008.02.084

Sharma, Vivek; Wikstroem, Marten; Laakkonen, Liisa
Modeling the active-site structure of the cbb(3)-type oxidase from Rhodobacter sphaeroides
BIOCHEMISTRY, 47:4221-4227, APR 8 2008
abstract, full text, DOI:10.1021/bi702088r

Coskuner, Orkid; Bergeron, Denis E.; Rincon, Luis; Hudgens, Jeffrey W.; Gonzalez, Carlos A.
Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe-III
JOURNAL OF PHYSICAL CHEMISTRY A, 112:2940-2947, APR 3 2008
abstract, full text, DOI:10.1021/jp711759q

Langham, Allison A.; Ahmad, Abdallah Sayyed; Kaznessis, Yiannis N.
On the nature of antimicrobial activity: A model for protegrin-1 pores
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:4338-4346, APR 2 2008
abstract, full text, DOI:10.1021/ja0780380

Potoff, Jeffrey J.; Issa, Zeena; Manke, Charles W., Jr.; Jena, Bhanu P.
Ca2+-dimethylphosphate complex formation: Providing insight into Ca2+-mediated local dehydration and membrane fusion in cells
CELL BIOLOGY INTERNATIONAL, 32:361-366, APR 2008
abstract, full text, DOI:10.1016/j.cellbi.2008.03.002

Alexiadis, Alessio; Kassinos, Stavros
The density of water in carbon nanotubes
CHEMICAL ENGINEERING SCIENCE, 63:2047-2056, APR 2008
abstract, full text, DOI:10.1016/j.ces.2007.12.035

Aldini, Giancarlo; Vistoli, Giulio; Regazzoni, Luca; Gamberoni, Luca; Facino, Roberto Maffei; Yamaguchi, Satoru; Uchida, Koji; Carini, Marina
Albumin is the main nucleophilic target of human plasma: A protective role against pro-atherogenic electrophilic reactive carbonyl species?
CHEMICAL RESEARCH IN TOXICOLOGY, 21:824-835, APR 2008
abstract, full text, DOI:10.1021/tx700349r

Martick, Monika; Lee, Tai-Sung; York, Darrin M.; Scott, William G.
Solvent structure and hammerhead ribozyme catalysis
CHEMISTRY & BIOLOGY, 15:332-342, APR 2008
abstract, full text, DOI:10.1016/j.chembiol.2008.03.010

MacKerell, Alexander D., Jr.; Nilsson, Lennart
Molecular dynamics simulations of nucleic acid-protein complexes
CURRENT OPINION IN STRUCTURAL BIOLOGY, 18:194-199, APR 2008
abstract, full text, DOI:10.1016/j.sbi.2007.12.012

Parr, Charity L.; Tanaka, Takuji; Xiao, Huogen; Yada, Rickey Y.
The catalytic significance of the proposed active site residues in Plasmodium falciparum histoaspartic protease
FEBS JOURNAL, 275:1698-1707, APR 2008
abstract, full text, DOI:10.1111/j.1742-4658.2008.06325.x

Mukhopadhyay, B. P.; Ghosh, B.; Bairagya, H. R.; Nandi, T. K.; Chakrabarti, B.; Bera, A. K.
Molecular modeling of the ternary complex of rusticyanin-cytochrome c(4)-cytochrome oxidase: An insight to possible H-bond mediated recognition and electron transfer reaction in T. ferrooxidans
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 25:543-551, APR 2008
abstract, full text

Singh, Anupama; Kushwaha, Hemant R.; Sharma, Pawan
Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv)
JOURNAL OF MOLECULAR MODELING, 14:249-263, APR 2008
abstract, full text, DOI:10.1007/s00894-008-0267-2

Sikdar, Debashis; Katti, Kalpana S.; Katti, Dinesh R.
Molecular interactions alter clay and polymer structure in polymer clay nanocomposites
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 8:1638-1657, APR 2008
abstract, full text, DOI:10.1166/jnn.2008.032

Connolly, M. J.; Roth, M. W.; Gray, Paul A.; Wexler, Carlos
Explicit hydrogen molecular dynamics simulations of hexane deposited onto graphite at various coverages
LANGMUIR, 24:3228-3234, APR 1 2008
abstract, full text, DOI:10.1021/1a703040a

Perez, Alberto; Lankas, Filip; Luque, F. Javier; Orozco, Modesto
Towards a molecular dynamics consensus view of B-DNA flexibility
NUCLEIC ACIDS RESEARCH, 36:2379-2394, APR 2008
abstract, full text, DOI:10.1093/nar/gkn082

Lin, Ying-Wu; Wang, Zhong-Hua; Ni, Feng-Yun; Huang, Zhong-Xian
Forced unfolding of apocytochrome b(5) by steered molecular dynamics simulation
PROTEIN JOURNAL, 27:197-203, APR 2008
abstract, full text, DOI:10.1007/s10930-007-9125-9

Cherezov, Vadim; Liu, Wei; Derrick, Jeremy P.; Luan, Binquan; Aksimentiev, Aleksei; Katritch, Vsevolod; Caffrey, Martin
In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:24-34, APR 2008
abstract, full text, DOI:10.1002/prot.21841

Shreif, Z.; Adhangale, P.; Cheluvaraja, S.; Perera, R.; Kuhn, R.; Ortoleva, P.
Enveloped viruses understood via multiscale simulation: computer-aided vaccine design
SCIENTIFIC MODELING AND SIMULATIONS, 15:363-380, APR 2008
abstract, full text, DOI:10.1007/s10820-008-9101-5

Bulo, Rosa E.; Jacob, Christoph R.; Visscher, Lucas
NMR solvent shifts of acetonitrile from frozen density embedding calculations
JOURNAL OF PHYSICAL CHEMISTRY A, 112:2640-2647, MAR 27 2008
abstract, full text, DOI:10.1021/jp710609m

Foley, Meredith C.; Schlick, Tamar
Simulations of DNA Pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:3967-3977, MAR 26 2008
abstract, full text, DOI:10.1021/ja077982t

Treptow, Werner; Marrink, S.i.e.w.e.r.t.-.J.; Tarek, Mounir
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:3277-3282, MAR 20 2008
abstract, full text, DOI:10.1021/jp709675e

Pereverzev, Yuriy V.; Gunnerson, Kirn N.; Prezhdo, Oleg V.; Sullivan, Philip A.; Liao, Yi; Olbricht, Benjamin C.; Akelaitis, Andrew J. P.; Jen, Alex K. -Y.; Dalton, Larry R.
Guest-host cooperativity in organic materials greatly enhances the nonlinear optical response
JOURNAL OF PHYSICAL CHEMISTRY C, 112:4355-4363, MAR 20 2008
abstract, full text, DOI:10.1021/jp077194q

Domene, Carmen; Vemparala, Satyavani; Furini, Simone; Sharp, Kim; Klein, Michael L.
The role of conformation in ion permeation in a K+ channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:3389-3398, MAR 19 2008
abstract, full text, DOI:10.1021/ja075164v

Bhattacharya, Supriyo; Hall, Spencer E.; Li, Hubert; Vaidehi, Nagarajan
Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation
BIOPHYSICAL JOURNAL, 94:2027-2042, MAR 15 2008
abstract, full text, DOI:10.1529/biophysj.107.117648

Catte, Andrea; Patterson, James C.; Bashtovyy, Denys; Jones, Martin K.; Gu, Feifei; Li, Ling; Rampioni, Aldo; Sengupta, Durba; Vuorela, Timo; Niemela, Perttu; Karttunen, Mikko; Marrink, Siewert Jan; Vattulainen, Ilpo; Segrest, Jere P.
Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations
BIOPHYSICAL JOURNAL, 94:2306-2319, MAR 15 2008
abstract, full text, DOI:10.1529/biophysj.107.115857

Eriksson, Mats; Lindhorst, Thisbe K.; Hartke, Bernd
Differential effects of oligosaccharides on the hydration of simple cations
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 105105, MAR 14 2008
abstract, full text, DOI:10.1063/1.2873147

Anselmi, Cecilia; Centini, Marisanna; Maggiore, Maria; Gaggelli, Nicola; Andreassi, Marco; Buonocore, Anna; Beretta, Giangiacomo; Facino, Roberto Maffei
Non-covalent inclusion of ferulic acid with alpha-cyclodextrin improves photo-stability and delivery: NMR and modeling studies
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 46:645-652, MAR 13 2008
abstract, full text, DOI:10.1016/j.jpba.2007.11.037

Zhou, Yonggang; Guan, Lan; Freites, J. Alfredo; Kaback, H. Ronald
Opening and closing of the periplasmic gate in lactose permease
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:3774-3778, MAR 11 2008
abstract, full text, DOI:10.1073/pnas.0800825105

Artali, Roberto; Del Pra, Antonio; Foresti, Elisabetta; Lesci, Isidoro Giorgio; Roveri, Norberto; Sabatino, Piera
Adsorption of human serum albumin on the chrysotile surface: a molecular dynamics and spectroscopic investigation
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 5:273-283, MAR 6 2008
abstract, full text, DOI:10.1098/rsif.2007.1137

Sikdar, Debashis; Katti, Dinesh R.; Katti, Kalpana S.
The role of interfacial interactions on the crystallinity and nanomechanical properties of clay-polymer nanocomposites: A molecular dynamics study
JOURNAL OF APPLIED POLYMER SCIENCE, 107:3137-3148, MAR 5 2008
abstract, full text, DOI:10.1002/app.27504

Celik, Leyla; Schiott, Birgit; Tajkhorshid, Ernad
Substrate binding and formation of an occluded state in the leucine transporter
BIOPHYSICAL JOURNAL, 94:1600-1612, MAR 1 2008
abstract, full text, DOI:10.1529/biophysj.107.117580

Jolley, Craig C.; Wells, Stephen A.; Frornme, Petra; Thorpe, M. F.
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
BIOPHYSICAL JOURNAL, 94:1613-1621, MAR 1 2008
abstract, full text, DOI:10.1529/biophysj.107.115949

Huang, Hung-Chung; Jupiter, Daniel; Qiu, Meikang; Briggs, James M.; VanBuren, Vincent
Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation
BIOPOLYMERS, 89:210-219, MAR 2008
abstract, full text, DOI:10.1002/bip.20893

Jouanna, Paul; Pedesseau, Laurent; Pepe, Gerard; Mainprice, David
Mass and momentum interface equilibrium by molecular modeling. Simulating AFM adhesion between (120) gypsum faces in a saturated solution and consequences on gypsum cohesion
CEMENT AND CONCRETE RESEARCH, 38:290-299, MAR 2008
abstract, full text, DOI:10.1016/j.cemconres.2007.09.022

Weronski, Pawel; Jiang, Yi; Rasmussen, Steew
Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine
COMPLEXITY, 13:10-17, MAR-APR 2008
abstract, full text, DOI:10.1002/cplx.20212

Henriques, E. S.; Solov'yov, A. V.
A rational method for probing macromolecules dissociation: the antibody-hapten system
EUROPEAN PHYSICAL JOURNAL D, 46:471-481, MAR 2008
abstract, full text, DOI:10.1140/epjd/e2008-00009-3

Nakano, Aiichiro; Kalia, Rajiv K.; Nomura, Ken-Ichi; Sharma, Ashish; Vashishta, Priya; Shimojo, Fuyuki; Van Duin, Adri C. T.; Goddard, William A., I.I.I.; Biswas, Rupak; Srivastava, Deepak; Yang, Lin H.
De novo ultrascale atomistic simulations on high-end parallel supercomputers
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 22:113-128, SPR 2008
abstract, full text, DOI:10.1177/1094342007085015

Hess, Berk; Kutzner, Carsten; van der Spoel, David; Lindahl, Erik
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:435-447, MAR 2008
abstract, full text, DOI:10.1021/ct700301q

Wan, Shunzhou; Flower, Darren R.; Coveney, Peter V.
Toward an atomistic understanding of the immune synapse: Large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex
MOLECULAR IMMUNOLOGY, 45:1221-1230, MAR 2008
abstract, full text, DOI:10.1016/j.molimm.2007.09.022

Zhao, Q.; Comer, J.; Dimitrov, V.; Yemenicioglu, S.; Aksimentiev, A.; Timp, G.
Stretching and unzipping nucleic acid hairpins using a synthetic nanopore
NUCLEIC ACIDS RESEARCH, 36:1532-1541, MAR 2008
abstract, full text, DOI:10.1093/nar/gkm1017

Zhmakin, A. I.
Physical aspects of cryobiology
PHYSICS-USPEKHI, 51:231-252, MAR 2008
abstract, full text, DOI:10.1070/PU2008v051n03ABEH006449

Yang, Sichun; Roux, Benoit
Src kinase conformational activation: Thermodynamics, pathways, and mechanisms
PLOS COMPUTATIONAL BIOLOGY, 4 Art. No. e1000047, MAR 2008
abstract, full text, DOI:10.1371/journal.pcbi.1000047

Ko, Youn Jo; Huh, June; Jo, Won Ho
Ion exclusion mechanism in aquaporin at an atomistic level
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70:1442-1450, MAR 2008
abstract, full text, DOI:10.1002/prot.21696

Lim, Bernard B. C.; Lee, Eric H.; Sotomayor, Marcos; Schulten, Klaus
Molecular basis of fibrin clot elasticity
STRUCTURE, 16:449-459, MAR 2008
abstract, full text, TCBG publications, DOI:10.1016/j.str.2007.12.019

Venkatramani, Ravindra; Radhakrishnan, Ravi
Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase
PHYSICAL REVIEW LETTERS, 100 Art. No. 088102, FEB 29 2008
abstract, full text, DOI:10.1103/PhysRevLett.100.088102

Stoica, Ileana; Sadiq, S. Kashif; Coveney, Peter V.
Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:2639-2648, FEB 27 2008
abstract, full text, DOI:10.1021/ja0779250

Zheng, Jie; Jang, Hyunbum; Nussinov, Ruth
beta(2)-microglobulin amyloid fragment organization and morphology and its comparison to A beta suggests that amyloid aggregation pathways are sequence specific
BIOCHEMISTRY, 47:2497-2509, FEB 26 2008
abstract, full text, DOI:10.1021/bi7019194

Perumal, Shiamalee; Antipova, Olga; Orgel, Joseph P. R. O.
Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:2824-2829, FEB 26 2008
abstract, full text, DOI:10.1073/pnas.0710588105

Gorfe, Alemayehu A.; Chang, Chia-En A.; Ivanov, Ivaylo; McCammon, J. Andrew
Dynamics of the acetylcholinesterase tetramer
BIOPHYSICAL JOURNAL, 94:1144-1154, FEB 15 2008
abstract, full text, DOI:10.1529/biophysj.107.117879

Qamar, Shahid; Williams, Phil M.; Lindsay, S. M.
Can an atomic force microscope sequence DNA using a nanopore?
BIOPHYSICAL JOURNAL, 94:1233-1240, FEB 15 2008
abstract, full text, DOI:10.1529/biophysj.107.108670

Anishkin, Andriy; Akitake, Bradley; Sukharev, Sergei
Characterization of the resting MscS: Modeling and analysis of the closed bacterial mechanosensitive channel of small conductance
BIOPHYSICAL JOURNAL, 94:1252-1266, FEB 15 2008
abstract, full text, DOI:10.1529/biophysj.107.110171

Wu, Licia N. Y.; Genge, Brian R.; Wuthier, Roy E.
Analysis and molecular modeling of the formation, structure, and activity of the phosphatidylserine-calcium-phosphate complex associated with biomineralization
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:3827-3838, FEB 15 2008
abstract, full text, DOI:10.1074/jbc.M707653200

Horejs, C.; Pum, D.; Sleytr, U. B.; Tscheliessnig, R.
Structure prediction of an S-layer protein by the mean force method
JOURNAL OF CHEMICAL PHYSICS, 128 Art. No. 065106, FEB 14 2008
abstract, full text, DOI:10.1063/1.2826375

Dalhaimer, Paul; Pollard, Thomas D.; Nolen, Brad J.
Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations
JOURNAL OF MOLECULAR BIOLOGY, 376:166-183, FEB 8 2008
abstract, full text, DOI:10.1016/j.jmb.2007.11.068

Zou, Hongling; Therien, Michael J.; Blasie, J. Kent
Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 112:1350-1357, FEB 7 2008
abstract, full text, DOI:10.1021/jp076643j

Corry, Ben
Designing carbon nanotube membranes for efficient water desalination
JOURNAL OF PHYSICAL CHEMISTRY B, 112:1427-1434, FEB 7 2008
abstract, full text, DOI:10.1021/jp709845u

Li, Zhenyu; Yu, Haibo; Zhuang, Wei; Mukamel, Shaul
Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation
CHEMICAL PHYSICS LETTERS, 452:78-83, FEB 4 2008
abstract, full text, DOI:10.1016/j.cplett.2007.12.022

Shen, Jia-Wei; Wu, Tao; Wang, Qi; Pan, Hai-Hua
Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces
BIOMATERIALS, 29:513-532, FEB 2008
abstract, full text, DOI:10.1016/j.biomaterials.2007.10.016

Henin, Jerome; Tajkhorshid, Emad; Schulten, Klaus; Chipot, Christophe
Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF
BIOPHYSICAL JOURNAL, 94:832-839, FEB 1 2008
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.115105

Landon, Melissa R.; Amaro, Rommie E.; Baron, Riccardo; Ngan, Chi Ho; Ozonoff, David; McCammon, J. Andrew; Vajda, Sandor
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
CHEMICAL BIOLOGY & DRUG DESIGN, 71:106-116, FEB 2008
abstract, full text, DOI:10.1111/j.1747-0285.2007.00614.x

El-Ghazawi, Tarek; El-Araby, Esam; Huang, Miaoqing; Gaj, Kris; Kindratenko, Volodymyr; Buell, Duncan
The promise of high-performance reconfigurable computing
COMPUTER, 41:69-+, FEB 2008
abstract, full text, DOI:10.1109/MC.2008.65

Solov'yov, I. A.; Yakubovich, A. V.; Solov'yov, A. V.; Greiner, W.
alpha-helix <-> random coil phase transition: analysis of ab initio theory predictions
EUROPEAN PHYSICAL JOURNAL D, 46:227-240, FEB 2008
abstract, full text, DOI:10.1140/epjd/e2007-00327-x

Landstroem, Jens; Nordmark, Eva-Lisa; Eklund, Robert; Weintraub, Andrej; Seckler, Robert; Widmalm, Goeran
Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies
GLYCOCONJUGATE JOURNAL, 25:137-143, FEB 2008
abstract, full text, DOI:10.1007/s10719-007-9065-9

Rodriguez-Ropero, Francisco; Zanuy, David; Casanovas, Jordi; Nussinov, Ruth; Aleman, Carlos
Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:333-343, FEB 2008
abstract, full text, DOI:10.1021/ci700291x

Carvacho, Ingrid; Gonzalez, Wendy; Torres, Yolima P.; Brauchi, Sebastian; Alvarez, Osvaldo; Gonzalez-Nilo, Fernando D.; Latorre, Ramon
Intrinsic electrostatic potential in the BK channel pore: Role in determining single channel conductance and block
JOURNAL OF GENERAL PHYSIOLOGY, 131:147-161, FEB 2008
abstract, full text, DOI:10.1085/jgp.200709862

Todman, Sarah J.; Halling-Brown, Mark D.; Davies, Matthew N.; Flower, Darren R.; Kayikci, Melis; Moss, David S.
Toward the atomistic simulation of T cell epitopes Automated construction of MHC: Peptide structures for free energy calculations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 26:957-961, FEB 2008
abstract, full text, DOI:10.1016/j.jmgm.2007.07.005

Beautrait, Alexandre; Leroux, Vincent; Chavent, Matthieu; Ghemtio, Leo; Devignes, Marie-Dominique; Smaiel-Tabbone, Malika; Cai, Wensheng; Shao, Xuegang; Moreau, Gilles; Bladon, Peter; Yao, Jianhua; Maigret, Bernard
Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment
JOURNAL OF MOLECULAR MODELING, 14:135-148, FEB 2008
abstract, full text, DOI:10.1007/s00894-007-0257-9

Lash, L. Leanne; Sanders, James M.; Akiyama, Nobuyuki; Shoji, Muneo; Postila, Pekka; Pentikainen, Olli T.; Sasaki, Makoto; Sakai, Ryuichi; Swanson, Geoffrey T.
Novel analogs and stereoisomers of the marine toxin neodysiherbaine with specificity for kainate receptors
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 324:484-496, FEB 2008
abstract, full text, DOI:10.1124/jpet.107.129890

Dalal, Shibani; Chikova, Anna; Jaeger, Joachim; Sweasy, Joann B.
The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient
NUCLEIC ACIDS RESEARCH, 36:411-422, FEB 2008
abstract, full text, DOI:10.1093/nar/gkm1053

Hytoenen, Vesa P.; Vogel, Viola
How force might activate talin's vinculin binding sites: SMD reveals a structural mechanism
PLOS COMPUTATIONAL BIOLOGY, 4 Art. No. e24, FEB 2008
abstract, full text, DOI:10.1371/journal.pcbi.0040024

Wang, Hai-Long; Cheng, Xiaolin; Taylor, Palmer; McCammon, J. Andrew; Sine, Steven M.
Control of cation permeation through the nicotinic receptor channel
PLOS COMPUTATIONAL BIOLOGY, 4 Art. No. e41, FEB 2008
abstract, full text, DOI:10.1371/journal.pcbi.0040041

Pentikaeinen, Ulla; Pentikaeinen, Olli T.; Mulholland, Adrian J.
Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70:498-508, FEB 1 2008
abstract, full text, DOI:10.1002/prot.21540

Yang, Lei; Song, Guang; Carriquiry, Alicia; Jernigan, Robert L.
Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
STRUCTURE, 16:321-330, FEB 2008
abstract, full text, DOI:10.1016/j.str.2007.12.011

Bleicher, Lucas; Aparicio, Ricardo; Nunes, Fabio M.; Martinez, Leandro; Gomes Dias, Sandra M.; Migliorini Figueira, Ana Carolina; Morim Santos, Maria Auxiliadora; Venturelli, Walter H.; da Silva, Rosangela; Donate, Paulo Marcos; Neves, Francisco A. R.; Simeoni, Luiz A.; Baxter, John D.; Webb, Paul; Skaf, Munir S.; Polikarpov, Igor
Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms
BMC STRUCTURAL BIOLOGY, 8 Art. No. 8, JAN 31 2008
abstract, full text, DOI:10.1186/1472-6807-8-8

Interlandi, Gianluca; Wetzel, Svava K.; Settanni, Giovanni; Plueckthun, Andreas; Caflisch, Amedeo
Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments
JOURNAL OF MOLECULAR BIOLOGY, 375:837-854, JAN 18 2008
abstract, full text, DOI:10.1016/j.jmb.2007.09.042

Spiegel, Katrin; Magistrato, Alessandra; Maurer, Patrick; Ruggerone, Paolo; Rothlisberger, Ursula; Carloni, Paolo; Reedijk, Jan; Klein, Michael L.
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:38-49, JAN 15 2008
abstract, full text, DOI:10.1002/jcc.20739

Shen, Miaoqing; Reitman, Zachary J.; Zhao, Yan; Moustafa, Ibrahim; Wang, Qixin; Arnold, Jamie J.; Pathak, Harsh B.; Cameron, Craig E.
Picornavirus genome replication - Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV3C(2)-3Dpol complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:875-888, JAN 11 2008
abstract, full text, DOI:10.1074/jbc.M707907200

Zhao, Xiongce; Payne, Christina M.; Cummings, Peter T.
Controlled translocation of DNA segments through nanoelectrode gaps from molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 112:8-12, JAN 10 2008
abstract, full text, DOI:10.1021/jp709652y

Larson, Richard H.; Salmon, John K.; Dror, Ron O.; Deneroff, Martin M.; Young, Cliff; Grossman, J. P.; Shan, Yibing; Klepeis, John L.; Shaw, David E.
High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation
2008 IEEE 14TH INTERNATIONAL SYMPOSIUM ON HIGH PEFORMANCE COMPUTER ARCHITECTURE, 303-314, 2008
abstract, full text

Kuskin, Jeffrey S.; Young, Cliff; Grossman, J. P.; Batson, Brannon; Deneroff, Martin M.; Dror, Ron O.; Shaw, David E.
Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation
2008 IEEE 14TH INTERNATIONAL SYMPOSIUM ON HIGH PEFORMANCE COMPUTER ARCHITECTURE, 315-326, 2008
abstract, full text

Alam, Sadaf R.; Agarwal, Pratul K.; Hampton, Scott S.; Ong, Hong; Vetter, Jeffrey S.
Impact of multicores on large-scale molecular dynamics simulations
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 544-550, 2008
abstract, full text

Dooley, Isaac; Mei, Chao; Kale, Laxmikant
NOISEMINER: An algorithm for scalable automatic computational noise and software interference detection
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 582-589, 2008
abstract, full text

Lee, Chee Wai; Mendes, Celso; Kale, Laxmikant V.
Towards scalable performance analysis and visualization through data reduction
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 590-597, 2008
abstract, full text

Bhatele, Abhinav; Kale, Laxmikant V.
Application-specific topology-aware mapping for three dimensional topologies
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 2196-2203, 2008
abstract, full text

Shi, Guochun; Kindratenko, Volodymyr
Implementation of NAMD molecular dynamics non-bonded force-field on the Cell Broadband Engine processor
2008 IEEE INTERNATIONAL SYMPOSIUM ON PARALLEL & DISTRIBUTED PROCESSING, VOLS 1-8, 2985-2992, 2008
abstract, full text

Sharma, Gaurav; Rege, Kaushal; Budil, David; Yarmush, Martin; Mavroidis, Constantinos
Design and Modeling of a Protein Based NanoGripper
2008 IEEE/RSJ INTERNATIONAL CONFERENCE ON ROBOTS AND INTELLIGENT SYSTEMS, VOLS 1-3, CONFERENCE PROCEEDINGS, 476-481, 2008
abstract, full text, DOI:10.1109/IROS.2008.4651051

Villarreal, Jason; Najjar, Walid A.
COMPILED HARDWARE ACCELERATION OF MOLECULAR DYNAMICS CODE
2008 INTERNATIONAL CONFERENCE ON FIELD PROGRAMMABLE AND LOGIC APPLICATIONS, VOLS 1 AND 2, 666-669, 2008
abstract, full text

Ding, Zhaohui; Wei, Xiaohui; Zhu, Yifan; Yuan, Yaoguang; Li, Wilfred W.; Tatebe, Osamu
Implementation of the Grid Workflow Scheduling for Data Intensive Applications as Scheduling Plug-ins
2008 SECOND INTERNATIONAL CONFERENCE ON FUTURE GENERATION COMMUNICATION AND NETWORKING SYMPOSIA, VOLS 1-5, PROCEEDINGS, 517-523, 2008
abstract, full text

Kozakiewicz, Anna; Neurnann, Piotr; Banach, Mariusz; Komoszyiski, Michal; Wojtczak, Andrzej
Modeling studies of potato nucleoside triphosphate diphosphohydrolase NTPDase1: an insight into the catalytic mechanism
ACTA BIOCHIMICA POLONICA, 55:141-150, 2008
abstract, full text

Charlet, L.; Chapron, Y.; Roman-Ross, G.; Hureau, C.; Hawkins, D. P.; Ragnarsdottir, K. V.
Prions, Metals, and Soils
ADSORPTION OF METALS BY GEOMEDIA II: VARIABLES, MECHANISMS, AND MODEL APPLICATIONS, 7:125-152, 2008
abstract, full text, DOI:10.1016/S1571-9197(07)07005-X

Fan, Anghong; Chinappi, Mauro
Multiscale analysis of interfacial shearing behavior between biocells and implant
ADVANCES IN HETEROGENEOUS MATERIAL MECHANICS 2008, 251-258, 2008
abstract, full text

Kosztin, Ioan; Schulten, Klaus
Molecular dynamics methods for bioelectronic systems in photosynthesis
Advances in Photosynthesis and Respiration, 26:445-464, 2008
abstract, full text, TCBG publications

Raiteri, Paolo; Bussi, Giovanni; Cucinotta, Clotilde S.; Credi, Alberto; Stoddart, J. Fraser; Parrinello, Michele
Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47:3536-3539, 2008
full text, DOI:10.1002/anie.200705207

Tian, Pu
Molecular dynamics simulations of nanoparticles
ANNUAL REPORTS ON THE PROGRESS OF CHEMISTRY 2008, VOL 104, SECTION C: PHYSICAL CHEMISTRY, 104:142-164, 2008
abstract, full text, DOI:10.1039/b7030897f

White, Stephen H.; von Heijne, Gunnar
How translocons select transmembrane helices
ANNUAL REVIEW OF BIOPHYSICS, 37:23-42, 2008
abstract, full text, DOI:10.1146/annurev.biophys.37.032807.125904

Frangeul, Antoine; Bussetta, Cecile; Deval, Jerome; Barral, Karine; Alvarez, Karine; Canard, Bruno
Gln151 of HIV-1 reverse transcriptase acts as a steric gate towards clinically relevant acyclic phosphonate nucleotide analogues
ANTIVIRAL THERAPY, 13:115-124, 2008
abstract, full text

Espinoza-Fonseca, L. Michel; Pedretti, Alessandro; Vistoli, Giulio
Structure and dynamics of the full-length M-1 muscarinic acetylcholine receptor studied by molecular dynamics simulations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 469:142-150, JAN 1 2008
abstract, full text, DOI:10.1016/j.abb.2007.09.002

Buldyrev, S. V.
Application of discrete molecular dynamics to protein folding and aggregation
ASPECTS OF PHYSICAL BIOLOGY: BIOLOGICAL WATER, PROTEIN SOLUTIONS, TRANSPORT AND REPLICATION, 752:97-131, 2008
abstract, full text, DOI:10.1007/978-3-540-78765-5-5

Al-Lazikani, Bissan; Hill, Emma E.; Morea, Veronica
Protein structure prediction
Bioinformatics:VOLUME II: STRUCTURE, FUNCTION AND APPLICATIONS, 453:33-85, 2008
abstract, full text

Linderoth, Lars; Andresen, Thomas L.; Jorgensen, Kent; Madsen, Robert; Peters, Guenther H.
Molecular basis of phospholipase A(2) activity toward phospholipids with sn-1 substitutions
BIOPHYSICAL JOURNAL, 94:14-26, JAN 1 2008
abstract, full text, DOI:10.1529/biophysj.107.110106

Atilgan, Canan; Aykut, Ayse Ozlem; Atilgan, Ali Rana
How a vicinal layer of solvent modulates the dynamics of proteins
BIOPHYSICAL JOURNAL, 94:79-89, JAN 1 2008
abstract, full text, DOI:10.1529/biophysj.107.116426

Torras, Juan; Zanuy, David; Crisma, Marco; Toniolo, Claudio; Betran, Oscar; Aleman, Carlos
Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: A molecular dynamics investigation
BIOPOLYMERS, 90:695-706, 2008
abstract, full text, DOI:10.1002/bip.21031

Searles, Debra J.; Evans, Denis J.
Fluctuation relations, free energy calculations and irreversibility
CHEMICAL MODELLING: APPLICATIONS AND THEORY, VOL 5: A REVIEW OF THE LITERATURE PUBLISHED BETWEEN JUNE 2005 AND MAY 2007, 5:182-207, 2008
full text, DOI:10.1039/b608839m

Zhang, Afang; Rodriguez-Ropero, Francisco; Zanuy, David; Aleman, Carlos; Meijer, E. W.; Schlueter, A. Dieter
A rigid, chiral, dendronized polymer with a thermally stable, right-handed helical conformation
CHEMISTRY-A EUROPEAN JOURNAL, 14:6924-6934, 2008
abstract, full text, DOI:10.1002/chem.200800325

Botta, Maurizio; Angeli, Lucilla; Radi, Marco; Maga, Giovanni
The fight against AlDS: New avenues for inhibiting reverse transcriptase (RT), an old target
Chemistry and Molecular Aspects of Drug Design and Action, 325-346, 2008
abstract, full text

Pedretti, Alessandro; De Luca, Laura; Sciarrillo, Cristina; Vistoli, Giulio
Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping
CHEMMEDCHEM, 3:79-90, JAN 2008
abstract, full text, DOI:10.1002/cmdc.200700197

Buehler, M. J.
Hierarchical nanomechanics of collagen fibrils: Atomistic and molecular modeling
Collagen: Structure and Mechanics, 175-247, 2008
abstract, full text, DOI:10.1007/978-0-387-73906-9_8

Pedersen, Ulf R.; Peters, Gunther H.; Schroder, Thomas B.; Dyre, Jeppe C.
Volume-energy correlations in the slow degrees of freedom of computer-simulated phospholipid membranes
COMPLEX SYSTEMS, 982:407-409, 2008
abstract, full text

Karttunen, Mikko; Rottler, Joerg; Vattulainen, Ilpo; Sagui, Celeste
Electrostatics in biomolecular simulations: Where are we now and where are we heading?
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:49-89, 2008
abstract, full text, DOI:10.1016/S1063-5823(08)00002-1

Fitch, Blake G.; Rayshubskiy, Aleksandr; Eleftheriou, Maria; Ward, T. J. Christopher; Giampapa, Mark; Pitman, Michael C.; Pitera, Jed; Swope, William C.; Germain, Robert S.
Blue Matter: Scaling of N-body simulations to one atom per node
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:159-180, 2008
abstract, full text, DOI:10.1016/S1063-5823(08)00006-9

Shih, Amy Y.; Freddolino, Peter L.; Arkhipov, Anton; Sligar, Stephen G.; Schulten, Klaus
Molecular modeling of the structural properties and formation of high-density lipoprotein particles
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:313-342, 2008
full text, TCBG publications, DOI:10.1016/S1063-5823(08)00011-2

Wang, Yi; Ohkubo, Y. Zenmei; Tajkhorshid, Emad
Gas conduction of lipid bilayers and membrane channels
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:343-367, 2008
abstract, full text, DOI:10.1016/S1063-5823(08)00012-4

Benkner, Siegfried; Schroeder, Christian; Lucka, Maria; Steinhauser, Othmar
Grid services for parallel molecular dynamics with NAMD and CHARMM
COMPUTATIONAL SCIENCE AND ITS APPLICATIONS - ICCSA 2008, PT 1, PROCEEDINGS, 5072:1036-1051, 2008
abstract, full text

Malawski, Maciej; Bartynski, Tomasz; Bubak, Marian
A tool for building collaborative applications by invocation of Grid operations
COMPUTATIONAL SCIENCE - ICCS 2008, PT 3, 5103:243-252, 2008
abstract, full text

Keten, Sinan; Buehler, Markus J.
Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 197:3203-3214, 2008
abstract, full text, DOI:10.1016/j.cma.2007.11.028

Yang, Soo I.; Tanaka, Takuji
Characterization of recombinant prolidase from Lactococcus lactis - changes in substrate specificity by metal cations, and allosteric behavior of the peptidase
FEBS JOURNAL, 275:271-280, JAN 2008
abstract, full text, DOI:10.1111/j.1742-4658.2007.06197.x

Kottakis, Filippos; Papadopoulos, Georgios; Pappa, Eleni V.; Cordopatis, Paul; Pentas, Stefanos; Choli-Papadopoulou, Theodora
Helicobacter pylori neutrophil-activating protein activates neutrophils by its C-terminal region even without dodecamer formation, which is a prerequisite for DNA protection - novel approaches against Helicobacter pylori inflammation
FEBS JOURNAL, 275:302-317, JAN 2008
abstract, full text, DOI:10.1111/j.1742-4658.2007.06201.x

Cohen, Jordi; Olsen, Kenneth W.; Schulten, Klaus
Finding gas migration pathways in proteins using implicit ligand sampling
GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B, 437:439-457, 2008
abstract, full text, TCBG publications, DOI:10.1016/S0076-6879(07)37022-5

Golden, Stephen D.; Olsen, Kenneth W.
Identification of ligand-binding pathways in truncated hemoglobins using locally enhanced sampling molecular dynamics
GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B, 437:459-475, 2008
abstract, full text, DOI:10.1016/S0076-6879(07)37023-7

Zhou, R.; Eleftheriou, M.; Hon, C. -C.; Germain, R. S.; Royyuru, A. K.; Berne, B. J.
Massively parallel molecular dynamics simulations of lysozyme unfolding
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:19-30, JAN-MAR 2008
abstract, full text

Fitch, B. G.; Rayshubskiy, A.; Eleftheriou, M.; Ward, T. J. C.; Giampapa, M. E.; Pitman, M. C.; Pitera, J. W.; Swope, W. C.; Germain, R. S.
Blue Matter: Scaling of N-body simulations to one atom per node
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:145-158, JAN-MAR 2008
abstract, full text

Kumar, S.; Huang, C.; Zheng, G.; Bohm, E.; Bhatele, A.; Phillips, J. C.; Yu, H.; Kale, L. V.
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:177-188, JAN-MAR 2008
abstract, full text

Tsujita, Yuichi; Arima, Tatsumi; Idemitsu, Kazuya; Suzuki, Yoshio; Kimura, Hideo
BUILDING AN APPLICATION-SPECIFIC GRID COMPUTING ENVIRONMENT USING ITBL FOR NUCLEAR MATERIAL ENGINEERING
ICONE16: PROCEEDING OF THE 16TH INTERNATIONAL CONFERENCE ON NUCLEAR ENGINEERING - 2008, VOL 2, 55-63, 2008
abstract, full text

Alam, S.; Barrett, R.; Bast, M.; Fahey, M. R.; Kuehn, J.; McCurdy, C.; Rogers, J.; Roth, P.; Sankaran, R.; Vetter, J. S.; Worley, P.; Yu, W.
Early Evaluation of IBM BlueGene/P
INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS, 303-314, 2008
abstract, full text

Tu, Tiankai; Rendleman, Charles A.; Borhani, David W.; Dror, Ron O.; Gullingsrud, Justin; Jensen, Morten O.; Klepeis, John L.; Maragakis, Paul; Miller, Patrick; Stafford, Kate A.; Shaw, David E.
A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories
INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS, 432-443, 2008
abstract, full text

Phillips, James C.; Stone, John E.; Schultent, Klaus
Adapting a Message-Driven Parallel Application to GPU-Accelerated Clusters
INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS, 444-452, 2008
abstract, full text

Sharma, Gaurav; Rege, Kaushal; Budil, David E.; Yarmush, Martin L.; Mavroidis, Constantinos
Reversible pH-controlled DNA-binding peptide nanotweezers: An in-silico study
INTERNATIONAL JOURNAL OF NANOMEDICINE, 3:505-521, 2008
abstract, full text

Falcon, Ayose; Faraboschi, Paolo; Ortega, Daniel
An adaptive synchronization technique for parallel simulation of networked clusters
ISPASS 2008: IEEE INTERNATIONAL SYMPOSIUM ON PERFORMANCE ANALYSIS OF SYSTEMS AND SOFTWARE, 22-31, 2008
abstract, full text, DOI:10.1109/ISPASS.2008.4510735

Colombres, Marcela; Garate, Jose A.; Lagos, Carlos F.; Araya-Secchi, Raul; Norambuena, Patricia; Quiroz, Soledad; Larrondo, Luis; Perez-Acle, Tomas; Eyzaguirre, Jaime
An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 22:19-28, JAN 2008
abstract, full text, DOI:10.1007/s10822-007-9149-4

Ghosh, Pijush; Katti, Dinesh R.; Katti, Kalpana S.
Mineral and protein-bound water and latching action control mechanical behavior at protein-mineral interfaces in biological nanocomposites
JOURNAL OF NANOMATERIALS, Art. No. 582973, 2008
abstract, full text, DOI:10.1155/2008/582973

Negi, Surendra S.; Carol, Andrew A.; Pandya, Shivangi; Braun, Werner; Anderson, Louise E.
Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts
JOURNAL OF STRUCTURAL BIOLOGY, 161:18-30, JAN 2008
abstract, full text, DOI:10.1016/j.jsb.2007.08.016

Pfeifer, Peter; Burress, Jacob W.; Wood, Mikael B.; Lapilli, Cintia M.; Barker, Sarah A.; Pobst, Jeffrey S.; Cepell, Raina J.; Wexler, Carlos; Shah, Parag S.; Gordon, Michael J.; Sup-Pes, Galen J.; Buckley, S. Philip; Radke, Darren J.; Ilavsky, Jan; Dillon, Anne C.; Parilla, Philip A.; Benham, Mi-Chael; Roth, Michael W.
High-surface-area biocarbon for reversible on-board storage of natural gas and hydrogen
LIFE-CYCLE ANALYSIS FOR NEW ENERGY CONVERSION AND STORAGE SYSTEMS, 1041:63-74, 2008
abstract, full text

Solares, Santiago D.
Characterization of deep nanoscale surface trenches with AFM using thin carbon nanotube probes in amplitude-modulation and frequency-force-modulation modes
MEASUREMENT SCIENCE AND TECHNOLOGY, 19 Art. No. 015503, JAN 2008
abstract, full text, DOI:10.1088/0957-0233/19/1/015503

Dubey, Devendra K.; Tomar, Vikas
Microstructure dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations
MECHANICS RESEARCH COMMUNICATIONS, 35:24-31, JAN-MAR 2008
abstract, full text, DOI:10.1016/j.mechrescom.2007.10.011

Jena, Bhanu P.
Understanding Membrane Fusion: Combining Experimental and Simulation Studies
METHODS IN NANO CELL BIOLOGY, 90:183-+, 2008
abstract, full text, DOI:10.1016/S0091-679X(08)00809-1

Shapiro, Bruce A.; Bindewald, Eckart; Kasprzak, Wojciech; Yingling, Yaroslava
Protocols for the In Silico Design of RNA Nanostructures
Methods in Molecular Biology, 474:93-115, 2008
abstract, full text

Buch, Idit; Tsai, Chung-Jung; Wolfson, Haim J.; Nussinov, Ruth
Self-Assembly of Fused Homo-Oligomers to Create Nanotubes
Methods in Molecular Biology, 474:117-131, 2008
abstract, full text

Bellesia, Giovanni; Lampoudi, Sotiria; Shea, Joan-Emma
Computational Methods in Nanostructure Design Replica Exchange Simulations of Self-Assembling Peptides
Methods in Molecular Biology, 474:133-151, 2008
abstract, full text

Lindahl, Erik R.
Molecular dynamics simulations
Methods in Molecular Biology, 443:3-23, 2008
abstract, full text, DOI:10.1007/978-1-59745-177-2_1

Guvench, Olgun; MacKerell, Alexander D., Jr.
Comparison of protein force fields for molecular dynamics simulations
Methods in Molecular Biology, 443:63-88, 2008
abstract, full text, DOI:10.1007/978-1-59745-177-2_4

Chipot, Christophe
Free energy calculations applied to membrane proteins
Methods in Molecular Biology, 443:121-144, 2008
abstract, full text, DOI:10.1007/978-1-59745-177-2_7

Biggin, Philip C.; Bond, Peter J.
Molecular dynamics simulations of membrane proteins
Methods in Molecular Biology, 443:147-160, 2008
abstract, full text, DOI:10.1007/978-1-59745-177-2_8

Morris, Garrett M.; Lim-Wilby, Marguerita
Molecular docking
Methods in Molecular Biology, 443:365-382, 2008
abstract, full text, DOI:10.1007/978-1-59745-177-2_19

Besseron, Xavier; Guitier, Thierry
Optimised Recovery with a Coordinated Checkpoint/Rollback Protocol for Domain Decomposition Applications
MODELLING, COMPUTATION AND OPTIMIZATION IN INFORMATION SYSTEMS AND MANAGEMENT SCIENCES, PROCEEDINGS, 14:497-506, 2008
abstract, full text

Karachevtsev, V. A.; Gladchenko, G. O.; Karachevtsev, M. V.; Glamazda, A. Yu.; Leontiev, V. S.; Lytvyn, O. S.; Dettlaff-Weglikowska, U.
RNA-Wrapped Carbon Nanotubes Aggregation Induced by Polymer Hybridization
MOLECULAR CRYSTALS AND LIQUID CRYSTALS, 497:339-351, 2008
abstract, full text, DOI:10.1080/15421400802458183

Ceraudo, Emilie; Murail, Samuel; Tan, Yossan-Var; Lacapere, Jean-Jacques; Neumann, Jean-Michel; Couvineau, Alain; Laburthe, Marc
The vasoactive intestinal peptide (VIP) alpha-helix up to C terminus interacts with the N-terminal ectodomain of the human VIP/Pituitary adenylate cyclase-activating peptide 1 receptor: Photoaffinity, molecular modeling, and dynamics
MOLECULAR ENDOCRINOLOGY, 22:147-155, JAN 2008
abstract, full text, DOI:10.1210/me.2007-0361

Alexiadis, Alessio; Kassinos, Stavros
Self-diffusivity, hydrogen bonding and density of different water models in carbon nanotubes
MOLECULAR SIMULATION, 34:671-678, 2008
abstract, full text, DOI:10.1080/08927020802073057

Flenner, Elijah; Marga, Francoise; Neagu, Adrian; Kosztin, Loan; Forgacs, Gabor
Relating biophysical properties across scales
MULTISCALE MODELING OF DEVELOPMENTAL SYSTEMS, 81:461-483, 2008
abstract, full text, DOI:10.1016/S0070-2153(07)81016-7

Sigalov, Grigori; Comer, Jeffrey; Timp, Gregory; Aksimentiev, Aleksei
Detection of DNA sequences using an alternating electric field in a nanopore capacitor
NANO LETTERS, 8:56-63, JAN 2008
abstract, full text, DOI:10.1021/nl071890k

Aksimentiev, Aleksei; Brunner, Robert; Cohen, Jordi; Comer, Jeffrey; Cruz-Chu, Eduardo; Hardy, David; Rajan, Aruna; Shih, Amy; Sigaloy, Grigori; Yin, Ying; Schulten, Klaus
Computer Modeling in Biotechnology A Partner in Development
Nanostructure Design: Methods and Protocols, 474:181-234, 2008
abstract, full text, TCBG publications

Krieger, Elmar; Leger, Laurent; Durrieu, Marie-Pierre; Taib, Nada; Bond, Peter; Laguerre, Michel; Lavery, Richard; Sansom, Mark S. P.; Baaden, Marc
Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex: a Grand Challenge Project on the DEISA HPC Infrastructure
PARALLEL COMPUTING: ARCHITECTURES, ALGORITHMS AND APPLICATIONS, 15:729-736, 2008
abstract, full text

Mederski, Jaroslaw; Mikulski, Lukasz; Bala, Piotr
Asynchronous parallel molecular dynamics simulations
PARALLEL PROCESSING AND APPLIED MATHEMATICS, 4967:439-446, 2008
abstract, full text

Kluszczynski, Rafal; Bala, Piotr
Supporting NAMD application on the grid using GPE
PARALLEL PROCESSING AND APPLIED MATHEMATICS, 4967:762-769, 2008
abstract, full text

Schulten, Klaus; Phillips, James C.; Kale, Laxmikant V.; Bhatele, Abhinav
Biomolecular Modeling in the Era of Petascale Computing
PETASCALE COMPUTING: ALGORITHMS AND APPLICATIONS, 165-+, 2008
full text, TCBG publications

Agarwal, Pratul K.; Alam, Sadaf Pl.; Geist, Al
Simulating Biomolecules on the Petascale Supercomputers
PETASCALE COMPUTING: ALGORITHMS AND APPLICATIONS, 211-+, 2008
full text

Ivanova, Anela; Jezierski, Grzegorz; Roesch, Notker
Electronic coupling between base pair dimers of LNA : DNA oligomers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:414-421, 2008
abstract, full text, DOI:10.1039/b712506b

Cai, Wensheng; Sun, Tingting; Shao, Xueguang; Chipot, Christophe
Can the anomalous aqueous solubility of beta-cyclodextrin be explained by its hydration free energy alone?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:3236-3243, 2008
abstract, full text, DOI:10.1039/b717509d

Blumberger, Jochen
Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:5651-5667, 2008
abstract, full text, DOI:10.1039/b807444e

Choi, Hojin; Kim, Jung Yun; Hong, Seungdo; Jang, Joonkyung; Ha, Man Yeong
CHARACTERISTICS OF THE WATER MENISCUS AT AFM TIP FOR VARIOUS SURFACE ENERGY
PROCEEDINGS OF THE 6TH INTERNATIONAL CONFERENCE ON NANOCHANNELS, MICROCHANNELS, AND MINICHANNELS, PTS A AND B, 1005-1011, 2008
abstract, full text

Southern, James; Pitt-Francis, Joe; Whiteley, Jonathan; Stokeley, Daniel; Kobashi, Hiromichi; Nobes, Ross; Kadooka, Yoshimasa; Gavaghan, David
Multi-scale computational modelling in biology and physiology
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 96:60-89, JAN-APR 2008
abstract, full text, DOI:10.1016/j.pbiomolbio.2007.07.019

Moustakas, Demetri T.
Application of docking methods to structure-based drug design
RSC Biomolecular Sciences, 155-180, 2008
full text

Crowley, M. F.; Uberbacher, E. C.; Brooks, C. L., I.I.I.; Walker, R. C.; Nimlos, M. R.; Himmel, M. E.
Developing improved MD codes for understanding processive cellulases - art. no. 012049
SCIDAC 2008: SCIENTIFIC DISCOVERY THROUGH ADVANCED COMPUTING, 125:12049-12049, 2008
abstract, full text, DOI:10.1088/1742-6596/125/1/012049

Weidemueller, Christian; Hauser, Karin
Impact of an electric field on P-type ATPases
SPECTROSCOPY-AN INTERNATIONAL JOURNAL, 22:319-325, 2008
abstract, full text, DOI:10.3233/SPE-2008-0343

Zheng, Xiaojing; Wintrode, Patrick L.; Chance, Mark R.
Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin
STRUCTURE, 16:38-51, JAN 2008
abstract, full text, DOI:10.1016/j.str.2007.10.019

Ohkubo, Y. Zenrnei; Tajkhorshid, Emad
Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors
STRUCTURE, 16:72-81, JAN 2008
abstract, full text, DOI:10.1016/j.str.2007.10.021

Jalkanen, K. J.; Gale, J. D.; Jalkanen, G. J.; McIntosh, D. F.; El-Azhary, A. A.; Jensen, G. M.
trans-1,2-dicyano-cyclopropane and other cyano-cyclopropane derivatives
THEORETICAL CHEMISTRY ACCOUNTS, 119:211-229, JAN 2008
abstract, full text, DOI:10.1007/s00214-007-0391-6

Mugnaini, Claudia; Alongi, Maddalena; Togninelli, Andrea; Gevariya, Harsukh; Brizzi, Antonella; Manetti, Fabrizio; Bernardini, Cesare; Angeli, Lucilla; Tafi, Andrea; Bellucci, Luca; Corelli, Federico; Massa, Silvio; Maga, Giovanni; Samuele, Alberta; Facchim, Marcella; Clotet-Codina, Imma; Armand-Ugon, Mercedes; Este, Jos A.; Botta, Maurizio
Dihydro-alkylthio-benzyl-oxopyrimidines as inhibitors of reverse transcriptase: Synthesis and rationalization of the biological data on both wild-type enzyme and relevant clinical mutants
JOURNAL OF MEDICINAL CHEMISTRY, 50:6580-6595, DEC 27 2007
abstract, full text, DOI:10.1021/jm0708230

Cheng, Mary Hongying; Liu, Lu Tian; Saladino, Alexander C.; Xu, Yan; Tang, Pei
Molecular dynamics simulations of ternary membrane mixture: Phosphatidylcholine, phosphatidic acid, and cholesterol
JOURNAL OF PHYSICAL CHEMISTRY B, 111:14186-14192, DEC 27 2007
abstract, full text, DOI:10.1021/jp075467b

Sadiq, A. Kashif; Wan, Shunzhou; Coveney, Peter V.
Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site
BIOCHEMISTRY, 46:14865-14877, DEC 25 2007
abstract, full text, DOI:10.1021/bi700864p

Curco, David; Nussinov, Ruth; Aleman, Carlos
Coarse-graining the self-assembly of beta-helical protein building blocks
JOURNAL OF PHYSICAL CHEMISTRY B, 111:14006-14011, DEC 20 2007
abstract, full text, DOI:10.1021/jp075386f

Hermans, Thomas M.; Broeren, Maarten A. C.; Gomopoulos, Nikos; Smeijers, A. F.; Mezari, Brahim; Van Leeuwen, Ellen N. M.; Vos, Matthijn R. J.; Magusin, Pieter C. M. M.; Hilbers, Peter A. J.; Van Genderen, Marcel H. P.; Sommerdijk, Nico A. J. M.; Fytas, George; Meijer, E. W.
Stepwise noncovalent synthesis leading to dendrimer-based assemblies in water
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:15631-15638, DEC 19 2007
abstract, full text, DOI:10.1021/ja074991t

Schmid, Franziska F-F.; Meuwly, Markus
All-atom simulations of structures and energetics of c-di-GMP-bound and free PleD
JOURNAL OF MOLECULAR BIOLOGY, 374:1270-1285, DEC 14 2007
abstract, full text, DOI:10.1016/j.jmb.2007.09.068

Campen, R. Kramer; Verde, Ana Vila; Kubicki, James D.
Influence of glycosidic linkage neighbors on disaccharide conformation in vacuum
JOURNAL OF PHYSICAL CHEMISTRY B, 111:13775-13785, DEC 13 2007
abstract, full text, DOI:10.1021/jp0730996

Hajjar, Eric; Korkmaz, Brice; Reuter, Nathalie
Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase
FEBS LETTERS, 581:5685-5690, DEC 11 2007
abstract, full text, DOI:10.1016/j.febslet.2007.11.029

Jayaraman, Saivenkataraman; Maginn, Edward J.
Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 214504, DEC 7 2007
abstract, full text, DOI:10.1063/1.2801539

Yu, Jin; Ha, Taekjip; Schulten, Klaus
How directional translocation is regulated in a DNA helicase motor
BIOPHYSICAL JOURNAL, 93:3783-3797, DEC 2007
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.109546

Spolnik, Pawel; Stopa, Barbara; Piekarska, Barbara; Jagusiak, Anna; Konieczny, Leszek; Rybarska, Janina; Krol, Marcin; Roterman, Irena; Urbanowicz, Barbara; Zieba-Palus, Janina
The use of rigid, fibrillar Congo red nanostructures for scaffolding protein assemblies and inducing the formation of amyloid-like arrangement of molecules
CHEMICAL BIOLOGY & DRUG DESIGN, 70:491-501, DEC 2007
abstract, full text, DOI:10.1111/j.1747-0285.2007.00589.x

Christensen, S.; Peters, G. H.; Hansen, F. Y.; Abildskov, J.
Thermodynamic models from fluctuation solution theory analysis of molecular simulations
FLUID PHASE EQUILIBRIA, 261:185-190, DEC 1 2007
abstract, full text, DOI:10.1016/j.fluid.2007.07.027

Hamacher, K.
Information theoretical measures to analyze, trajectories in rational molecular design
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2576-2580, DEC 2007
abstract, full text, DOI:10.1002/jcc.20759

Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Hardy, David J.; Trabuco, Leonardo G.; Schulten, Klaus
Accelerating molecular modeling applications with graphics processors
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2618-2640, DEC 2007
abstract, full text, TCBG publications, DOI:10.1002/jcc.20829

Alberto Guevara-Salazar, J.; Espinoza-Fonseca, Michel; Beltran, Hiram I.; Correa-Basurto, Jose; Zavala, Delia Quintana; Trujillo-Ferrara, Jose G.
The electronic influence on the active site-directed inhibition of acetylcholinesterase by N-aryl-substituted succinimides
JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 51:222-227, OCT-DEC 2007
abstract, full text

Akitake, Bradley; Anishkin, Andriy; Liu, Naili; Sukharev, Sergei
Straightening and sequential buckling of the pore-lining helices define the gating cycle of MscS
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 14:1141-1149, DEC 2007
abstract, full text, DOI:10.1038/nsmb1341

Ma, Buyong; Levine, Arnold J.
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements
NUCLEIC ACIDS RESEARCH, 35:7733-7747, DEC 2007
abstract, full text, DOI:10.1093/nar/gkm890

Starzec, Anna; Ladam, Patrick; Vassy, Roger; Badache, Sabah; Bouchemal, Nadia; Navaza, Alda; Du Penhoat, Catherine Herve; Perret, Gerard Y.
Structure-function analysis of the antiangiogenic ATWLPPR peptide inhibiting VEGF(165) binding to neuropilin-1 and molecular dynamics simulations of the ATWLPPR/neuropilin-1 complex
PEPTIDES, 28:2397-2402, DEC 2007
abstract, full text, DOI:10.1016/j.peptides.2007.09.013

Xiao, Huogen; Tanaka, Takuji; Ogawa, Masahiro; Yada, Rickey Y.
Expression and enzymatic characterization of the soluble recombinant plasmepsin I from Plasmodium falciparum
PROTEIN ENGINEERING DESIGN & SELECTION, 20:625-633, DEC 2007
abstract, full text, DOI:10.1093/protein/gzm066

Cui, Shuxun; Yu, Jin; Kuehner, Ferdinand; Schulten, Klaus; Gaub, Hermann E.
Double-stranded DNA dissociates into single strands when dragged into a poor solvent
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:14710-14716, NOV 28 2007
abstract, full text, TCBG publications, DOI:10.1021/ja074776c

Best, Robert B.; Merchant, Kusai A.; Gopich, Irina V.; Schuler, Benjamin; Bax, Ad; Eaton, William A.
Effect of flexibility and cis residues in single-molecule FRET studies of polyproline
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:18964-18969, NOV 27 2007
abstract, full text, DOI:10.1073/pnas.0709567104

Li, Zhenyu; Abramavicius, Darius; Zhuang, Wei; Mukamel, Shaul
Two-dimensional electronic correlation spectroscopy of the n pi* and pi pi* protein backbone transitions: A simulation study
CHEMICAL PHYSICS, 341:29-36, NOV 15 2007
abstract, full text, DOI:10.1016/j.chemphys.2007.03.029

Simona, F.; Magistrato, A.; Vera, D. M. A.; Garau, G.; Vila, A. J.; Carloni, P.
Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 69:595-605, NOV 15 2007
abstract, full text, DOI:10.1002/prot.21476

Schug, Alexander; Whitford, Paul C.; Levy, Yaakov; Onuchic, Jose N.
Mutations as trapdoors to two competing native conformations of the Rop-dimer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:17674-17679, NOV 6 2007
abstract, full text, DOI:10.1073/pnas.0706077104

Kim, Han Ie; Jung, Jinwon; Lee, Eun-Saem; Kim, Yong-Chul; Lee, Weontae; Lee, Seung-Taek
Molecular dissection of the interaction between the SH3 domain and the SH2-Kinase Linker region in PTK6
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 362:829-834, NOV 3 2007
abstract, full text, DOI:10.1016/j.bbrc.2007.08.055

Ivanova, Anela; Jezierski, Grzegorz; Vladimirov, Egor; Roesch, Notker
Structure of rhodamine 6G-DNA complexes from molecular dynamics Simulations
BIOMACROMOLECULES, 8:3429-3438, NOV 2007
abstract, full text, DOI:10.1021/bm7005499

Legge, E. Sue; Treutlein, Herbert; Howlett, Geoffrey J.; Yarovsky, Irene
Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II
BIOPHYSICAL CHEMISTRY, 130:102-113, NOV 2007
abstract, full text, DOI:10.1016/j.bpc.2007.08.002

Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Tsai, Chung-Jun; Nussinov, Ruth
Modeling the Alzheimer A beta(17-42) fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities
BIOPHYSICAL JOURNAL, 93:3046-3057, NOV 2007
abstract, full text, DOI:10.1529/biophysj.107.110700

Luan, Binquan; Caffrey, Martin; Aksimentiev, Aleksei
Structure refinement of the OpcA adhesin using molecular dynamics
BIOPHYSICAL JOURNAL, 93:3058-3069, NOV 2007
abstract, full text, DOI:10.1529/biophysj.107.106724

Cohen, Jordi; Schulten, Klaus
O-2 migration pathways are not conserved across proteins of a similar fold
BIOPHYSICAL JOURNAL, 93:3591-3600, NOV 2007
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.108712

Chen, Kun-Ming; Spratt, Thomas E.; Stanley, Bruce A.; De Cotiis, Dan A.; Bewley, Maria C.; Flanagan, John M.; Desai, Dhimant; Das, Arunangshu; Fiala, Emerich S.; Amin, Shantu; El-Bayoumy, Karam
Inhibition of nuclear Factor-kappa B DNA binding by organoselenocyanates through covalent modification of the p50 subunit
CANCER RESEARCH, 67:10475-10483, NOV 1 2007
abstract, full text, DOI:10.1158/0008-5472.CAN-07-2510

Christensen, Steen; Peters, Gunther H.; Hansen, Flemming Y.; O'Connell, John P.; Abildskov, Jens
State conditions transferability of vapor-liquid equilibria via fluctuation solution theory with correlation function integrals from molecular dynamics simulation
FLUID PHASE EQUILIBRIA, 260:169-176, NOV 1 2007
abstract, full text, DOI:10.1016/j.fluid.2007.06.026

Stanton, Courtney L.; Kuo, I-Feng W.; Mundy, Christopher J.; Laino, Teodoro; Houk, K. N.
QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5 '-monophosphate decarboxylase using two different QM regions: Acceleration too small to explain rate of enzyme catalysis
JOURNAL OF PHYSICAL CHEMISTRY B, 111:12573-12581, NOV 1 2007
abstract, full text, DOI:10.1021/jp074858n

Zanuy, David; Rodriguez-Ropero, Francisco; Nussinov, Ruth; Aleman, Carlos
Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study
JOURNAL OF STRUCTURAL BIOLOGY, 160:177-189, NOV 2007
abstract, full text, DOI:10.1016/j.jsb.2007.07.014

Amaro, Rommie E.; Swift, Robert V.; McCammon, J. Andrew
Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei
PLOS NEGLECTED TROPICAL DISEASES, 1 Art. No. e68, NOV 2007
abstract, full text, DOI:10.1371/journal.pntd.0000068

Fort, Joana; de la Ballina, Laura R.; Burghardt, Hans E.; Ferrer-Costa, Carles; Turnay, Javier; Ferrer-Orta, Cristina; Uson, Isabel; Zorzano, Antonio; Fernandez-Recio, Juan; Orozco, Modesto; Lizarbe, Maria Antonia; Fita, Ignacio; Palacin, Manuel
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:31444-31452, OCT 26 2007
abstract, full text, DOI:10.1074/jbc.M704524200

Raman, E. Prabhu; Takeda, Takako; Barsegov, Valer; Klimov, Dmitri K.
Mechanical unbinding of A beta peptides from amyloid fibrils
JOURNAL OF MOLECULAR BIOLOGY, 373:785-800, OCT 26 2007
abstract, full text, DOI:10.1016/j.jmb.2007.08.034

Zhao, Xiongce; Payne, Christina M.; Cummings, Peter T.; Lee, James W.
Single-strand DNA molecule translocation through nanoelectrode gaps
NANOTECHNOLOGY, 18 Art. No. 424018, OCT 24 2007
abstract, full text, DOI:10.1088/0957-4484/18/42/424018

Yakovlev, Vasily A.; Barani, Igor J.; Rabender, Christopher S.; Black, Stephen M.; Leach, J. Kevin; Graves, Paul R.; Kellogg, Glen E.; Mikkelsen, Ross B.
Tyrosine nitration of I kappa B alpha: A novel mechanism for NF-kappa B activation
BIOCHEMISTRY, 46:11671-11683, OCT 23 2007
abstract, full text, DOI:10.1021/bi701107z

Milac, A. L.; Buchete, N. V.; Fritz, T. A.; Hummer, G.; Tabak, L. A.
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine: Polypeptide N-acetylgalactosaminyltransferase-2
JOURNAL OF MOLECULAR BIOLOGY, 373:439-451, OCT 19 2007
abstract, full text, DOI:10.1016/j.jmb.2007.08.028

Spiegel, Katrin; Magistrato, Alessandra; Carloni, Paolo; Reedijk, Jan; Klein, Michael L.
Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11873-11876, OCT 18 2007
abstract, full text, DOI:10.1021/jp0762323

Gorfe, Alemayehu A.; Babakhani, Arneh; McCammon, J. Andrew
H-ras protein in a bilayer: Interaction and structure perturbation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:12280-12286, OCT 10 2007
abstract, full text, DOI:10.1021/ja073949v

Widge, Alik S.; Matsuoka, Yoky; Kurnikova, Maria
Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers
LANGMUIR, 23:10672-10681, OCT 9 2007
abstract, full text, DOI:10.1021/1a070214v

Gumbart, James; Schulten, Klaus
Structural determinants of lateral gate opening in the protein translocon
BIOCHEMISTRY, 46:11147-11157, OCT 2 2007
abstract, full text, TCBG publications, DOI:10.1021/bi700835d

Seeber, Michele; Cecchini, Marco; Rao, Francesco; Settanni, Giovanni; Caflisch, Amedeo
Wordom: a program for efficient analysis of molecular dynamics simulations
BIOINFORMATICS, 23:2625-2627, OCT 1 2007
abstract, full text, DOI:10.1093/bioinformatics/btm378

Zanuy, David; Rodriguez-Ropero, Francisco; Haspel, Nurit; Zheng, Jie; Nussinov, Ruth; Aleman, Carlos
Stability of tubular structures based on beta-helical proteins: Self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences
BIOMACROMOLECULES, 8:3135-3146, OCT 2007
abstract, full text, DOI:10.1021/bm700561t

Lagerqvist, Johan; Zwolak, Michael; Di Ventra, Massimiliano
Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
BIOPHYSICAL JOURNAL, 93:2384-2390, OCT 2007
abstract, full text, DOI:10.1529/biophysj.106.102269

Radhakrishnan, Ravi
Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage
BIOPHYSICAL JOURNAL, 93:2391-2399, OCT 2007
abstract, full text, DOI:10.1529/biophysj.107.104661

Cheng, Xiaolin; Ivanov, Ivaylo; Wang, Hailong; Sine, Steven M.; McCammon, J. Andrew
Nanosecond-timescale conformational dynamics of the human alpha 7 nicotinic acetylcholine receptor
BIOPHYSICAL JOURNAL, 93:2622-2634, OCT 2007
abstract, full text, DOI:10.1529/biophysj.107.109843

Thomas, Michael; Jayatilaka, Dylan; Corry, Ben
The predominant role of coordination number in potassium channel selectivity
BIOPHYSICAL JOURNAL, 93:2635-2643, OCT 2007
abstract, full text, DOI:10.1529/biophysj.107.108167

Damjanovic, Ana; Schlessman, Jamie L.; Fitch, Carolyn A.; Garcia, Angel E.; Garcia-Moreno, Bertrand
Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins
BIOPHYSICAL JOURNAL, 93:2791-2804, OCT 2007
abstract, full text, DOI:10.1529/biophysj.107.104182

Pant, Kartikeya; Dutta, Udayan
Software packages for studying diffusion pathways of gases in proteins
Biophysical Reviews and Letters, 2:273-286, OCT 2007
abstract, full text, DOI:10.1142/S1793048007000544

Gorfe, Alemayehu A.; Caflisch, Amedeo
Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier
FASEB JOURNAL, 21:3279-3287, OCT 2007
abstract, full text, DOI:10.1096/fj.07-8292com

Mukhopadhyay, B. P.; Ghosh, B.; Bairagya, H. R.; Bera, A. K.; Nandi, T. K.; Das, S. B.
Modeling study of rusticyanin-cytochrome C-4 complex: An insight to possible H-bond mediated recognition and electron - Transfer process
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 25:157-164, OCT 2007
abstract, full text

Siggel, Lorenz; Bulo, Rosa E.; Molnar, Ferenc; Weiss, Horst; Taeger, Tilman
Leather relates collagen modeling: The challenges of modeling hierarchical structures
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 102:333-336, OCT 2007
full text

Wells, David B.; Abramkina, Volha; Aksimentiev, Aleksei
Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 125101, SEP 28 2007
abstract, full text, DOI:10.1063/1.2770738

Moroni, Elisabetta; Caselle, Michele; Fogolari, Federico
Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes
BMC STRUCTURAL BIOLOGY, 7 Art. No. 61, SEP 27 2007
abstract, full text, DOI:10.1186/1472-6807-7-61

Ivanova, Anela; Roesch, Notker
The structure of LNA : DNA hybrids from molecular dynamics simulations: The effect of locked nucleotides
JOURNAL OF PHYSICAL CHEMISTRY A, 111:9307-9319, SEP 27 2007
abstract, full text, DOI:10.1021/jp073198j

Shih, Amy Y.; Arkhipov, Anton; Freddolino, Peter L.; Sligar, Stephen G.; Schulten, Klaus
Assembly of lipids and proteins into lipoprotein particles
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11095-11104, SEP 27 2007
abstract, full text, TCBG publications, DOI:10.1021/jp072320b

Mottamal, Madhusoodanan; Shen, Sui; Guembe, Cristina; Krilov, Goran
Solvation of transmembrane proteins by isotropic membrane mimetics: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11285-11296, SEP 27 2007
abstract, full text, DOI:10.1021/jp0740245

Patra, Swarna M.; Bastug, Turgut; Kuyucak, Serdar
Binding of organic cations to gramicidin a channel studied with AutoDock and molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11303-11311, SEP 27 2007
abstract, full text, DOI:10.1021/jp0742281

Liu, Yuqi; Henry, Gillian D.; Hegde, Rashmi S.; Baleja, James D.
Solution structure of the hDIg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 Papillomavirus E6 protein
BIOCHEMISTRY, 46:10864-10874, SEP 25 2007
abstract, full text, DOI:10.1021/bi700879k

Porter, Corrine J.; Matthews, Jacqueline M.; Mackay, Joel P.; Pursglove, Sharon E.; Schmidberger, Jason W.; Leedman, Peter J.; Pero, Stephanie C.; Krag, David N.; Wilce, Matthew C. J.; Wilce, Jacqueline A.
Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation
BMC STRUCTURAL BIOLOGY, 7 Art. No. 58, SEP 25 2007
abstract, full text, DOI:10.1186/1472-6807-7-58

Zhou, Hailong; Wu, Tao; Dong, Xiuli; Wang, Qi; Shen, Jiawei
Adsorption mechanism of BMP-7 on hydroxyapatite (001) surfaces
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 361:91-96, SEP 14 2007
abstract, full text, DOI:10.1016/j.bbrc.2007.06.169

Dehez, Francois; Tarek, Mounir; Chipot, Christophe
Energetics of ion transport in a peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10633-10635, SEP 13 2007
abstract, full text, DOI:10.1021/jp075308s

Henthorn, David B.; Peppas, Nicholas A.
Molecular simulations of recognitive behavior of molecularly imprinted intelligent polymeric networks
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 46:6084-6091, SEP 12 2007
abstract, full text, DOI:10.1021/ie0613691

Jo, Sunhwan; Kim, Taehoon; Im, Wonpil
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
PLOS ONE, 2 Art. No. e880, SEP 12 2007
abstract, full text, DOI:10.1371/journal.pone.0000880

Curco, David; Nussinov, Ruth; Aleman, Carlos
Coarse-grained representation of beta-helical protein building blocks
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10538-10549, SEP 6 2007
abstract, full text, DOI:10.1021/jp072832q

Roy, Arijit; Taraphder, Srabani
Identification of proton-transfer pathways in human carbonic anhydrase II
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10563-10576, SEP 6 2007
abstract, full text, DOI:10.1021/jp073499t

Bender, Gretchen M.; Lehmann, Andreas; Zou, Hongling; Cheng, Hong; Fry, H. Christopher; Engel, Don; Therien, Michael J.; Blasie, J. Kent; Roder, Heinrich; Saven, Jeffrey G.; DeGrado, William F.
De novo design of a single-chain diphenylporphyrin metalloprotein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:10732-10740, SEP 5 2007
abstract, full text, DOI:10.1021/ja071199j

Hemp, James; Han, Huazhi; Roh, Jung Hyeob; Kaplan, Samuel; Martinez, Todd J.; Gennis, Robert B.
Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb(3) oxidase) of heme-copper oxygen reductases
BIOCHEMISTRY, 46:9963-9972, SEP 4 2007
abstract, full text, DOI:10.1021/bi700659y

Jones, Peter M.; Turner, Kylie M.; Djordjevic, Julianne T.; Sorrell, Tania C.; Wright, Lesley C.; George, Anthony M.
Role of conserved active site residues in catalysis by phospholipase B1 from Cryptococcus neoformans
BIOCHEMISTRY, 46:10024-10032, SEP 4 2007
abstract, full text, DOI:10.1021/bi7009508

Zhuang, Wei; Abrarnavicius, Darius; Voronine, Dirnitrii V.; Mukarmel, Shaul
Simulation of two-dimensional infrared spectroscopy of amyloid fibrils
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:14233-14236, SEP 4 2007
abstract, full text, DOI:10.1073/pnas.0700392104

Mazzini, S.; Fernandez-Vidal, M.; Galbusera, V.; Castro-Roman, F.; Bellucci, M. C.; Ragg, E.; Haro, I.
3D-Structure of the interior fusion peptide of HGV/GBV-C by 1H NMR, CD and molecular dynamics studies
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 465:187-196, SEP 1 2007
abstract, full text, DOI:10.1016/j.abb.2007.05.024

Tuukkanen, Anne; Kaila, Ville R. I.; Laakkonen, L'isa; Hummer, Gerhard; Wikstrom, Marten
Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1767:1102-1106, SEP 2007
abstract, full text, DOI:10.1016/j.bbabio.2007.06.010

Wierzbicki, Andrzej; Dalal, Pranav; Cheatham, Thomas E., I.I.I.; Knickelbein, Jared E.; Haymet, A. D. J.; Madura, Jeffry D.
Antifreeze proteins at the Ice/Water interface: Three calculated discriminating properties for orientation of type I proteins
BIOPHYSICAL JOURNAL, 93:1442-1451, SEP 2007
abstract, full text, DOI:10.1529/biophysj.107.105189

Lee, Eric H.; Hsin, Jen; Mayans, Olga; Schulten, Klaus
Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model
BIOPHYSICAL JOURNAL, 93:1719-1735, SEP 2007
abstract, full text, TCBG publications, DOI:10.1529/biophysj.107.105528

Sliozberg, Yelena; Abrams, Cameron F.
Spontaneous conformational changes in the e. coli GroEL subunit from all-atom molecular dynamics Simulations
BIOPHYSICAL JOURNAL, 93:1906-1916, SEP 2007
abstract, full text, DOI:10.1529/biophys.107.108043

Jang, Hyunbum; Zheng, Jie; Nussinov, Ruth
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process
BIOPHYSICAL JOURNAL, 93:1938-1949, SEP 2007
abstract, full text, DOI:10.1529/biophysj.107.110148

Espinoza-Fonseca, L. Michel; Kast, David; Thomas, David D.
Molecular dynamics Simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin
BIOPHYSICAL JOURNAL, 93:2083-2090, SEP 2007
abstract, full text, DOI:10.1529/biophysj.106.095802

Boghosian, Bruce; Coveney, Peter; Dong, Suchuan; Finn, Lucas; Jha, Shantenu; Karniadakis, George; Karonis, Nicholas
NEKTAR, SPICE and Vortonics: using federated grids for large scale scientific applications
CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS, 10:351-364, SEP 2007
abstract, full text, DOI:10.1007/s10586-007-0029-4

Merelli, Ivan; Morra, Giulia; Milanesi, Luciano
Evaluation of a grid based molecular dynamics approach for polypeptide simulations
IEEE TRANSACTIONS ON NANOBIOSCIENCE, 6:229-234, SEP 2007
abstract, full text, DOI:10.1109/TNB.2007.903483

Yesylevskyy, Semen O.
ProtSqueeze: Simple and effective automated tool for setting up membrane protein simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 47:1986-1994, SEP-OCT 2007
abstract, full text, DOI:10.1021/ci600553y

Jojart, Balazs; Martinek, Tamas A.
Performance of the general amber force field in modeling aqueous POPC membrane bilayers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2051-2058, SEP 2007
abstract, full text, DOI:10.1002/jcc.20748

Kutzner, Carsten; Van der Spoel, David; Fechner, Martin; Lindahl, Erik; Schmitt, Udo W.; De Groot, Bert L.; Grubmuller, Helmut
Software news and update - Speeding up parallel GROMACS on high-latency networks
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2075-2084, SEP 2007
abstract, full text, DOI:10.1002/jcc.20703

Rivail, L.; Chipot, C.; Maigret, B.; Bestel, I.; Sicsic, S.; Tarek, M.
Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 817:19-26, SEP 1 2007
abstract, full text, DOI:10.1016/j.theochem.2007.04.012

Nilsson, Lina M.; Yakovenko, Olga; Tchesnokova, Veronika; Thomas, Wendy E.; Schembri, Mark A.; Vogel, Viola; Klemm, Per; Sokurenko, Evgeni V.
The cysteine bond in the Escherichia coli FimH adhesin is critical for adhesion under flow conditions
MOLECULAR MICROBIOLOGY, 65:1158-1169, SEP 2007
abstract, full text, DOI:10.1111/j.1365-2958.2007.05858.x

Delgado-Buscalioni, R.; De Fabritiis, G.
Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids
PHYSICAL REVIEW E, 76 Art. No. 036709, SEP 2007
abstract, full text, DOI:10.1103/PhysRevE.76.036709

Szarecka, Agnieszka; Xu, Yan; Tang, Pei
Dynamics of heteropentameric nicotinic acetylcholine receptor: Implications of the gating mechanism
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:948-960, SEP 2007
abstract, full text, DOI:10.1002/prot.21462

Levin, Elena J.; Kondrashov, Dmitry A.; Wesenberg, Gary E.; Phillips, George N., Jr.
Ensemble refinement of protein crystal structures: Validation and application
STRUCTURE, 15:1040-1052, SEP 2007
abstract, full text, DOI:10.1016/j.str.2007.06.019

Herrera, Fernando E.; Zucchelli, Silvia; Jezierska, Aneta; Lavina, Zeno Scotto; Gustincich, Stefano; Carloni, Paolo
On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson disease - A combined computational and in vitro study
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:24905-24914, AUG 24 2007
abstract, full text, DOI:10.1074/jbc.M701013200

Anavi-Goffer, Sharon; Fleischer, Daniel; Hurst, Dow P.; Lynch, Diane L.; Barnett-Norris, Judy; Shi, Shanping; Lewis, Deborah L.; Mukhopadhyay, Somnath; Howlett, Allyn C.; Reggio, Patricia H.; Abood, Mary E.
Helix 8 Leu in the CB1 cannabinoid receptor contributes to selective signal transduction mechanisms
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:25100-25113, AUG 24 2007
abstract, full text, DOI:10.1074/jbc.M703388200

Asthagiri, D.; Ashbaugh, H. S.; Piryatinski, A.; Paulaitis, M. E.; Pratt, L. R.
Non-van der waals treatment of the hydrophobic solubilities of CF4
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:10133-10140, AUG 22 2007
abstract, full text, DOI:10.1021/ja071037n

Zhu, Hui; May, Volkhard; Roeder, Beate; Madjet, Mohamed Ei-Amine; Renger, Thomas
The pheophorbide-a DAB dendrimer P-4 in solution: MD-simulations based studies of exciton states
CHEMICAL PHYSICS LETTERS, 444:118-124, AUG 17 2007
abstract, full text, DOI:10.1016/j.cplett.2007.06.126

Kelkar, Manish S.; Maginn, Edward J.
Calculating the enthalpy of vaporization for ionic liquid clusters
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9424-9427, AUG 16 2007
abstract, full text, DOI:10.1021/jp073253o

Rapedius, Markus; Fowler, Philip W.; Shang, Lijun; Sansom, Mark S. P.; Tucker, Stephen J.; Baukrowitz, Thomas
H bonding at the helix-bundle crossing controls gating in Kir potassium channels
NEURON, 55:602-614, AUG 16 2007
abstract, full text, DOI:10.1016/j.neuron.2007.07.026

Fang, Bin; Martyna, Glenn; Deng, Yuefan
A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer
COMPUTER PHYSICS COMMUNICATIONS, 177:362-377, AUG 15 2007
abstract, full text, DOI:10.1016/j.cpc.2007.01.011

Budiman, Michael E.; Knaggs, Michael H.; Fetrow, Jacquelyn S.; Alexander, Rebecca W.
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:670-689, AUG 15 2007
abstract, full text, DOI:10.1002/prot.21426

Saam, Jan; Ivanov, Igor; Walther, Matthias; Holzhuetter, Hermann-Georg; Kuhn, Hartmut
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:13319-13324, AUG 14 2007
abstract, full text, DOI:10.1073/pnas.0702401104

Aprikian, Pavel; Tchesnokova, Veronika; Kidd, Brian; Yakovenko, Olga; Yarov-Yarovoy, Vladimir; Trinchina, Elena; Vogel, Viola; Thomas, Wendy; Sokurenko, Evgeni
Interdomain interaction in the FimH adhesin of Escherichia coli regulates the affinity to mannose
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:23437-23446, AUG 10 2007
abstract, full text, DOI:10.1074/jbc.M702037200

Ashbaugh, Henry S.; Pratt, Lawrence R.
Contrasting nonaqueous against aqueous solvation on the basis of scaled-particle theory
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9330-9336, AUG 9 2007
abstract, full text, DOI:10.1021/jp071969d

Jones, Peter M.; George, Anthony M.
Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette - A computational study of the MJ0796 dimer
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:22793-22803, AUG 3 2007
abstract, full text, DOI:10.1074/jbc.M700809200

Fuentes-Cabrera, Miguel; Zhao, Xiongce; Kent, P. R. C.; Sumpter, Bobby G.
Electronic structure of xDNA
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9057-9061, AUG 2 2007
abstract, full text, DOI:10.1021/jp0729056

Vistoli, Giulio; Pedretti, Alessandro; Testa, Bernard; Matucci, Rosanna
The conformational and property space of acetylcholine bound to muscarinic receptors: An entropy component accounts for the subtype selectivity of acetylcholine
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 464:112-121, AUG 1 2007
abstract, full text, DOI:10.1016/j.abb.2007.04.022

Dong, Xiuli; Wang, Qi; Wu, Tao; Pan, Haihua
Understanding adsorption-desorption dynamics of BMP-2 on hydroxyapatite (001) surface
BIOPHYSICAL JOURNAL, 93:750-759, AUG 2007
abstract, full text, DOI:10.1529/biophysj.106.103168

Zheng, Xiange; Diraviyam, Karthikeyan; Sept, David
Nucleotide effects on the structure and dynamics of actin
BIOPHYSICAL JOURNAL, 93:1277-1283, AUG 2007
abstract, full text, DOI:10.1529/biophysj.107.109215

Geroult, Sebastien; Hooda, Manisha; Virdee, Satpal; Waksman, Gabriel
Prediction of solvation sites at the interface of src SH2 domain complexes using molecular dynamics simulations
CHEMICAL BIOLOGY & DRUG DESIGN, 70:87-99, AUG 2007
abstract, full text, DOI:10.1111/j.1747-0285.2007.00545.x

Villoutreix, Bruno O.; Renault, Nicolas; Lagorce, David; Sperandio, Olivier; Montes, Matthieu; Miteva, Maria A.
Free resources to assist structure-based virtual ligand screening experiments
CURRENT PROTEIN & PEPTIDE SCIENCE, 8:381-411, AUG 2007
abstract, full text

Lou, Jizhong; Yago, Tadayuki; Mcever, Rodger P.; Zhu, Cheng
The sliding-rebinding mechanism for catch bonds
JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS, 46:5528-5535, AUG 2007
abstract, full text, DOI:10.1143/JJAP.46.55281

Roumen, Luc; Sanders, Marijn P. A.; Pieterse, Koen; Hilbers, Peter A. J.; Plate, Ralf; Custers, Erica; de Gooyer, Marcel; Smits, Jos F. M.; Beugels, Ilona; Emmen, Judith; Ottenheijm, Harry C. J.; Leysen, Dirk; Hermans, J. J. R.
Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 21:455-471, AUG 2007
abstract, full text, DOI:10.1007/s10822-007-9128-9

Gong, Haipeng; Shen, Yang; Rose, George D.
Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly
PROTEIN SCIENCE, 16:1515-1521, AUG 2007
abstract, full text, DOI:10.1110/ps.072988407

Venkat, Anurag Setty; Corni, Stefano; Di Felice, Rosa
Etectronic coupling between azurin and gold at different protein/substrate orientations
SMALL, 3:1431-1437, AUG 2007
abstract, full text, DOI:10.1002/smll.200700001

Peters, Baron; Beckham, Gregg T.; Trout, Bernhardt L.
Extensions to the likelihood maximization approach for finding reaction coordinates
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 034109, JUL 21 2007
abstract, full text, DOI:10.1063/1.2748396

Krzysko, K. A.; Kolinski, M.; Filipek, S.
Molecular modelling of the complex of oligomeric rhodopsin and its G protein
JOURNAL OF PHYSICS-CONDENSED MATTER, 19 Art. No. 285204, JUL 18 2007
abstract, full text, DOI:10.1088/0953-8984/19/28/285204

Neelov, Alexey; Ghasemi, S. Alireza; Goedecker, Stefan
Particle-particle, particle-scaling function algorithm for electrostatic problems in free boundary conditions
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 024109, JUL 14 2007
abstract, full text, DOI:10.1063/1.2746328

Solares, Santiago D.; Crone, Joshua C.
Real-time simulation of isolated biomolecule characterization with frequency and force modulation atomic force microscopy
JOURNAL OF PHYSICAL CHEMISTRY C, 111:10029-10034, JUL 12 2007
abstract, full text, DOI:10.1021/jp0718350

Coskuner, Orkid
Preferred conformation of the glycosidic linkage of methyl-beta-mannose
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 015101, JUL 7 2007
abstract, full text, DOI:10.1063/1.2747238

Ivanov, Ivaylo; Cheng, Xiaolin; Sine, Steven M.; McCammon, J. Andrew
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:8217-8224, JUL 4 2007
abstract, full text, DOI:10.1021/ja070778l

Zhang, Dajun; Chippada, Uday; Jordan, Kenneth
Effect of the structural water on the mechanical properties of collagen-like microfibrils: A molecular dynamics study
ANNALS OF BIOMEDICAL ENGINEERING, 35:1216-1230, JUL 2007
abstract, full text, DOI:10.1007/s10439-007-9296-8

Dawelbait, Gihan; Winter, Christof; Zhang, Yanju; Pilarsky, Christian; Gruetzmann, Robert; Heinrich, Joerg-Christian; Schroeder, Michael
Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data
BIOINFORMATICS, 23:I115-I124, JUL 1 2007
abstract, full text, DOI:10.1093/bioinformatics/btm188

Haspel, Nurit; Zanuy, David; Zheng, Jie; Aleman, Carlos; Wolfson, Haim; Nussinov, Ruth
Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer
BIOPHYSICAL JOURNAL, 93:245-253, JUL 2007
abstract, full text, DOI:10.1529/biophysj.106.100644

Gumbart, James; Wiener, Michael C.; Tajkhorshid, Emad
Mechanics of force propagation in TonB-dependent outer membrane transport
BIOPHYSICAL JOURNAL, 93:496-504, JUL 2007
abstract, full text, DOI:10.1529/biophysj.107.104158

Cilurzo, Francesco; Selmin, Francesca; Vistoli, Giulio; Minghetti, Paola; Montanari, Luisa
Binary polymeric blends to microencapsulate nitroflurbiprofen: Physicochemical and in silico studies
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 31:202-210, JUL 2007
abstract, full text, DOI:10.1016/j.ejps.2007.03.010

Skeel, Robert D.; Hardy, David J.; Phillips, James C.
Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 225:1-5, JUL 1 2007
full text, DOI:10.1016/j.jcp.2007.03.010

Cyr, Eric C.; Bond, Stephen D.
Using the method of weighted residuals to compute potentials of mean force
JOURNAL OF COMPUTATIONAL PHYSICS, 225:714-729, JUL 1 2007
abstract, full text, DOI:10.1016/j.jcp.2006.12.015

Mamonov, Artem B.; Coalson, Rob D.; Zeidel, Mark L.; Mathai, John C.
Water and deuterium oxide permeability through aquaporin 1: MD predictions and experimental verification
JOURNAL OF GENERAL PHYSIOLOGY, 130:111-116, JUL 2007
abstract, full text, DOI:10.1085/jgp.200709810

Boiteux, Celine; Kraszewski, Sebastian; Ramseyer, Christophe; Girardet, Claude
Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives
JOURNAL OF MOLECULAR MODELING, 13:699-713, JUL 2007
abstract, full text, DOI:10.1007/s00894-007-0202-y

Orlowski, Slawomir; Nowak, Wieslaw
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin
JOURNAL OF MOLECULAR MODELING, 13:715-723, JUL 2007
abstract, full text, DOI:10.1007/s00894-007-0203-x

Peplowski, Lukasz; Kubiak, Karina; Nowak, Wieslaw
Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides
JOURNAL OF MOLECULAR MODELING, 13:725-730, JUL 2007
abstract, full text, DOI:10.1007/s00894-007-0181-z

Kuang, Zhifeng; Mahankali, Uma; Beck, Thomas L.
Proton pathways and H+/Cl- stoichiometry in bacterial chloride transporters
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:26-33, JUL 2007
abstract, full text, DOI:10.1002/prot.21441

Krol, Marcin; Tournier, Alexander L.; Bates, Paul A.
Flexible relaxation of rigid-body docking solutions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:159-169, JUL 2007
abstract, full text, DOI:10.1002/prot.21391

Ni, Feng-Yun; Cai, Bin; Ding, Zhi-Chun; Zheng, Fei; Zhang, Ming-Jie; Wu, Hou-Ming; Sun, Hong-Zhe; Huang, Zhong-Xian
Structural prediction of the beta-domain of metallothionein-3 by molecular dynamics simulation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:255-266, JUL 2007
abstract, full text, DOI:10.1002/prot.21404

Wang, Boyang; Kral, Petr
Chemically tunable nanoscale propellers of liquids
PHYSICAL REVIEW LETTERS, 98 Art. No. 266102, JUN 29 2007
abstract, full text, DOI:10.1103/PhysRevLett.98.266102

Bellesia, Giovanni; Shea, Joan-Emma
Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates
JOURNAL OF CHEMICAL PHYSICS, 126 Art. No. 245104, JUN 28 2007
abstract, full text, DOI:10.1063/1.2739547

Floquet, Nicolas; Mouilleron, Stephane; Daher, Rasha; Maigret, Bernard; Badet, Bernard; Badet-Denisot, Marie-Ange
Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): Molecular dynamics simulations and kinetic studies of protein mutants
FEBS LETTERS, 581:2981-2987, JUN 26 2007
abstract, full text, DOI:10.1016/j.febslet.2007.05.068

Johnson, Bryan J.; Cohen, Jordi; Welford, Richard W.; Pearson, Arwen R.; Schulten, Klaus; Klinman, Judith P.; Wilmot, Carrie M.
Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:17767-17776, JUN 15 2007
abstract, full text, TCBG publications, DOI:10.1074/jbc.M701308200

Tucinska-Daneluti, Agata M.; Gorecki, Adam; Czubaty, Alicja; Kowalska-Loth, Barbara; Girstun, Agnieszka; Murawska, Magdalena; Lesyng, Bogdan; Staron, Krzysztof
RRM proteins-interacting with the cap region of topoisomerase I
JOURNAL OF MOLECULAR BIOLOGY, 369:1098-1112, JUN 15 2007
abstract, full text, DOI:10.1016/j.jmb.2007.04.017

O'Brien, Edward P.; Dima, Ruxandra I.; Brooks, Bernard; Thirumalai, D.
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:7346-7353, JUN 13 2007
abstract, full text, DOI:10.1021/ja069232+

Glykos, Nicholas M.
On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 63:705-713, JUN 2007
abstract, full text, DOI:10.1107/S0907444907014928

Hill, Cheryl L.; Hung, Lee Chiang; Smith, Derek J.; Verma, Chandra S.; Grogan, Gideon
On the resolution of chiral substrates by a retro-claisenase enzyme: Biotransformations of heteroannular bicyclic beta-diketones by 6-oxocamphor hydrolase
ADVANCED SYNTHESIS & CATALYSIS, 349:1353-1360, JUN 2007
abstract, full text, DOI:10.1002/adsc.200700046

Sonne, Jacob; Jensen, Morten O.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Gunther H.
Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension
BIOPHYSICAL JOURNAL, 92:4157-4167, JUN 2007
abstract, full text, DOI:10.1529/biophysj.106.087130

Jorgensen, Anne Marie; Tagmose, Lena; Jorgensen, Anne Marie M.; Bogeso, Klaus P.; Peters, Guenther H.
Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system
CHEMMEDCHEM, 2:827-840, JUN 2007
abstract, full text, DOI:10.1002/cmdc.200600243

De Fabritiis, G.
Performance of the Cell processor for biomolecular simulations
COMPUTER PHYSICS COMMUNICATIONS, 176:660-664, JUN 2007
abstract, full text, DOI:10.1016/j.cpc.2007.02.107

Waibel, Benjamin; Scheiber, Josef; Meier, Claudia; Hammitzsch, Manuela; Baumann, Knut; Scriba, Gerhard K. E.; Holzgrabe, Ulrike
Comparison of cyclodextrin-dipeptide inclusion complexes in the absence and presence of urea by means of capillary electrophoresis, nuclear magnetic resonance and molecular modeling
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18, 2921-2930, JUN 2007
abstract, full text, DOI:10.1002/ejoc.200700052

Buehler, Markus J.
Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture
JOURNAL OF MECHANICS OF MATERIALS AND STRUCTURES, 2:1019-1057, JUN 2007
abstract, full text, DOI:10.2140/jomms.2007.2.1019

Xaplanteri, Maria A.; Papadopoulos, Georgios; Leontiadou, Fotini; Choli-Papadopoulou, Theodora; Kalpaxis, Dimitrios L.
The contribution of the zinc-finger motif to the function of Thermus thermophilus ribosomal protein S14
JOURNAL OF MOLECULAR BIOLOGY, 369:489-497, JUN 1 2007
abstract, full text, DOI:10.1016/j.jmb.2007.03.056

Zhao, Q.; Sigalov, G.; Dimitrov, V.; Dorvel, B.; Mirsaidov, U.; Sligar, S.; Aksimentiev, A.; Timp, G.
Detecting SNPs using a synthetic nanopore
NANO LETTERS, 7:1680-1685, JUN 2007
abstract, full text, DOI:10.1021/nl070668c

Shih, Amy Y.; Freddolino, Peter L.; Sligar, Stephen G.; Schulten, Klaus
Disassembly of nanodiscs with cholate
NANO LETTERS, 7:1692-1696, JUN 2007
abstract, full text, TCBG publications, DOI:10.1021/nl0706906

Burden, Conrad J.; Oakley, Aaron J.
Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations
PHYSICAL BIOLOGY, 4:79-90, JUN 2007
abstract, full text, DOI:10.1088/1478-3975/4/2/002

Oberhofer, Harald; Dellago, Christoph; Boresch, Stefan
Single molecule pulling with large time steps
PHYSICAL REVIEW E, 75 Art. No. 061106, JUN 2007
abstract, full text, DOI:10.1103/PhysRevE.75.061106

Raman, E. Prabhu; Barsegov, Valeri; Klimov, Dmitri K.
Folding of tandem-linked domains
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67:795-810, JUN 2007
abstract, full text, DOI:10.1002/prot.21339

Sotomayor, Marcos; Schulten, Klaus
Single-molecule experiments in vitro and in silico
SCIENCE, 316:1144-1148, MAY 25 2007
abstract, full text, TCBG publications, DOI:10.1126/science.1137591

Budi, Akin; Legge, F. Sue; Treutlein, Herbert; Yarovsky, Irene
Effect of frequency on insulin response to electric field stress
JOURNAL OF PHYSICAL CHEMISTRY B, 111:5748-5756, MAY 24 2007
abstract, full text, DOI:10.1021/jp067248g

Guo, Jun-Tao; Jaromczyk, Jerzy W.; Xu, Ying
Analysis of chameleon sequences and their implications in biological processes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67:548-558, MAY 15 2007
abstract, full text, DOI:10.1002/prot.21285

Takeda, Takako; Klimov, Dmitri K.
Dissociation of A beta(16-22) amyloid fibrils probed by molecular dynamics
JOURNAL OF MOLECULAR BIOLOGY, 368:1202-1213, MAY 11 2007
abstract, full text, DOI:10.1016/j.jmb.2007.02.066

Kelkar, Manish S.; Maginn, Edward J.
Effect of temperature and water content on the shear viscosity of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide as studied by atomistic simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:4867-4876, MAY 10 2007
abstract, full text, DOI:10.1021/jp0686893

Sass, Hans-Juergen; Schmid, Franziska Fang-Fang; Grzesiek, Stephan
Correlation of protein structure and dynamics to scalar couplings across hydrogen bonds
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:5898-5903, MAY 9 2007
abstract, full text, DOI:10.1021/ja068336h

Ramos, Lavoisier S.; Chen, Min-Hsuan; Knox, Barry E.; Birge, Robert R.
Regulation of photoactivation in vertebrate short wavelength visual pigments: Protonation of the retinylidene Schiff base and a counterion switch
BIOCHEMISTRY, 46:5330-5340, MAY 8 2007
abstract, full text, DOI:10.1021/bi700138g

Munson, Keith; Law, Richard J.; Sachs, George
Analysis of the gastric H,K ATPase for ion pathways and inhibitor binding sites
BIOCHEMISTRY, 46:5398-5417, MAY 8 2007
abstract, full text, DOI:10.1021/bi062305h

Buchete, Nicolae-Viorel; Hummer, Gerhard
Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils
BIOPHYSICAL JOURNAL, 92:3032-3039, MAY 1 2007
abstract, full text, DOI:10.1529/biophysj.106.100404

Weronski, Pawel; Jiang, Yi; Rasmussen, Steen
Molecular dynamics study of small PNA molecules in lipid-water system
BIOPHYSICAL JOURNAL, 92:3081-3091, MAY 1 2007
abstract, full text, DOI:10.1529/biophysj.106.097352

Lamoureux, Guillaume; Klein, Michael L.; Berneche, Simon
A stable water chain in the hydrophobic pore of the AmtB ammonium transporter
BIOPHYSICAL JOURNAL, 92:L82-L84, MAY 1 2007
abstract, full text, DOI:10.1529/biophysj.106.102756

Sorensen, Jesper; Hamelberg, Donald; Schiott, Birgit; McCammon, J. Andrew
Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism
BIOPOLYMERS, 86:73-82, MAY 2007
abstract, full text, DOI:10.1002/bip.20705

Fowler, Philip W.; Geroult, Sebastien; Jha, Shantenu; Waksman, Gabriel; Coveney, Peter V.
Rapid, accurate, and precise calculation of relative binding affinities for the SH2 domain using a computational grid
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:1193-1202, MAY-JUN 2007
abstract, full text, DOI:10.1021/ct6003017

Chen, Xin; Deng, Yuefan
Long-time molecular dynamics simulations of botulinum biotoxin type-A at different pH values and temperatures
JOURNAL OF MOLECULAR MODELING, 13:559-572, MAY 2007
abstract, full text, DOI:10.1007/s00894-007-0178-7

Bulo, Rosa E.; Donadio, Davide; Laio, Alessandro; Molnar, Ferenc; Rieger, Jens; Parrinello, Michele
"Site binding" of Ca2+ ions to polyacrylates in water: A molecular dynamics study of coiling and aggregation
MACROMOLECULES, 40:3437-3442, MAY 1 2007
abstract, full text, DOI:10.1021/ma062467l

Rueda, Manuel; Chacon, Pablo; Orozco, Modesto
Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
STRUCTURE, 15:565-575, MAY 2007
abstract, full text, DOI:10.1016/j.str.2007.03.013

Tayefeh, Sascha; Kloss, Thomas; Thiel, Gerhard; Hertel, Brigitte; Moroni, Anna; Kast, Stefan M.
Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels
BIOCHEMISTRY, 46:4826-4839, APR 24 2007
abstract, full text, DOI:10.1021/bi602468r

Wang, Zhong-Hua; Lin, Ying-Wu; Rosell, Federico I.; Ni, Feng-Yun; Lu, Hao-Jie; Yang, Peng-Yuan; Tan, Xiang-Shi; Li, Xiao-Yuan; Huang, Zhong-Xian; Mauk, A. Grant
Converting cytochrome c into a peroxidase-like metalloenzyme by molecular design
CHEMBIOCHEM, 8:607-609, APR 16 2007
full text, DOI:10.1002/cbic.200600547

Pedretti, Alessandro; Vistoli, Giulio
Modeling of human ghrelin receptor (hGHS-R1a) in its close state and validation by molecular docking
BIOORGANIC & MEDICINAL CHEMISTRY, 15:3054-3064, APR 15 2007
abstract, full text, DOI:10.1016/j.bmc.2007.01.057

Johnson, Colin P.; Gaetani, Massimiliano; Ortiz, Vanessa; Bhasin, Nishant; Harper, Sandy; Gallagher, Patrick G.; Speicher, David W.; Discher, Dennis E.
Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding
BLOOD, 109:3538-3543, APR 15 2007
abstract, full text, DOI:10.1182/blood-2006-07-038588

Christensen, S.; Peters, G. H.; Hansen, F. Y.; O'Connell, J. P.; Abildskov, J.
Generation of thermodynamic data for organic liquid mixtures from molecular simulations
MOLECULAR SIMULATION, 33:449-457, APR 15 2007
abstract, full text, DOI:10.1080/08927020601177109

Klauda, Jeffery B.; Brooks, Bernard R.
Sugar binding in lactose permease: Anomeric state of a disaccharide influences binding structure
JOURNAL OF MOLECULAR BIOLOGY, 367:1523-1534, APR 13 2007
abstract, full text, DOI:10.1016/j.jmb.2007.02.001

Migliore, Agostino; Corni, Stefano; Di Felice, Rosa; Molinari, Elisa
Water-mediated electron transfer between protein redox centers
JOURNAL OF PHYSICAL CHEMISTRY B, 111:3774-3781, APR 12 2007
abstract, full text, DOI:10.1021/jp068773i

Zoellner, Andy; Pasquinelli, Melissa A.; Bernhardt, Rita; Beratan, David N.
Protein phosphorylation and intermolecular electron transfer: A joint experimental and computational study of a hormone biosynthesis pathway
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:4206-4216, APR 11 2007
abstract, full text, DOI:10.1021/ja064803j

Ou, Tian-Miao; Lu, Yu-Jing; Zhang, Chi; Huang, Zhi-Shu; Wang, Xiao-Dong; Tan, Jia-Heng; Chen, Yuan; Ma, Dik-Lung; Wong, Kwok-Yin; Tang, Johnny Cheuk-On; Chan, Albert Sun-Chi; Gu, Lian-Quan
Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives
JOURNAL OF MEDICINAL CHEMISTRY, 50:1465-1474, APR 5 2007
abstract, full text, DOI:10.1021/jm0610088

Sinkovits, Andras F.; Bryksa, Brian C.; Tanaka, Takuji; Yada, Rickey Y.
Understanding the structure-function role of specific catalytic residues in a model food related enzyme: Pepsin
ENZYME AND MICROBIAL TECHNOLOGY, 40:1175-1180, APR 3 2007
abstract, full text, DOI:10.1016/j.enzmictec.2006.08.029

Zhou, Ruhong; Eleftheriou, Maria; Royyuru, Ajay K.; Berne, Bruce J.
Destruction of long-range interactions by a single mutation in lysozyme
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:5824-5829, APR 3 2007
abstract, full text, DOI:10.1073/pnas.0701249104

Jang, Hyunbum; Ma, Buyong; Nussinov, Ruth
Conformational study of the protegrin-I (PG-I) dimer interaction with lipid bilayers and its effect
BMC STRUCTURAL BIOLOGY, 7 Art. No. 21, APR 2 2007
abstract, full text, DOI:10.1186/1472-6807-7-21

Floquet, Nicolas; Richez, Celine; Durand, Philippe; Maigret, Bernard; Badet, Bernard; Badet-Denisot, Marie-Ange
Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 17:1966-1970, APR 1 2007
abstract, full text, DOI:10.1016/j.bmcl.2007.01.052

Katti, Dinesh R.; Schmidt, Steven R.; Ghosh, Pijush; Katti, Kalpana S.
Molecular modeling of the mechanical behavior and interactions in dry and slightly hydrated sodium montmorillonite interlayer
CANADIAN GEOTECHNICAL JOURNAL, 44:425-435, APR 2007
abstract, full text, DOI:10.1139/T06-127

Tsigelny, Igor F.; Bar-On, Pazit; Sharikov, Yuriy; Crews, Leslie; Hashimoto, Makoto; Miller, Mark A.; Keller, Steve H.; Platoshyn, Oleksandr; Yuan, Jason X. -J.; Masliah, Eliezer
Dynamics of alpha-synuclein aggregation and inhibition of pore-like oligomer development by beta-synuclein
FEBS JOURNAL, 274:1862-1877, APR 2007
abstract, full text, DOI:10.1111/j.1742-4658.2007.05733.x

Wang, Boyang; Kral, Petr
Optimal atomistic modifications of material surfaces: Design of selective nesting sites for biomolecules
SMALL, 3:580-584, APR 2007
full text, DOI:10.1002/smll.200600433

Leroux, Vincent; Gresh, Nohad; Liu, Wang-Qing; Garbay, Christiane; Maigret, Bernard
Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 806:51-66, MAR 31 2007
abstract, full text, DOI:10.1016/j.theochem.2006.11.010

Zanuy, David; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Aleman, Carlos
Use of constrained synthetic amino acids in beta-helix proteins for conformational control
JOURNAL OF PHYSICAL CHEMISTRY B, 111:3236-3242, MAR 29 2007
abstract, full text, DOI:10.1021/jp065025k

Fowler, Philip W.; Balali-Mood, Kia; Deol, Sundeep; Coveney, Peter V.; Sansom, Mark S. P.
Monotopic enzymes and lipid bilayers: A comparative study
BIOCHEMISTRY, 46:3108-3115, MAR 20 2007
abstract, full text, DOI:10.1021/bi602455n

Casanovas, Jordi; Zanuy, David; Nussinov, Ruth; Aleman, Carlos
Intrinsic conformational characteristics of alpha,alpha-diphenylglycine
JOURNAL OF ORGANIC CHEMISTRY, 72:2174-2181, MAR 16 2007
abstract, full text, DOI:10.1021/jo0624905

Knaggs, Michael H.; Salsbury, Freddie R., Jr.; Edgell, Marshall Hall; Fetrow, Jacquelyn S.
Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 92:2062-2079, MAR 15 2007
abstract, full text, DOI:10.1529/biophysj.106.081950

Coveney, P. V.; Saksena, R. S.; Zasada, S. J.; McKeown, M.; Pickles, S.
The application hosting environment: Lightweight middleware for grid-based computational science
COMPUTER PHYSICS COMMUNICATIONS, 176:406-418, MAR 15 2007
abstract, full text, DOI:10.1016/j.cpc.2006.11.011

Karain, Wael I.; Ajarmah, Basem; Qaraeen, Nael I.
The dynamics of inter-residue distances in bovine pancreatic trypsin inhibitor
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 376:394-400, MAR 15 2007
abstract, full text, DOI:10.1016/j.physa.2006.10.070

Bastug, Turgut; Kuyucak, Serdar
Free energy simulations of single and double ion occupancy in gramicidin A
JOURNAL OF CHEMICAL PHYSICS, 126 Art. No. 105103, MAR 14 2007
abstract, full text, DOI:10.1063/1.2710267

Solares, Santiago D.
Single biomolecule imaging with frequency and force modulation in tapping-mode atomic force microscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 111:2125-2129, MAR 8 2007
abstract, full text, DOI:10.1021/jp070067+

Orlowski, Jerzy; Boniecki, Michal; Bujnicki, Janusz M.
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
BIOINFORMATICS, 23:527-530, MAR 2007
abstract, full text, DOI:10.1093/bioinformatics/btm007

Ghosh, Pijush; Katti, Dinesh R.; Katti, Kalpana S.
Mineral proximity influences mechanical response of proteins in biological mineral-protein hybrid systems
BIOMACROMOLECULES, 8:851-856, MAR 2007
abstract, full text, DOI:10.1021/bm060942h

Lou, Jizhong; Zhu, Cheng
A structure-based sliding-rebinding mechanism for catch bonds
BIOPHYSICAL JOURNAL, 92:1471-1485, MAR 1 2007
abstract, full text, DOI:10.1529/biophysj.106.097048

Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Zuccato, Pierfrancesco; Pieri, Lidia; Faccioli, Pietro; Bellotti, Vittorio; Esposito, Gennaro
Molecular dynamics simulation suggests possible interaction patterns at early steps of beta(2)-microglobulin aggregation
BIOPHYSICAL JOURNAL, 92:1673-1681, MAR 1 2007
abstract, full text, DOI:10.1529/biophysj.106.098483

Balog, Erika; Laberge, Monique; Fidy, Judit
The influence of interdomain interactions on the intradomain motions in yeast phosphoglycerate kinase: A molecular dynamics study
BIOPHYSICAL JOURNAL, 92:1709-1716, MAR 1 2007
abstract, full text, DOI:10.1529/biophysj.106.093195

Linderoth, Lars; Peters, Guenther H.; Jorgensen, Kent; Madsen, Robert; Andresen, Thomas L.
Synthesis of sn-1 functionalized phospholipids as substrates for secretory phospholipase A(2)
CHEMISTRY AND PHYSICS OF LIPIDS, 146:54-66, MAR 2007
full text, DOI:10.1016/j.chemphyslip.2006.12.006

Dalle-Donne, Isabella; Carini, Marina; Vistoli, Giulio; Gamberoni, Luca; Giustarini, Daniela; Colombo, Roberto; Facino, Roberto Maffei; Rossi, Ranieri; Milzani, Aldo; Aldini, Giancarlo
Actin Cys374 as a nucleophilic target of alpha,beta-unsaturated aldehydes
FREE RADICAL BIOLOGY AND MEDICINE, 42:583-598, MAR 1 2007
abstract, full text, DOI:10.1016/j.freeradbiomed.2006.11.026

Palmer, Bruce; Kathmann, Shawn; Krishnan, Manojkumar; Tipparaju, Vinod; Nieplocha, Jarek
The use of processor groups in molecular dynamics simulations to sample free-energy states
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:583-592, MAR-APR 2007
abstract, full text, DOI:10.1021/ct600260u

Dal Peraro, M. D.; Spiegel, Katrin; Lamoureux, Guillaume; De Vivo, Marco; DeGrado, William F.; Klein, Michael L.
Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:444-453, MAR 2007
abstract, full text, DOI:10.1016/j.jsb.2006.10.019

Sanbonmatsu, K. Y.; Tung, C. -S.
High performance computing in biology: Multimillion atom simulations of nanoscale systems
JOURNAL OF STRUCTURAL BIOLOGY, 157:470-480, MAR 2007
abstract, full text, DOI:10.1016/j.jsb.2006.10.023

Wang, Yi; Cohen, Jordi; Boron, Walter F.; Schulten, Klaus; Tajkhorshid, Emad
Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 157:534-544, MAR 2007
abstract, full text, TCBG publications, DOI:10.1016/j.jsb.2006.11.008

Shih, Amy Y.; Freddolino, Peter L.; Arkhipov, Anton; Schulten, Klaus
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:579-592, MAR 2007
abstract, full text, TCBG publications, DOI:10.1016/j.jsb.2006.08.006

Calderon, Christopher P.
On the use of local diffusion models for path ensemble averaging in potential of mean force computations
JOURNAL OF CHEMICAL PHYSICS, 126 Art. No. 084106, FEB 28 2007
abstract, full text, DOI:10.1063/1.2567098

Tagami, K.; Tsukada, M.
Simulated non-contact AFM images of an alcohol molecule in an alkanethiol self-assembled monolayer
NANOTECHNOLOGY, 18 Art. No. 084005, FEB 28 2007
abstract, full text, DOI:10.1088/0957-4484/18/8/084005

Amaro, Rommie E.; Sethi, Anurag; Myers, Rebecca S.; Davisson, V. Jo; Luthey-Schulten, Zaida A.
A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
BIOCHEMISTRY, 46:2156-2173, FEB 27 2007
abstract, full text, DOI:10.1021/bi061708e

Kim, Kyoungtae; McCully, Michelle E.; Bhattacharya, Nandini; Butler, Boyd; Sept, David; Cooper, John A.
Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein - Implications for how capping protein binds the actin filament
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:5871-5879, FEB 23 2007
abstract, full text, DOI:10.1074/jbc.M609850200

Gorfe, Alemayehu A.; Hanzal-Bayer, Michael; Abankwa, Daniel; Hancock, John F.; McCammon, J. Andrew
Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer
JOURNAL OF MEDICINAL CHEMISTRY, 50:674-684, FEB 22 2007
abstract, full text, DOI:10.1021/jm061053f

Wei, Kai; Liu, Lei; Cheng, Yu-Hui; Fu, Yao; Guo, Qing-Xiang
Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1514-1516, FEB 22 2007
abstract, full text, DOI:10.1021/jp070120u

Zou, Hongling; Strzalka, Joseph; Xu, Ting; Tronin, Andrey; Blasie, J. Kent
Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1823-1833, FEB 22 2007
abstract, full text, DOI:10.1021/jp0666378

Muralidhara, B. K.; Negi, Surendra S.; Halpert, James R.
Dissecting the thermodynamics and cooperativity of ligand binding in cytochrome P450eryF
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:2015-2024, FEB 21 2007
abstract, full text, DOI:10.1021/ja066303w

Celik, Leyla; Lund, Julie Davey Dalsgaard; Schiott, Birgit
Conformational dynamics of the estrogen receptor alpha: Molecular dynamics simulations of the influence of binding site structure on protein dynamics
BIOCHEMISTRY, 46:1743-1758, FEB 20 2007
abstract, full text, DOI:10.1021/bi061656t

Golosov, Andrei A.; Karplus, Martin
Probing polar solvation dynamics in proteins: A molecular dynamics simulation analysis
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1482-1490, FEB 15 2007
abstract, full text, DOI:10.1021/jp065493u

Fishelovitch, Dan; Hazan, Carina; Shaik, Sason; Wolfson, Haim J.; Nussinov, Ruth
Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:1602-1611, FEB 14 2007
abstract, full text, DOI:10.1021/ja066007j

Bulo, Rosa E.; Siggel, Lorenz; Molnar, Ferenc; Weiss, Horst
Modeling of bovine Type-I collagen fibrils: Interaction with pickling and retanning agents
MACROMOLECULAR BIOSCIENCE, 7:234-240, FEB 12 2007
abstract, full text, DOI:10.1002/mabi.200600208

Isgro, Timothy A.; Schulten, Klaus
Association of nuclear pore FG-repeat domains to NTF2 import and export complexes
JOURNAL OF MOLECULAR BIOLOGY, 366:330-345, FEB 9 2007
abstract, full text, TCBG publications, DOI:10.1016/j.jmb.2006.11.048

Kutteh, Ramzi; Vandenberg, Jamie I.; Kuyucak, Serdar
Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1090-1098, FEB 8 2007
abstract, full text, DOI:10.1021/jp066294d

Yamazaki, Takeshi; Imai, Takashi; Hirata, Fumio; Kovalenko, Andriy
Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1206-1212, FEB 8 2007
abstract, full text, DOI:10.1021/jp064615f

Zheng, Jie; Zanuy, David; Haspel, Nurit; Tsai, Chung-Jung; Aleman, Carlos; Nussinov, Ruth
Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues
BIOCHEMISTRY, 46:1205-1218, FEB 6 2007
abstract, full text, DOI:10.1021/bi061674a

Zhao, Xiuli; Sun, Miao; Zhao, Jin; Leyva, J. Alfonso; Zhu, Hongwen; Yang, Wei; Zeng, Xuan; Ao, Yang; Liu, Qing; Liu, Guoyang; Lo, Wilson H. Y.; Jabs, Ethylin Wang; Amzel, L. Mario; Shan, Xiangnian; Zhang, Xue
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome
AMERICAN JOURNAL OF HUMAN GENETICS, 80:361-371, FEB 2007
abstract, full text, DOI:10.1086/511387

Zanuy, David; Aleman, Carlos
Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammonium
BIOMACROMOLECULES, 8:663-671, FEB 2007
abstract, full text, DOI:10.1021/bm060927c

Pickholz, Monica; Oliveira, Osvaldo N., Jr.; Skaf, Munir S.
Interactions of chlorpromazine with phospholipid monolayers: Effects of the ionization state of the drug
BIOPHYSICAL CHEMISTRY, 125:425-434, FEB 2007
abstract, full text, DOI:10.1016/j.bpc.2006.10.010

Sotomayor, Marcos; Vasquez, Valeria; Perozo, Eduardo; Schulten, Klaus
Ion conduction through MscS as determined by electrophysiology and simulation
BIOPHYSICAL JOURNAL, 92:886-902, FEB 2007
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.095232

Nakano, Aiichiro; Kalia, Rajiv K.; Nomura, Ken-ichi; Sharma, Ashish; Vashishta, Priya; Shimojo, Fuyuki; van Duin, Adri C. T.; Goddard, William A.; Biswas, Rupak; Srivastava, Deepak
A divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactions
COMPUTATIONAL MATERIALS SCIENCE, 38:642-652, FEB 2007
abstract, full text, DOI:10.1016/j.commatsci.2006.04.012

Taboureau, Olivier; Olsen, Ole Hvilsted
Computational study of coagulation factor VIIa's affinity for phospholipid membranes
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 36:133-144, FEB 2007
abstract, full text, DOI:10.1007/s00249-006-0114-2

Grabe, Michael; Lai, Helen C.; Jain, Monika; Jan, Yuh Nung; Jan, Lily Yeh
Structure prediction for the down state of a potassium channel voltage sensor
NATURE, 445:550-553, FEB 1 2007
abstract, full text, DOI:10.1038/nature05494

De Fabritiis, G.; Serrano, M.; Delgado-Buscalioni, R.; Coveney, P. V.
Fluctuating hydrodynamic modeling of fluids at the nanoscale
PHYSICAL REVIEW E, 75 Art. No. 026307, FEB 2007
abstract, full text, DOI:10.1103/PhysRevE.75.026307

Orlowski, Slawomir; Nowak, Wieslaw
Oxygen diffusion in minihemoglobin from Cerebratulus lacteus: a locally enhanced sampling study
THEORETICAL CHEMISTRY ACCOUNTS, 117:253-258, FEB 2007
abstract, full text, DOI:10.1007/s00214-006-0139-8

Ivanov, Ivaylo; Tainer, John A.; McCammon, J. Andrew
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:1465-1470, JAN 30 2007
abstract, full text, DOI:10.1073/pnas.0603468104

Lippert, Ross A.; Bowers, Kevin J.; Dror, Ron O.; Eastwood, Michael P.; Gregersen, Brent A.; Klepeis, John L.; Kolossvary, Istvan; Shaw, David E.
A common, avoidable source of error in molecular dynamics integrators
JOURNAL OF CHEMICAL PHYSICS, 126 Art. No. 046101, JAN 28 2007
full text, DOI:10.1063/1.2431176

Pogorelov, Taras V.; Autenrieth, Felix; Roberts, Elijah; Luthey-Schulten, Zaida A.
Cytochrome c(2) exit strategy: Dissociation studies and evolutionary implications
JOURNAL OF PHYSICAL CHEMISTRY B, 111:618-634, JAN 25 2007
abstract, full text, DOI:10.1021/jp064973i

Chen, Xin; Wang, Qi; Shen, Jiawei; Pan, Haihua; Wu, Tao
Adsorption of leucine-rich amelogenin protein on hydroxyapatite (001) surface through -COO- claws
JOURNAL OF PHYSICAL CHEMISTRY C, 111:1284-1290, JAN 25 2007
abstract, full text, DOI:10.1021/jp0646630

Subramanian, Shyamsundar; Boder, Eric T.; Discher, Dennis E.
Phylogenetic divergence of CD47 interactions with human signal regulatory protein alpha reveals locus of species specificity - Implications for the binding site
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:1805-1818, JAN 19 2007
abstract, full text, DOI:10.1074/jbc.M603923200

Korkmaz, Brice; Hajjar, Eric; Kalupov, Timofey; Reuter, Nathalie; Brillard-Bourdet, Michele; Moreau, Thierry; Juliano, Luiz; Gauthier, Francis
Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase - A kinetic and molecular modeling analysis
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:1989-1997, JAN 19 2007
abstract, full text, DOI:10.1074/jbc.M608700200

Reyes-Vivas, Horacio; Diaz, Adelaida; Peon, Jorge; Mendoza-Hernandez, Guillermo; Hernandez-Alcantara, Gloria; De la Mora-De la Mora, Ignacio; Enriquez-Flores, Sergio; Dominguez-Ramirez, Lenin; Lopez-Velazquez, Gabriel
Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity
JOURNAL OF MOLECULAR BIOLOGY, 365:752-763, JAN 19 2007
abstract, full text, DOI:10.1016/j.jmb.2006.10.053

De Vivo, Marco; Ensing, Bernd; Dal Peraro, Matteo; Gomez, German A.; Christianson, David W.; Klein, Michael L.
Proton shuttles and phosphatase activity in soluble epoxide hydrolase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:387-394, JAN 17 2007
abstract, full text, DOI:10.1021/ja066150c

Rueda, Manuel; Ferrer-Costa, Caries; Meyer, Tim; Perez, Alberto; Camps, Jordi; Hospital, Adam; Gelpi, Josep Lluis; Orozco, Modesto
A consensus view of protein dynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:796-801, JAN 16 2007
abstract, full text, DOI:10.1073/pnas.0605534104

Sun, Yudong; McKeever, Steve; Balali-Mood, Kia; Sansom, Mark S. P.
Integrating multi-level molecular simulations across heterogeneous resources
2007 8TH IEEE/ACM INTERNATIONAL CONFERENCE ON GRID COMPUTING, 98-105, 2007
abstract, full text

Feng, Gang; Lu, Hui
Computer simulation of I27 translocation through ClpY reveals a critical role of protein mechanical strength and local stability
2007 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-16, 1213-1216, 2007
abstract, full text, DOI:10.1109/IEMBS.2007.4352515

Alam, Sadaf R.; Vetter, Jeffrey S.; Smith, Melissa C.
An application specific memory characterization technique for co-processor accelerators
2007 IEEE INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES, AND PROCESSORS, 353-358, 2007
abstract, full text, DOI:10.1109/ASAP.2007.4459289

Leonard, Jud; Purkayastha, Avi; Reilly, Matt; Mohan, Tushar
The Software Interface for a Cluster Interconnect Based on the Kautz Digraph
2007 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING, 187-193, 2007
abstract, full text, DOI:10.1109/CLUSTR.2007.4629231

Ferreira, Pedro Gabriel; Silva, Candida G.; Brito, Rui M. M.; Azevedo, Paulo J.
A closer look on protein unfolding Simulations through hierarchical clustering
2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 461-468, 2007
abstract, full text

Cickovski, Trevor; Sweet, Chris; Izaguirre, Jesus A.
MDL, a domain-specific language for molecular dynamics
40th Annual Simulation Symposium, Proceedings, 256-264, 2007
abstract, full text, DOI:10.1109/ANSS.2007.26

Castro-Roman, Francisco
Dynamic structure of lipid membranes: Lamellar diffraction in concert with molecular dynamics simulations
ADVANCED SUMMER SCHOOL IN PHYSICS 2007: FRONTIERS IN CONTEMPORARY PHYSICS, 960:107-112, 2007
abstract, full text

Gorfe, Alemayehu A.; Babakhani, Arneh; McCammon, J. Andrew
Free energy profile of h-ras membrane anchor upon membrane insertion
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 46:8234-8237, 2007
full text, DOI:10.1002/anie.200702379

Clarke, A. S.; Hamm, S. M.; Cardenas, A. E.
Extending Atomistic Time Scale Simulations by Optimization of the Action
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 3, 3:15-30, 2007
full text, DOI:10.1016/S1574-1400(07)03002-2

Uppuluri, Prem; Singh, Sachin; Joshi, Uday
RemoteFS: Accessing remote file systems for desktop grid computing
APPLIED COMPUTING 2007, VOL 1 AND 2, 1203-1204, 2007
abstract, full text

Dittrich, Markus; Yu, Jin; Schulten, Klaus
PcrA helicase, a molecular motor studied from the electronic to the functional level
ATOMISTIC APPROACHES IN MODERN BIOLOGY: FROM QUANTUM CHEMISTRY TO MOLECULAR SIMULATIONS, 268:319-347, 2007
abstract, full text, TCBG publications, DOI:10.1007/128_2006_086

Fajer, Mikolai I.; Sale, Kenneth L.; Fajer, Piotr G.
Molecular modeling of spin labels
ESR Spectroscopy in Membrane Biophysics, 27:253-259, 2007
full text

Pedersen, Ulf R.; Peters, Gunther H.; Westh, Peter
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
BIOPHYSICAL CHEMISTRY, 125:104-111, JAN 2007
abstract, full text, DOI:10.1016/j.bpc.2006.07.005

Aird, A.; Wrachtrup, J.; Schulten, K.; Tietz, C.
Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation
BIOPHYSICAL JOURNAL, 92:23-33, JAN 2007
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.084715

Jaud, Simon; Tobias, Douglas J.; Falke, Joseph J.; White, Stephen H.
Self-induced docking site of a deeply embedded peripheral membrane protein
BIOPHYSICAL JOURNAL, 92:517-524, JAN 2007
abstract, full text, DOI:10.1529/biophysj.106.090704

Zanuy, David; Aleman, Carlos
Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation
CHEMISTRY-A EUROPEAN JOURNAL, 13:2695-2700, 2007
abstract, full text, DOI:10.1002/chem.200601130

Chang, Theresa; Pieterse, Koen; Broeren, Maarten A. C.; Kooijman, Huub; Spek, Anthony L.; Hilbers, Peter A. I.; Meijer, E. W.
Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics Simulations
CHEMISTRY-A EUROPEAN JOURNAL, 13:7883-7889, 2007
abstract, full text, DOI:10.1002/chem.200700572

Kobler, Rene; Koeckerbauer, Thomas; Omasits, Ulrich; Neumann, Martin; Schreiner, Wolfgang; Volkert, Jens
Interactive molecular dynamics simulations on the grid
COMPUTER AIDED SYSTEMS THEORY- EUROCAST 2007, 4739:443-447, 2007
abstract, full text

Patra, Michael; Hyvonen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko
Long-range interactions and parallel scalability in molecular simulations
COMPUTER PHYSICS COMMUNICATIONS, 176:14-22, JAN 1 2007
abstract, full text, DOI:10.1016/j.cpc.2006.07.017

Carrieri, Antonio; Fano, Alessandra
The in silico insights of alpha-adrenergic receptors over the last decade: Methodological approaches and structural features of the 3D models
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 7:195-205, 2007
abstract, full text, DOI:10.2174/156802607779318181

Cachau, Raul E.; Gonzalez-Nilo, Fernando D.; Ventura, Oscar N.; Fritts, Martin J.
In-silico nanobio-design. A new frontier in computational biology
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 7:1537-1540, 2007
abstract, full text, DOI:10.2174/156802607782194680

Choi, Youngjin; Jeong, Karpjoo; Kim, Dongkwang; Lee, Jonghyun; Lim, Sang Boem; Jung, Seunho; Heo, Daeyoung; Hwang, Suntae; Byeon, Ok-Hwan
Glyco-MGrid: A collaborative molecular simulation grid for e-glycomics
E-SCIENCE 2007: THIRD IEEE INTERNATIONAL CONFERENCE ON E-SCIENCE AND GRID COMPUTING, PROCEEDINGS, 213-220, 2007
abstract, full text

Veloso, C. J. M.; Silveira, C. H.; Melo, R. C.; Ribeiro, C.; Lopes, J. C. D.; Santoro, M. M.; Meira, W., Jr.
On the characterization of energy networks of proteins
GENETICS AND MOLECULAR RESEARCH, 6:799-820, 2007
abstract, full text

Kowadlo, Gideon; Hall, Nathan E.; Burgess, Antony W.
De novo design of beta-helical polypeptides
GROWTH FACTORS, 25:168-190, 2007
abstract, full text, DOI:10.1080/08977190701679772

Dynowski, M.; Ludewig, U.
TrpAQP: Computer simulations to determine the selectivity of aquaporins
High Performance Computing in Science and Engineering '06, 187-197, 2007
abstract, full text, DOI:10.1007/978-3-540-36183-1_14

Poghosyan, Armen H.; Gharabekyan, Hrant H.; Shahinyan, Aram A.
Molecular dynamics simulations of DMPC/DPPC mixed bilayers
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 18:73-89, JAN 2007
abstract, full text, DOI:10.1142/S0129183107010267

Morrow, Timothy I.; Maginn, Edward J.
Molecular Simulation of Mixtures Containing Imidazolium- and Pyridinium-Based Ionic Liquids and 1-Butanol
IONIC LIQUIDS IV: NOT JUST SOLVENTS ANYMORE, 975:102-125, 2007
abstract, full text

Shaw, David E.; Deneroff, Martin M.; Dror, Ron O.; Kuskin, Jeffrey S.; Larson, Richard H.; Salmon, John K.; Young, Cliff; Batson, Brannon; Bowers, Kevin J.; Chao, Jack C.; Eastwood, Michael P.; Gagliardo, Joseph; Grossman, J. P.; Ho, C. Richard; Ierardi, Douglas J.; Kolossvary, Istvan; Klepeis, John L.; Layman, Timothy; McLeavey, Christine; Moraes, Mark A.; Mueller, Rolf; Priest, Edward C.; Shan, Yibing; Spengler, Jochen; Theobald, Michael; Towles, Brian; Wang, Stanley C.
Anton, a Special-Purpose Machine for Molecular Dynamics Simulation
ISCA'07: 34TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE, CONFERENCE PROCEEDINGS, 1-12, 2007
abstract, full text

Rosales-Leon, L.; Ortega-Lule, G.; Ruiz-Ordaz, B.
Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25:585-594, JAN 2007
abstract, full text, DOI:10.1016/j.jmgm.2006.04.001

Nagata, Toshi
Automated design of protecting molecules for metal nanoparticles by combinatorial molecular simulations
JOURNAL OF ORGANOMETALLIC CHEMISTRY, 692:225-233, JAN 1 2007
abstract, full text, DOI:10.1016/j.jorganchem.2006.05.058

Pestryaev, E.M.
Parallel - vectorial algorithm of molecular dynamics
Mathematical Models and Computer Simulations, 19:62-70, 2007
abstract, full text

Wan, Shunzhou; Coveney, Peter V.; Flower, Darren R.
Molecular dynamics Simulations - Bring biomolecular structures alive on a computer
Methods in Molecular Biology, 409:321-339, 2007
abstract, full text

Allen, Michael P.
Educational aspects of molecular simulation
MOLECULAR PHYSICS, 105:157-166, JAN-FEB 2007
abstract, full text, DOI:10.1080/00268970601138721

Chatterjee, S.; Gersten, B.; Thakur, S.; Burin, A.
Molecular dynamics simulations of a single stranded (ss) DNA
MOLECULAR SIMULATION, 33:573-576, 2007
abstract, full text, DOI:10.1080/08927020601067524

Poghosyan, A. H.; Yeghiazaryan, G. A.; Gharabekyan, H. H.; Koetz, J.; Shahinyan, A. A.
A molecular dynamics study of Na-dodecylsulfate/water liquid crystalline phase
MOLECULAR SIMULATION, 33:1155-1163, 2007
abstract, full text, DOI:10.1080/08927020701613631

Pappalardo, Matteo; Milardi, Danilo; Grasso, Domenico; La Rosa, Carmelo
Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species
NEW JOURNAL OF CHEMISTRY, 31:901-905, 2007
abstract, full text, DOI:10.1039/b700764g

Sun, Lin; Le, Chinh; Saied, Faisal; Murthy, Jayathi Y.
Performance of a parallel molecular dynamics program for computation of thermal properties
NUMERICAL HEAT TRANSFER PART B-FUNDAMENTALS, 51:315-331, 2007
abstract, full text, DOI:10.1080/10407790601144748

Karachevtsev, V. A.; Glamazda, A. Yu.; Karachevtsev, M. V.; Lytvynb, O. S.; Dettlaff-Weglikowska, U.
Emission of carbon nanotube-DNA-GOX bionanohybrid for glucose detection - art. no. 679625
PHOTONICS NORTH 2007, PTS 1 AND 2, 6796:79625-79625, 2007
abstract, full text, DOI:10.1117/12.778902

Bellesia, Giovanni; Fedorov, Maxim V.; Timoshenko, Edward G.
Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 373:455-476, JAN 1 2007
abstract, full text, DOI:10.1016/j.physa.2006.06.011

Tagami, Katsunori; Tsukada, Masaru
Atomistic simulation of compression of single human serum albumin molecule by AFM tip
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON NANOSCIENCE AND TECHNOLOGY, 61:1122-1126, 2007
abstract, full text, DOI:10.1088/1742-6596/61/1/222

Stitham, Jeremiah; Arehart, Eric J.; Gleim, Scott R.; Douville, Karen L.; Hwa, John
Human prostacyclin receptor structure and function from naturally-occurring and synthetic mutations
PROSTAGLANDINS & OTHER LIPID MEDIATORS, 82:95-108, JAN 2007
abstract, full text, DOI:10.1016/j.prostaglandins.2006.05.010

Reymond, Cedric; Ouellet, Jonathan; Bisaillon, Martin; Perreault, Jean-Pierre
Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop
RNA-A PUBLICATION OF THE RNA SOCIETY, 13:44-54, JAN 2007
abstract, full text, DOI:10.1261/rna.263407

Ngo, Jacky Chi Ki; Gullingsrud, Justin; Giang, Kayla; Yeh, Melinda Jean; Fu, Xiang-Dong; Adams, Joseph A.; McCammon, J. Andrew; Ghosh, Gourisankar
SR protein kinase 1 is resilient to inactivation
STRUCTURE, 15:123-133, JAN 2007
abstract, full text, DOI:10.1016/j.str.2006.11.011

Lakhiaev, A. V.; Nalian, A.; Koenig, K.; Idell, S.
Thrombin-thrombomodulin inhibits prourokinase-mediated pleural mesothelial cell-dependent fibrinolysis
THROMBOSIS RESEARCH, 120:715-725, 2007
abstract, full text, DOI:10.1016/j.thromres.2006.12.001

Cavallari, Manuela; Calzolari, Arrigo; Garbesi, Anna; Di Felice, Rosa
Stability and migration of metal ions in G4-wires by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26337-26348, DEC 28 2006
abstract, full text, DOI:10.1021/jp064522y

Hwang, Hyonseok; Schatz, George C.; Ratner, Mark A.
Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26448-26460, DEC 28 2006
abstract, full text, DOI:10.1021/jp0657888

Zhang, Zhiyong; Boyle, Paul C.; Lu, Bao-Yuan; Chang, Jui-Yoa; Wriggers, Willy
Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations
BIOCHEMISTRY, 45:15269-15278, DEC 26 2006
abstract, full text, DOI:10.1021/bi0615083

Wang, Boyang; Kral, Petr
Coulombic dragging of molecules on surfaces induced by separately flowing liquids
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:15984-15985, DEC 20 2006
full text, DOI:10.1021/ja066431k

Espinoza-Fonseca, L. Michel; Trujillo-Ferrara, Jose G.
Toward a rational design of selective multi-trypanosomatid inhibitors: A computational docking study
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:6288-6292, DEC 15 2006
abstract, full text, DOI:10.1016/j.bmcl.2006.09.029

Yao, Shenggen; Liu, Ming S.; Masters, Seth L.; Zhang, Jian-Guo; Babon, Jeffrey J.; Nicola, Nicos A.; Nicholson, Sandra E.; Norton, Raymond S.
Dynamics of the SPRY domain-containing SOCS box protein 2: Flexibility of key functional loops
PROTEIN SCIENCE, 15:2761-2772, DEC 2006
abstract, full text, DOI:10.1110/ps.062477806

Arkhipov, Anton; Freddolino, Peter L.; Schulten, Klaus
Stability and dynamics of virus capsids described by coarse-grained modeling
STRUCTURE, 14:1767-1777, DEC 2006
abstract, full text, TCBG publications, DOI:10.1016/j.str.2006.10.003

Yin, Ying; Jensen, Morten O.; Tajkhorshid, Emad; Schulten, Klaus
Sugar binding and protein conformational changes in lactose permease
BIOPHYSICAL JOURNAL, 91:3972-3985, DEC 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.085993

Nygaard, Thomas P.; Rovira, Carme; Peters, Gunther H.; Jensen, Morten O.
Ammonium recruitment and ammonia transport by E-coli ammonia channel AmtB
BIOPHYSICAL JOURNAL, 91:4401-4412, DEC 2006
abstract, full text, DOI:10.1529/biophysj.106.089714

Arkhipov, Anton; Freddolino, Peter L.; Imada, Katsumi; Namba, Keiichi; Schulten, Klaus
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
BIOPHYSICAL JOURNAL, 91:4589-4597, DEC 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.093443

Thevenard, Jessica; Floquet, Nicolas; Ramont, Laurent; Prost, Elise; Nuzillard, Jean-Marc; Dauchez, Manuel; Yezid, Hocine; Alix, Alain J. P.; Maquart, Francois-Xavier; Brassart-Plasco, Sylvie
Structural and antitumor properties of the YSNSG cyclopeptide derived from tumstatin
CHEMISTRY & BIOLOGY, 13:1307-1315, DEC 2006
abstract, full text, DOI:10.1016/j.chembiol.2006.10.007

Seminario, Jorge M.; Ma, Yuefei; Tarigopula, Vandana
The nanocell: A chemically assembled molecular electronic circuit
IEEE SENSORS JOURNAL, 6:1614-1626, DEC 2006
abstract, full text, DOI:10.1109/JSEN.2006.884163

Stitham, Jeremiah; Gleim, Scott R.; Douville, Karen; Arehart, Eric; Hwa, John
Versatility and differential roles of cysteine residues in human prostacyclin receptor structure and function
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:37227-37236, DEC 1 2006
abstract, full text, DOI:10.1074/jbc.M604042200

Humeres, Eduardo; Mascayano, Carolina; Riadi, Gonzalo; Gonzalez-Nilo, Fernando
Molecular dynamics simulation of the aqueous solvation shell of cellulose and xanthate ester derivatives
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 19:896-901, DEC 2006
abstract, full text, DOI:10.1002/poc.1074

Noda, Kazuhiro; Nakamura, Miho; Nishida, Ryoko; Yoneda, Yukari; Yamaguchi, Yoko; Tamura, Yuichi; Nakamura, Hiroaki; Yasunaga, Takuo
Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using a virtual reality system
JOURNAL OF PLASMA PHYSICS, 72:1037-1040, DEC 2006
abstract, full text, DOI:10.1017/S0022377806005174

Castro-Roman, Francisco; Benz, Ryan W.; White, Stephen H.; Tobias, Douglas J.
Investigation of finite system size effects in molecular dynamics simulations of lipid bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 110:24157-24164, NOV 30 2006
abstract, full text, DOI:10.1021/jp064746g

Bazeley, Peter S.; Prithivi, Sridevi; Struble, Craig A.; Povinelli, Richard J.; Sem, Daniel S.
Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:2698-2708, NOV 27 2006
abstract, full text, DOI:10.1021/ci600267k

Khurana, Ekta; Nielsen, Steven O.; Klein, Michael L.
Gemini surfactants at the air/water interface: A fully atomistic molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:22136-22142, NOV 9 2006
abstract, full text, DOI:10.1021/jp063343d

Cruz-Chu, Eduardo R.; Aksimentiev, Aleksei; Schulten, Klaus
Water-silica force field for simulating nanodevices
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21497-21508, NOV 2 2006
abstract, full text, TCBG publications, DOI:10.1021/jp063896o

Jensen, Jan K.; Malmendal, Anders; Schiott, Birgit; Skeldal, Sune; Pedersen, Katrine E.; Celik, Leyla; Nielsen, Niels Chr.; Andreasen, Peter A.; Wind, Troels
Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library
BIOCHEMICAL JOURNAL, 399:387-396, NOV 1 2006
abstract, full text, DOI:10.1042/BJ20060533

Foley, Meredith C.; Arora, Karunesh; Schlick, Tamar
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda
BIOPHYSICAL JOURNAL, 91:3182-3195, NOV 2006
abstract, full text, DOI:10.1529/biophysj.106.092080

Streiff, John H.; Allen, Thomas W.; Atanasova, Elena; Juranic, Nenad; Macura, Slobodan; Penheiter, Alan R.; Jones, Keith A.
Prediction of volatile anesthetic binding sites in proteins
BIOPHYSICAL JOURNAL, 91:3405-3414, NOV 2006
abstract, full text, DOI:10.1529/biophysj.106.082586

Paramore, Sterling; Voth, Gregory A.
Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules
BIOPHYSICAL JOURNAL, 91:3436-3445, NOV 2006
abstract, full text, DOI:10.1529/biophysj.106.091108

Benz, Ryan W.; Nanda, Hirsh; Castro-Roman, Francisco; White, Stephen H.; Tobias, Douglas J.
Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations
BIOPHYSICAL JOURNAL, 91:3617-3629, NOV 2006
abstract, full text, DOI:10.1529/bipohysj.106.084483

Freddolino, Peter L.; Dittrich, Markus; Schulten, Klaus
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins
BIOPHYSICAL JOURNAL, 91:3630-3639, NOV 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.088609

Espinoza-Fonseca, L. M.; Trujillo-Ferrara, Jose G.
Conformational changes of the p53-binding cleft of MDM2 revealed by molecular dynamics simulations
BIOPOLYMERS, 83:365-373, NOV 2006
abstract, full text, DOI:10.1002/bip.20566

Grandi, Fabio; Sandal, Massimo; Guarguaglini, Giovanni; Capriotti, Emidio; Casadio, Rita; Samori, Bruno
Hierarchical mechanochemical switches in angiostatin
CHEMBIOCHEM, 7:1774-1782, NOV 2006
abstract, full text, DOI:10.1002/cbic.200600227

Wang, Kai; Chang, Anthony; Kale, Laxmikant V.; Dantzig, Jonathan A.
Parallelization of a level set method for simulating dendritic growth
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 66:1379-1386, NOV 2006
abstract, full text, DOI:10.1016/j.jpdc.2006.02.005

Ivanov, Ivaylo; Chapados, Brian R.; McCammon, J. Andrew; Tainer, John A.
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications
NUCLEIC ACIDS RESEARCH, 34:6023-6033, NOV 2006
abstract, full text, DOI:10.1093/nar/gkl744

Mueller, Marcus; Katsov, Kirill; Schick, Michael
Biological and synthetic membranes: What can be learned from a coarse-grained description?
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 434:113-176, NOV 2006
abstract, full text, DOI:10.1016/j.physrep.2006.08.003

Aleman, Carlos; Zanuy, David; Casanovas, Jordi; Cativiela, Carlos; Nussinov, Ruth
Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21264-21271, OCT 26 2006
abstract, full text, DOI:10.1021/jp062804s

Blumberger, Jochen; Klein, Michael L.
Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:13854-13867, OCT 25 2006
abstract, full text, DOI:10.1021/ja063852t

Puklin-Faucher, Eileen; Gao, Mu; Schulten, Klaus; Vogel, Viola
How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation
JOURNAL OF CELL BIOLOGY, 175:349-360, OCT 23 2006
abstract, full text, TCBG publications, DOI:10.1083/jcb.200602071

Trzaskowski, Bartosz; Jalbout, Abraham F.; Adamowicz, Ludwik
Molecular dynamics studies of protein-fragment models encapsulated into carbon nanotubes
CHEMICAL PHYSICS LETTERS, 430:97-100, OCT 19 2006
abstract, full text, DOI:10.1016/j.cplett.2006.08.125

Yraola, Francesc; Garcia-Vicente, Silvia; Fernandez-Recio, Juan; Albericio, Fernando; Zorzano, Antonio; Marti, Luc; Royo, Miriam
New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: Analysis by SARs and computational docking
JOURNAL OF MEDICINAL CHEMISTRY, 49:6197-6208, OCT 19 2006
abstract, full text, DOI:10.1021/jm051076e

Klauda, Jeffery B.; Brooks, Bernard R.; Pastor, Richard W.
Dynamical motions of lipids and a finite size effect in simulations of bilayers
JOURNAL OF CHEMICAL PHYSICS, 125 Art. No. 144710, OCT 14 2006
abstract, full text, DOI:10.1063/1.2354486

Yeong, Sui Sum; Zhu, Yimin; Smith, Derek; Verma, Chandra; Lim, Wee Guan; Tan, Bee Jen; Li, Qiu Tian; Cheung, Nam Sang; Cai, Minnie; Zhu, Yi-Zhun; Zhou, Shu-Feng; Tan, Seng-Lai; Duan, Wei
The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase C alpha
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:30768-30781, OCT 13 2006
abstract, full text, DOI:10.1074/jbc.M511278200

Bhattacharya, Nandini; Ghosh, Shatadal; Sept, David; Cooper, John A.
Binding of myotrophin/V-1 to actin-capping protein - Implications for how capping protein binds to the filament barbed end
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:31021-31030, OCT 13 2006
abstract, full text, DOI:10.1074/jbc.M606278200

Adhangale, Parag S.; Gaver, Donald P., I.I.I.
Equation of state for a coarse-grained DPPC monolayer at the air/water interface
MOLECULAR PHYSICS, 104:3011-3019, OCT 10 2006
abstract, full text, DOI:10.1080/00268970600935101

Blood, Philip D.; Voth, Gregory A.
Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:15068-15072, OCT 10 2006
abstract, full text, DOI:10.1073/pnas.0603917103

Casanovas, Jordi; Zanuy, David; Nussinov, Ruth; Aleman, Carlos
Identification of the intrinsic conformational properties of 1-aminocyclobutane-1-carboxylic acid
CHEMICAL PHYSICS LETTERS, 429:558-562, OCT 5 2006
abstract, full text, DOI:10.1016/j.cplett.2006.08.062

Liu, Ming S.; Todd, B. D.; Sadus, Richard J.
Dynamic and coordinating domain motions in the active subunits of the F-1-ATPase molecular motor
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:1553-1560, OCT 2006
abstract, full text, DOI:10.1016/j.bbapap.2006.08.005

Roh, J. H.; Curtis, J. E.; Azzam, S.; Novikov, V. N.; Peral, I.; Chowdhuri, Z.; Gregory, R. B.; Sokolov, A. P.
Influence of hydration on the dynamics of lysozyme
BIOPHYSICAL JOURNAL, 91:2573-2588, OCT 2006
abstract, full text, DOI:10.1529/biophysj.106.082214

Fiorin, G.; Pastore, A.; Carloni, P.; Parrinello, M.
Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail
BIOPHYSICAL JOURNAL, 91:2768-2777, OCT 2006
abstract, full text, DOI:10.1529/biophysj.106.086611

Vemparala, Satyavani; Saiz, Leonor; Eckenhoff, Roderic G.; Klein, Michael L.
Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles
BIOPHYSICAL JOURNAL, 91:2815-2825, OCT 2006
abstract, full text, DOI:10.1529/biophysj.106.085324

Jang, Hyunbum; Ma, Buyong; Woolf, Thomas B.; Nussinov, Ruth
Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect
BIOPHYSICAL JOURNAL, 91:2848-2859, OCT 2006
abstract, full text, DOI:10.1529/biophysj.106.084046

Kikuzawa, Yoshihiro; Nagata, Toshi; Tahara, Tahei; Ishii, Kunihiko
Photo- and redox-active dendritic molecules with soft, layered nanostructures
CHEMISTRY-AN ASIAN JOURNAL, 1:516-528, OCT 2006
abstract, full text, DOI:10.1002/asia.200600134

Papadopoulos, G.; Grudinin, S.; Kalpaxis, D. L.; Choli-Papadopoulou, T.
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 35:675-683, OCT 2006
abstract, full text, DOI:10.1007/s00249-006-0076-4

Buehler, Markus J.
Large-scale hierarchical molecular modeling of nanostructured biological materials
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:603-623, OCT 2006
abstract, full text

De Fabritiis, G.; Delgado-Buscalioni, R.; Coveney, P. V.
Multiscale modeling of liquids with molecular specificity
PHYSICAL REVIEW LETTERS, 97 Art. No. 134501, SEP 29 2006
abstract, full text, DOI:10.1103/PhysRevLett.97.134501

Khurana, Ekta; Nielsen, Steven O.; Ensing, Bernd; Klein, Michael L.
Self-assembling cyclic peptides: Molecular dynamics studies of dimers in polar and nonpolar solvents
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18965-18972, SEP 28 2006
abstract, full text, DOI:10.1021/jp057471y

Jun, Sangmi; Becker, James S.; Yonkunas, Mike; Coalson, Rob; Saxena, Sunil
Unfolding of alanine-based peptides using electron spin resonance distance measurements
BIOCHEMISTRY, 45:11666-11673, SEP 26 2006
abstract, full text, DOI:10.1021/bi061195b

Bichet, Delphine; Grabe, Michael; Jan, Yuh Nung; Jan, Lily Yeh
Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:14355-14360, SEP 26 2006
abstract, full text, DOI:10.1073/pnas.0606660103

Grabe, Michael; Bichet, Delphine; Qian, Xiang; Jan, Yuh Nung; Jan, Lily Yeh
K+ channel selectivity depends on kinetic as well as thermodynamic factors
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:14361-14366, SEP 26 2006
abstract, full text, DOI:10.1073/pnas.0606662103

Lou, Jizhong; Yago, Tadayuki; Klopocki, Arkadiusz G.; Mehta, Padmaja; Chen, Wei; Zarnitsyna, Veronika I.; Bovin, Nicolai V.; Zhu, Cheng; McEver, Rodger P.
Flow-enhanced adhesion regulated by a selectin interdomain hinge
JOURNAL OF CELL BIOLOGY, 174:1107-1117, SEP 25 2006
abstract, full text, DOI:10.1083/jcb.200606056

Ma, Kan; Forbes, Jeffrey G.; Gutierrez-Cruz, Gustavo; Wang, Kuan
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways - The clustering of novel overlap ligand motifs in the elastic PEVK segment
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:27539-27556, SEP 15 2006
abstract, full text, DOI:10.1074/jbc.M604525200

Cadena, Cesar; Maginn, Edward J.
Molecular simulation study of some thermophysical and transport properties of triazolium-based ionic liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18026-18039, SEP 14 2006
abstract, full text, DOI:10.1021/jp0629036

Muriel Sanchez, Veronica; Crespo, Alejandro; Gutkind, J. Silvio; Gustavo Turjanski, Adrian
Investigation of the catalytic mechanism of farnesyl pyrophosphate synthase by computer simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18052-18057, SEP 14 2006
abstract, full text, DOI:10.1021/jp063099q

Glykos, Nicholas M.; Papanikolau, Yannis; Vlassi, Metaxia; Kotsifaki, Dina; Cesareni, Giovanni; Kokkinidis, Michael
Loopless rop: Structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein
BIOCHEMISTRY, 45:10905-10919, SEP 12 2006
abstract, full text, DOI:10.1021/bi060833n

Tuukkanen, Anne; Verkhovsky, Michael I.; Laakkonen, Liisa; Wikstrom, Marten
The K-pathway revisited: A computational study on cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:1117-1121, SEP-OCT 2006
abstract, full text, DOI:10.1016/j.bbabio.2006.05.041

Meyer, Grischa R.; Gullingsrud, Justin; Schulten, Klaus; Martinac, Boris
Molecular dynamics study of MscL interactions with a curved lipid bilayer
BIOPHYSICAL JOURNAL, 91:1630-1637, SEP 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.080721

Cohen, Jordi; Arkhipov, Anton; Braun, Rosemary; Schulten, Klaus
Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin
BIOPHYSICAL JOURNAL, 91:1844-1857, SEP 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.085746

Yu, Jin; Ha, Taekjip; Schulten, Klaus
Structure-based model of the stepping motor of PcrA helicase
BIOPHYSICAL JOURNAL, 91:2097-2114, SEP 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.088203

Khalili-Araghi, Fatemeh; Tajkhorshid, Emad; Schulten, Klaus
Dynamics of K+ ion conduction through Kv1.2
BIOPHYSICAL JOURNAL, 91:L2-L4, SEP 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.106.091926

Lu, Zhenyu; Hu, Hao; Yang, Weitao; Marszaleky, Piotr E.
Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method
BIOPHYSICAL JOURNAL, 91:L57-L59, SEP 2006
abstract, full text, DOI:10.1529/biophysj.106.090324

George, Anthony M.; Jones, Peter M.
Molecular Dynamics Simulations and Analysis of ABC Transporters
CURRENT COMPUTER-AIDED DRUG DESIGN, 2:203-214, SEP 2006
abstract, full text, DOI:10.2174/157340906778226427

Salapura, Valentina; Walkup, Robert; Gara, Alan
Exploiting workload parallelism for performance and power optimization in Blue Gene
IEEE MICRO, 26:67-81, SEP-OCT 2006
abstract, full text, DOI:10.1109/MM.2006.89

Seminario, Jorge A.; Yan, Liurning; Ma, Yuefei
Encoding and transport of information in molecular and biomolecular systems
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 5:436-440, SEP 2006
abstract, full text, DOI:10.1109/TNANO.2006.880905

Gao, Qi; Tagami, Katsuori; Fujihira, Masamichi; Tsukada, Masaru
Quenching mechanism of mechanically compressed green fluorescent protein studied by CASSCF/AM1
JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS & EXPRESS LETTERS, 45:L929-L931, SEP 2006
abstract, full text, DOI:10.1143/JJAP.45.L929

Ghosh, Pijush; Katti, Dinesh R.; Katti, Kalpana S.
Impact of beta-sheet conformations on the mechanical response of protein in biocomposites
MATERIALS AND MANUFACTURING PROCESSES, 21:676-682, SEP-OCT 2006
abstract, full text, DOI:10.1080/10426910600611706

Alonso, Hernan; Bliznyuk, Andrey A.; Gready, Jill E.
Combining docking and molecular dynamic simulations in drug design
MEDICINAL RESEARCH REVIEWS, 26:531-568, SEP 2006
abstract, full text, DOI:10.1002/med.20067

Gan, Yong; Chen, Zhen
Molecular Dynamics Simulation of the Size Effect of Carbon Nanotubes on the Bulk Modulus of a Lipid Bilayer
Molecular & Cellular Biomechanics, 3:89-94, SEP 2006
abstract, full text

Cheng, Xiaolin; Wang, Hailong; Grant, Barry; Sine, Steven M.; McCammon, J. Andrew
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors
PLOS COMPUTATIONAL BIOLOGY, 2:1173-1184, SEP 2006
abstract, full text, DOI:10.1371/journal.pcbi.0020134

Yu, Jin; Yool, Andrea J.; Schulten, Klaus; Tajkhorshid, Emad
Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1
STRUCTURE, 14:1411-1423, SEP 2006
abstract, full text, TCBG publications, DOI:10.1016/j.str.2006.07.006

Sikdar, Debashis; Katti, Dinesh R.; Katti, Kalpana S.
A molecular model for epsilon-caprolactam-based intercalated polymer clay nanocomposite: Integrating modeling and experiments
LANGMUIR, 22:7738-7747, AUG 29 2006
abstract, full text, DOI:10.1021/la060243q

Mitra, Arpita; Sept, David
Binding and interaction of dinitroanilines with apicomplexan and kinetoplastid alpha-tubulin
JOURNAL OF MEDICINAL CHEMISTRY, 49:5226-5231, AUG 24 2006
abstract, full text, DOI:10.1021/jm060472+

Henin, Jerome; Schulten, Klaus; Chipot, Christophe
Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:16718-16723, AUG 24 2006
abstract, full text, TCBG publications, DOI:10.1021/jp0601116

Moskovsky, A.A.; Vanovschi, V.V.; Konyukhov, S.S.; Nemukhin, A.V.
Implementation of the replica-exchange molecular dynamics method for rigid bodies
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:2208-2213, AUG 15 2006
abstract, full text, DOI:10.1002/qua.20940

Rebelo, Susana L.; Bainbridge, Susan E.; Amel-Kashipaz, Mohammad R.; Radford, Paul M.; Powell, Richard J.; Todd, Ian; Tighe, Patrick J.
Modeling of tumor necrosis factor receptor superfamily 1A mutants associated with tumor necrosis factor receptor-associated periodic syndrome indicates misfolding consistent with abnormal function
ARTHRITIS AND RHEUMATISM, 54:2674-2687, AUG 2006
abstract, full text, DOI:10.1002/art.21964

Treptow, Werner; Tarek, Mounir
Molecular restraints in the permeation pathway of ion channels
BIOPHYSICAL JOURNAL, 91:L26-L28, AUG 2006
abstract, full text, DOI:10.1529/biophysj.106.087437

Poghosyan, Armen H.; Yeghiazaryan, Grigor A.; Charabekyan, Hrant H.; Shahinyan, Aram A.
The GROMACS and NAMD software packages comparison
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 1:736-743, AUG 2006
abstract, full text

Gorecki, A.; Trylska, J.; Lesyng, B.
Causal relations in molecular dynamics from the multi-variate autoregressive model
EUROPHYSICS LETTERS, 75:503-509, AUG 2006
abstract, full text, DOI:10.1209/epl/i2006-10129-2

Weetman, Philip; Wartak, Marek S.
Advanced approach to modelling quantum well semiconductor lasers based on the quantum Boltzmann equation: Green's function approach
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:463-478, AUG 2006
abstract, full text

Krystek, Stanley R., Jr.; Kimura, S. Roy; Tebben, Andrew J.
Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:463-470, AUG 2006
abstract, full text, DOI:10.1007/s10822-006-9065-z

Lynch, Diane L.; Reggio, Patricia H.
Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:495-509, AUG 2006
abstract, full text, DOI:10.1007/s10822-006-9068-9

Buehler, Markus J.
Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly
JOURNAL OF MATERIALS RESEARCH, 21:1947-1961, AUG 2006
abstract, full text, DOI:10.1557/JMR.2006.0236

Gullingsrud, J.; Babakhani, A.; McCammon, J. A.
Computational investigation of pressure profiles in lipid bilayers with embedded proteins
MOLECULAR SIMULATION, 32:831-838, AUG-SEP 2006
abstract, full text, DOI:10.1080/08927020600779350

Zhang, Qingmin; Lu, Zhenyu; Hu, Hao; Yang, Weitao; Marszalek, Piotr E.
Direct detection of the formation of V-amylose helix by single molecule force spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:9387-9393, JUL 26 2006
abstract, full text, DOI:10.1021/ja057693+

Fowler, Philip W.; Coveney, Peter V.
A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer
BIOPHYSICAL JOURNAL, 91:401-410, JUL 15 2006
abstract, full text, DOI:10.1529/biophysj.105.077784

Asthagiri, D.; Pratt, Lawrence R.; Paulaitis, Michael E.
Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity
JOURNAL OF CHEMICAL PHYSICS, 125 Art. No. 024701, JUL 14 2006
abstract, full text, DOI:10.1063/1.2205853

Gracheva, M.E.; Aksimentiev, A.; Leburton, J.P.
Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
NANOTECHNOLOGY, 17:3160-3165, JUL 14 2006
abstract, full text, DOI:10.1088/0957-4484/17/13/014

Bravaya, Ksenia; Bochenkova, Anastasia; Grigorenko, Bella; Topol, Igor; Burt, Stanley; Nemukhin, Alexander
Molecular modeling the reaction mechanism of serine-carboxyl peptidases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1168-1175, JUL 11 2006
abstract, full text, DOI:10.1021/ct6000686

Zuckerman, Daniel M.; Lyman, Edward
A second look at canonical sampling of biomolecules using replica exchange simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1200-1202, JUL 11 2006
abstract, full text, DOI:10.1021/ct0600464

Bastug, Turgut; Patra, Swarna M.; Kuyucak, Serdar
Finite system and periodicity effects in free energy simulations of membrane proteins
CHEMICAL PHYSICS LETTERS, 425:320-323, JUL 10 2006
abstract, full text, DOI:10.1016/j.cplett.2006.05.036

Henin, Jerome; Chipot, Christophe
Hydrogen-bonding patterns of cholesterol in lipid membranes
CHEMICAL PHYSICS LETTERS, 425:329-335, JUL 10 2006
abstract, full text, DOI:10.1016/j.cplett.2006.04.115

Starovoitova, V.; Budarz, T.E.; Wyllie, G.R.A.; Scheidt, W.R.; Sturhahn, W.; Alp, E.E.; Prohofsky, E.W.; Durbin, S.M.
Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin
JOURNAL OF PHYSICAL CHEMISTRY B, 110:13277-13282, JUL 6 2006
abstract, full text, DOI:10.1021/jp060345p

Lyman, Edward; Zuckerman, Daniel M.
Ensemble-based convergence analysis of biomolecular trajectories
BIOPHYSICAL JOURNAL, 91:164-172, JUL 2006
abstract, full text, DOI:10.1529/biophysj.106.082941

Belessi, Chrysoula J.; Davi, Frederic B.; Stamatopoulos, Kostas E.; Degano, Massimo; Andreou, Thanassis M.; Moreno, Carol; Merle-Beral, Helene; Crespo, Marta; Laoutaris, Nikolaos P.; Montserrat, Emili; Caligaris-Cappio, Federico; Anagnostopoulos, Achilles Z.; Ghia, Paolo
IGHV gene insertions and deletions in chronic lymphocytic leukemia: "CLL-biased" deletions in a subset of cases with stereotyped receptors
EUROPEAN JOURNAL OF IMMUNOLOGY, 36:1963-1974, JUL 2006
abstract, full text, DOI:10.1002/eji.200535751

Janosi, Lorant; Kosztin, Ioan; Damjanovic, Ana
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
JOURNAL OF CHEMICAL PHYSICS, 125 Art. No. 014903, JUL 1 2006
abstract, full text, DOI:10.1063/1.2210481

Moretti, S.; Macchiarulo, A.; De Falco, V.; Avenia, N.; Barbi, F.; Carta, C.; Cavaliere, A.; Melillo, R. M.; Passeri, L.; Santeusanio, F.; Tartaglia, M.; Santoro, M.; Puxeddu, E.
Biochemical and molecular characterization of the novel BRAF(V599Ins) mutation detected in a classic papillary thyroid carcinoma
ONCOGENE, 25:4235-4240, JUL 2006
abstract, full text, DOI:10.1038/sj.onc.1209448

Zikic, Radomir; Krstic, Predrag S.; Zhang, X. -G.; Fuentes-Cabrera, Miguel; Wells, Jack; Zhao, Xiongce
Characterization of the tunneling conductance across DNA bases
PHYSICAL REVIEW E, 74 Art. No. 011919, JUL 2006
abstract, full text, DOI:10.1103/PhysRevE.74.011919

Interlandi, G.; Settanni, G.; Caflisch, A.
Unfolding transition state and intermediates of the tumor suppressor p16(INK4a) investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:178-192, JUL 1 2006
abstract, full text, DOI:10.1002/prot.20953

Haspel, Nurit; Zanuy, David; Aleman, Carlos; Wolfson, Haim; Nussinov, Ruth
De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs
STRUCTURE, 14:1137-1148, JUL 2006
abstract, full text, DOI:10.1016/j.str.2006.05.016

Liu, Z.W.; Xu, Y.; Tang, P.
Steered molecular dynamics simulations of Na+ permeation across the gramicidin a channel
JOURNAL OF PHYSICAL CHEMISTRY B, 110:12789-12795, JUN 29 2006
abstract, full text, DOI:10.1021/jp060688n

Samel, S.A.; Wagner, B.; Marahiel, M.A.; Essen, L.O.
The thioesterase domain of the fengycin biosynthesis cluster: A structural base for the macrocyclization of a non-ribosomal lipopeptide
JOURNAL OF MOLECULAR BIOLOGY, 359:876-889, JUN 16 2006
abstract, full text, DOI:10.1016/j.jmb.2006.03.062

Paliwal, A.; Asthagiri, D.; Pratt, L. R.; Ashbaugh, H. S.; Paulaitis, M. E.
An analysis of molecular packing and chemical association in liquid water using quasichemical theory
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 224502, JUN 14 2006
abstract, full text, DOI:10.1063/1.2202350

Bastug, T.; Kuyucak, S.
Molecular dynamics simulations of calcium binding in gramicidin A
CHEMICAL PHYSICS LETTERS, 424:82-85, JUN 12 2006
abstract, full text, DOI:10.1016/j.cplett.2006.04.024

Karain, W.I.; Qaraeen, N.I.; Ajarmah, B.
A stochastic model for correlated protein motions
PHYSICS LETTERS A, 354:497-500, JUN 12 2006
abstract, full text, DOI:10.1016/j.physleta.2006.01.073

Bastug, T.; Kuyucak, S.
Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations
BIOPHYSICAL JOURNAL, 90:3941-3950, JUN 2006
abstract, full text, DOI:10.1529/biphysj.105.074633

Catte, A.; Patterson, J.C.; Jones, M.K.; Jerome, W.G.; Bashtovyy, D.; Su, Z.C.; Gu, F.F.; Chen, J.G.; Aliste, M.P.; Harvey, S.C.; Li, L.; Weinstein, G.; Segrest, J.P.
Novel changes in discoidal high density lipoprotein morphology: A molecular dynamics study
BIOPHYSICAL JOURNAL, 90:4345-4360, JUN 2006
abstract, full text, DOI:10.1529/biophysj.105.071456

Zhu, Y.M.; Smith, D.; Verma, C.; Lim, W.G.; Tan, B.J.; Armstrong, J.S.; Zhou, S.F.; Chan, E.; Tan, S.L.; Zhu, Y.Z.; Cheung, N.S.; Duan, W.
The very C-terminus of protein kinase C epsilon is critical for the full catalytic competence but its hydrophobic motif is dispensable for the interaction with 3-phosphoinositide-dependent kinase-1
CELLULAR SIGNALLING, 18:807-818, JUN 2006
abstract, full text, DOI:10.1016/j.cellsig.2005.07.005

Bastug, T.; Patra, S.M.; Kuyucak, S.
Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields
CHEMISTRY AND PHYSICS OF LIPIDS, 141:197-204, JUN 2006
abstract, full text, DOI:10.1016/j.chemphyslip.2006.02.012

Xu, L.N.; Zhang, L.L.; Gu, Z.; Zhou, L.X.
Full electronic structure calculation of the biological activity in P173L enzyme
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:1544-1550, JUN 2006
abstract, full text, DOI:10.1002/qua.20915

Vasenkov, Alex V.; Fedoseyev, Alex I.; Kolobov, Vladimir I.; Choi, Hyuk Soon; Hong, Ki-Ha; Kim, Kwanghee; Kim, Jongseob; Lee, Hyo Sug; Shin, Jai Kwang
Computational framework for modeling of multi-scale processes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:453-458, JUN 2006
abstract, full text

Pedretti, A.; Villa, M.; Pallavicini, M.; Valoti, E.; Vistoli, G.
Construction of human ghrelin receptor (hGHS-R1a) model using a fragmental prediction approach and validation through docking analysis
JOURNAL OF MEDICINAL CHEMISTRY, 49:3077-3085, JUN 1 2006
abstract, full text, DOI:10.1021/jm058053k

Vistoli, G.; Pedretti, A.; Cattaneo, M.; Aldini, G.; Testa, B.
Homology modeling of human serum carnosinase, a potential medicinal target, and MD simulations of its allosteric activation by citrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:3269-3277, JUN 1 2006
abstract, full text, DOI:10.1021/jm0602099

Jacobsen, R.B.; Sale, K.L.; Ayson, M.J.; Novak, P.; Hong, J.H.; Lane, P.; Wood, N.L.; Kruppa, G.H.; Young, M.M.; Schoeniger, J.S.
Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry
PROTEIN SCIENCE, 15:1303-1317, JUN 2006
abstract, full text, DOI:10.1110/ps.052040406

Zanuy, D.; Casanovas, J.; Aleman, C.
Conformational features of an actuator containing calix[4] arene and thiophene: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:9876-9881, MAY 25 2006
abstract, full text, DOI:10.1021/jp060680d

James, S.; Maresca, K.P.; Allis, D.G.; Valliant, J.F.; Eckelman, W.; Babich, J.W.; Zubieta, J.
Extension of the single amino acid chelate concept (SAAC) to bifunctional biotin analogues for complexation of the M(CO)(3)(+1) core (M = Tc and Re): Syntheses, characterization, biotinidase stability, and avidin binding
BIOCONJUGATE CHEMISTRY, 17:579-589, MAY 17 2006
abstract, full text, DOI:10.1021/bc050297w

Sharma, V.; Puustinen, A.; Wikstrom, M.; Laakkonen, L.
Sequence analysis of the cbb(3) oxidases and an atomic model for the Rhodobacter sphaeroides enzyme
BIOCHEMISTRY, 45:5754-5765, MAY 9 2006
abstract, full text, DOI:10.1021/bi060169a

Pickholz, M.; Oliveira, O.N.; Skaf, M.S.
Molecular dynamics simulations of neutral chlorpromazine in zwitterionic phospholipid monolayers
JOURNAL OF PHYSICAL CHEMISTRY B, 110:8804-8814, MAY 4 2006
abstract, full text, DOI:10.1021/jp056678o

Pedersen, Ulf R.; Leidy, Chad; Westh, Peter; Peters, Gunther H.
The effect of calcium on the properties of charged phospholipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1758:573-582, MAY 2006
abstract, full text, DOI:10.1016/j.bbamem.2006.03.035

Vasil'ev, S.; Bruce, D.
A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function
BIOPHYSICAL JOURNAL, 90:3062-3073, MAY 2006
abstract, full text, DOI:10.1529/biophysj.105.076075

Gao, M.; Schulten, K.
Onset of anthrax toxin pore formation
BIOPHYSICAL JOURNAL, 90:3267-3279, MAY 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.105.079376

Sotomayor, M.; van der Straaten, T.A.; Ravaioli, U.; Schulten, K.
Electrostatic properties of the mechanosensitive channel of small conductance MscS
BIOPHYSICAL JOURNAL, 90:3496-3510, MAY 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.105.080069

Adcock, Stewart A.; McCammon, J. Andrew
Molecular dynamics: Survey of methods for simulating the activity of proteins
CHEMICAL REVIEWS, 106:1589-1615, MAY 2006
full text, DOI:10.1021/cr040426m

Limbach, H.J.; Arnold, A.; Mann, B.A.; Holm, C.
ESPResSo - an extensible simulation package for research on soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 174:704-727, MAY 1 2006
abstract, full text, DOI:10.1016/j.cpc.2005.10.005

Yio, X.; Diamond, M.; Zhang, J.Y.; Weinstein, H.; Wang, L.H.; Werther, L.; Itzkowitz, S.
Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways
GASTROENTEROLOGY, 130:1696-1706, MAY 2006
abstract, full text, DOI:10.1053/j.gastro.2006.01.040

Gu, Y.; VanCourt, T.; Herbordt, M.C.
Accelerating molecular dynamics simulations with configurable circuits
IEE PROCEEDINGS-COMPUTERS AND DIGITAL TECHNIQUES, 153:189-195, MAY 2006
abstract, full text, DOI:10.1049/ip-cdt:20050182

Sild, Sulev; Maran, Uko; Lomaka, Andre; Karelson, Mati
Open computing grid for molecular science and engineering
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:953-959, MAY 2006
abstract, full text, DOI:10.1021/ci050354f

Manetti, F.; Tintori, C.; Armand-Ugon, M.; Clotet-Codina, I.; Massa, S.; Ragno, R.; Este, J.A.; Botta, M.
A combination of molecular dynamics and docking calculations to explore the binding mode of ADS-J1, a polyanionic compound endowed with anti-HIV-1 activity
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:1344-1351, MAY 2006
abstract, full text, DOI:10.1021/ci050414h

Lopez, Carlos F.; Nielsen, Steven O.; Srinivas, Goundla; DeGrado, William F.; Klein, Michael L.
Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:649-655, MAY 2006
abstract, full text, DOI:10.1021/ct050298p

Rodinger, T.; Howell, P.L.; Pomes, R.
Distributed replica sampling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:725-731, MAY 2006
abstract, full text, DOI:10.1021/ct050302x

Siggel, L.; Molnar, F.
Computer modelling of a type-1 collagen fibril in water. 1. Model development and validation
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 101:179-+, MAY 2006
abstract, full text

Espinoza-Fonseca, L.M.; Trujillo-Ferrara, J.G.
Transient stability of the helical pattern of region F19-L22 of the N-terminal domain of p53: A molecular dynamics simulation study
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 343:110-116, APR 28 2006
abstract, full text, DOI:10.1016/j.bbrc.2006.02.129

Eike, D.M.; Maginn, E.J.
Atomistic simulation of solid-liquid coexistence for molecular systems: Application to triazole and benzene
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 164503, APR 28 2006
abstract, full text, DOI:10.1063/1.2188400

Hamacher, K.; Hubsch, A.; McCammon, J.A.
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 164907, APR 28 2006
abstract, full text, DOI:10.1063/1.2185645

Kezuka, Y.; Ohishi, M.; Itoh, Y.; Watanabe, J.; Mitsutomi, M.; Watarabe, T.; Nonaka, T.
Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037
JOURNAL OF MOLECULAR BIOLOGY, 358:472-484, APR 28 2006
abstract, full text, DOI:10.1016/j.jmb.2006.02.013

Mathews, D.H.; Case, D.A.
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair
JOURNAL OF MOLECULAR BIOLOGY, 357:1683-1693, APR 14 2006
abstract, full text, DOI:10.1016/j.jmb.2006.01.054

Zhao, X.G.; Cummings, P.T.
Molecular dynamics study of carbon nanotube oscillators revisited
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 134705, APR 7 2006
abstract, full text, DOI:10.1063/1.2185623

Cecchini, M.; Curcio, R.; Pappalardo, M.; Melki, R.; Caflisch, A.
A molecular dynamics approach to the structural characterization of amyloid aggregation
JOURNAL OF MOLECULAR BIOLOGY, 357:1306-1321, APR 7 2006
abstract, full text, DOI:10.1016/j.jmb.2006.01.009

Hwang, H.; Schatz, G.C.; Ratner, M.A.
Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6999-7008, APR 6 2006
abstract, full text, DOI:10.1021/jp055740e

Jensen, M.O.; Mouritsen, O.G.
Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF
BIOPHYSICAL JOURNAL, 90:2270-2284, APR 2006
abstract, full text, DOI:10.1529/biophysj.105.073965

Bastug, T.; Gray-Weale, A.; Patra, S.M.; Kuyucak, S.
Role of protein flexibility in ion permeation: A case study in gramicidin A
BIOPHYSICAL JOURNAL, 90:2285-2296, APR 2006
abstract, full text, DOI:10.1529/biophysj.105.073205

Gumbart, J.; Schulten, K.
Molecular dynamics studies of the archaeal translocon
BIOPHYSICAL JOURNAL, 90:2356-2367, APR 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.105.075291

Anishkin, A.; Sukharev, S.; Colombini, M.
Searching for the molecular arrangement of transmembrane ceramide channels
BIOPHYSICAL JOURNAL, 90:2414-2426, APR 2006
abstract, full text, DOI:10.1529/biophysj.105.071977

Ramirez, E.; Santana, A.; Cruz, A.; Plasencia, I.; Lopez, G.E.
Molecular dynamics of surfactant protein C: From single molecule to heptameric aggregates
BIOPHYSICAL JOURNAL, 90:2698-2705, APR 2006
abstract, full text, DOI:10.1529/biophysj.105.073270

Clark, M.G.; Teply, J.; Haarer, B.K.; Viggiano, S.C.; Sept, D.; Amberg, D.C.
A genetic dissection of Aip1p's interactions leads to a model for Aip1p-cofilin cooperative activities
MOLECULAR BIOLOGY OF THE CELL, 17:1971-1984, APR 2006
abstract, full text, DOI:10.1091/mbc.E05-10-0956

Lagerqvist, J.; Zwolak, M.; Di Ventra, M.
Fast DNA sequencing via transverse electronic transport
NANO LETTERS, 6:779-782, APR 2006
abstract, full text, DOI:10.1021/nl0601076

Fitch, C.A.; Whitten, S.T.; Hilser, V.J.; Garcia-Moreno, B.
Molecular mechanisms of pH-driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:113-126, APR 1 2006
abstract, full text, DOI:10.1002/prot.20797

Janosi, L.; Keer, H.; Kosztin, I.; Ritz, T.
Influence of subunit structure on the oligomerization state of light-harvesting complexes: A free energy calculation study
CHEMICAL PHYSICS, 323:117-128, MAR 31 2006
abstract, full text, DOI:10.1016/j.chemphys.2005.08.038

Yu, Y.M.; Chipot, C.; Cai, W.S.; Shao, X.G.
Molecular dynamics study of the inclusion of cholesterol into cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6372-6378, MAR 30 2006
abstract, full text, DOI:10.1021/jp056751a

Spijker, P.; Vaidehi, N.; Freddolino, P.L.; Hilbers, P.A.J.; Goddard, W.A.
Dynamic behavior of fully solvated beta 2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:4882-4887, MAR 28 2006
abstract, full text, DOI:10.1073/pnas.0511329103

Kawatsu, T.; Beratan, D.N.; Kakitani, T.
Conformationally averaged score functions for electronic propagation in proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:5747-5757, MAR 23 2006
abstract, full text, DOI:10.1021/jp052194g

Romanov, S.; Wiesner, R.; Myagkova, G.; Kuhn, H.; Ivanov, I.
Affinity Labeling of the rabbit 12/15-lipoxygenase using azido derivatives of arachidonic acid
BIOCHEMISTRY, 45:3554-3562, MAR 21 2006
abstract, full text, DOI:10.1021/bi052152i

Pophristic, V.; Vemparala, S.; Ivanov, I.; Liu, Z.W.; Klein, M.L.; DeGrado, W.F.
Controlling the shape and flexibility of arylamides: A combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3517-3526, MAR 2 2006
abstract, full text, DOI:10.1021/jp054306+

Baer, M.; Schreiner, E.; Kohlmeyer, A.; Rousseau, R.; Marx, D.
Inverse temperature transition of a biomimetic elastin model: Reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3576-3587, MAR 2 2006
abstract, full text, DOI:10.1021/jp054805a

Shih, A.Y.; Arkhipov, A.; Freddolino, P.L.; Schulten, K.
Coarse grained protein-lipid model with application to lipoprotein particles
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3674-3684, MAR 2 2006
abstract, full text, TCBG publications, DOI:10.1021/jp0550816

Espinoza-Fonseca, L.M.; Trujillo-Ferrara, J.G.
The existence of a second allosteric site on the M-1 muscarinic acetylcholine receptor and its implications for drug design
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:1217-1220, MAR 1 2006
abstract, full text, DOI:10.1016/j.bmcl.2005.11.097

Meyer, T.; Ferrer-Costa, C.; Perez, A.; Rueda, M.; Bidon-Chanal, A.; Luque, F.J.; Laughton, C.A.; Orozco, M.
Essential dynamics: A tool for efficient trajectory compression and management
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:251-258, MAR-APR 2006
abstract, full text, DOI:10.1021/ct050285b

Yan, L.M.; Ma, Y.F.; Seminario, J.M.
Encoding information using molecular vibronics
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 6:675-684, MAR 2006
abstract, full text, DOI:10.1166/jnn.2006.087

Chipot, C.; Tarek, M.
Interaction of a peptide nanotube with a water-membrane interface
PHYSICAL BIOLOGY, 3:S20-S25, MAR 2006
abstract, full text, DOI:10.1088/1478-3975/3/1/S03

Lu, D.Y.; Aksimentiev, A.; Shih, A.Y.; Cruz-Chu, E.; Freddolino, P.L.; Arkhipov, A.; Schulten, K.
The role of molecular modeling in bionanotechnology
PHYSICAL BIOLOGY, 3:S40-S53, MAR 2006
abstract, full text, TCBG publications, DOI:10.1088/1478-3975/3/1/S05

Balaeff, A.; Mahadevan, L.; Schulten, K.
Modeling DNA loops using the theory of elasticity
PHYSICAL REVIEW E, 73 Art. No. 031919, MAR 2006
abstract, full text, TCBG publications, DOI:10.1103/PhysRevE.73.031919

Freddolino, P.L.; Arkhipov, A.S.; Larson, S.B.; McPherson, A.; Schulten, K.
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
STRUCTURE, 14:437-449, MAR 2006
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.11.014

Lee, E.H.; Gao, M.; Pinotsis, N.; Wilmanns, M.; Schulten, K.
Mechanical strength of the titin Z1Z2-telethonin complex
STRUCTURE, 14:497-509, MAR 2006
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.12.005

Hajjar, E.; Korkmaz, B.; Gauthier, F.; Brandsdal, B.O.; Witko-Sarsat, V.; Reuter, N.
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:1248-1260, FEB 23 2006
abstract, full text, DOI:10.1021/jm051018t

Zhuang, W.; Abramavicius, D.; Hayashi, T.; Mukamel, S.
Simulation protocols for coherent femtosecond vibrational spectra of peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3362-3374, FEB 23 2006
abstract, full text, DOI:10.1021/jp055813u

Sapay, N.; Montserret, R.; Chipot, C.; Brass, V.; Moradpour, D.; Deleage, G.; Penin, F.
NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural. protein 5A from bovine viral diarrhea virus
BIOCHEMISTRY, 45:2221-2233, FEB 21 2006
abstract, full text, DOI:10.1021/bi0517685

Cadena, C.; Zhao, Q.; Snurr, R.Q.; Maginn, E.J.
Molecular modeling and experimental studies of the thermodynamic and transport properties of pyridinium-based ionic liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 110:2821-2832, FEB 16 2006
abstract, full text, DOI:10.1021/jp056235k

Ivanov, I.; Vemparala, S.; Pophristic, V.; Kuroda, K.; DeGrado, W.F.; McCammon, J.A.; Klein, M.L.
Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:1778-1779, FEB 15 2006
full text, DOI:10.1021/ja0564665

Kosztin, I.; Barz, B.; Janosi, L.
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 124 Art. No. 064106, FEB 14 2006
abstract, full text, DOI:10.1063/1.2166379

Gracheva, M.E.; Xiong, A.L.; Aksimentiev, A.; Schulten, K.; Timp, G.; Leburton, J.P.
Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
NANOTECHNOLOGY, 17:622-633, FEB 14 2006
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/17/3/002

Tornroth-Horsefield, S.; Wang, Y.; Hedfalk, K.; Johanson, U.; Karlsson, M.; Tajkhorshid, E.; Neutze, R.; Kjellbom, P.
Structural mechanism of plant aquaporin gating
NATURE, 439:688-694, FEB 9 2006
abstract, full text, DOI:10.1038/nature04316

Corry, B.
An energy-efficient gating mechanism in the acetylcholine receptor channel suggested by molecular and Brownian dynamics
BIOPHYSICAL JOURNAL, 90:799-810, FEB 2006
abstract, full text, DOI:10.1529/biophysj.105.067868

Heng, J.B.; Aksimentiev, A.; Ho, C.; Marks, P.; Grinkova, Y.V.; Sligar, S.; Schulten, K.; Timp, G.
The electromechanics of DNA in a synthetic nanopore
BIOPHYSICAL JOURNAL, 90:1098-1106, FEB 2006
abstract, full text, TCBG publications, DOI:10.1529/biophysj.105.070672

Bronson, J.; Lee, O.S.; Saven, J.G.
Molecular dynamics simulation of WSK-3, a computationally designed, water-soluble variant of the integral membrane protein KcsA
BIOPHYSICAL JOURNAL, 90:1156-1163, FEB 2006
abstract, full text, DOI:10.1529/biophysj.105.068965

Henin, J.; Maigret, B.; Tarek, M.; Escrieut, C.; Fourmy, D.; Chipot, C.
Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor
BIOPHYSICAL JOURNAL, 90:1232-1240, FEB 2006
abstract, full text, DOI:10.1529/biophysj.105.070599

Kale, L.V.; Zheng, G.B.; Lee, C.W.; Kumar, S.
Scaling applications to massively parallel machines using Projections performance analysis tool
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 22:347-358, FEB 2006
abstract, full text, DOI:10.1016/j.future.2004.11.020

Mezei, M.; Filizola, M.
TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:97-107, FEB 2006
abstract, full text, DOI:10.1007/s10822-006-9039-1

Seroka, P.; Plosinski, M.; Czub, J.; Sowinski, P.; Pawlak, J.
Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol
MAGNETIC RESONANCE IN CHEMISTRY, 44:132-138, FEB 2006
abstract, full text, DOI:10.1002/mrc.1735

Legge, F.S.; Budi, A.; Treutlein, H.; Yarovsky, I.
Protein flexibility: Multiple molecular dynamics simulations of insulin chain B
BIOPHYSICAL CHEMISTRY, 119:146-157, JAN 20 2006
abstract, full text, DOI:10.1016/j.bpc.2005.08.002

Martinez, L.; Webb, P.; Polikarpov, I.; Skaf, M.S.
Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands
JOURNAL OF MEDICINAL CHEMISTRY, 49:23-26, JAN 12 2006
abstract, full text, DOI:10.1021/jm050805n

Casanovas, J.; Zanuy, D.; Aleman, C.
Conducting polymer actuator mechanism based on the conformational flexibility of calix[4]arene
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:1103-1105, 2006
full text, DOI:10.1002/anie.200503304

Dixon, M.F.
A runtime adaptive load balancing algorithm for particle simulations
APPLIED PARALLEL COMPUTING: STATE OF THE ART IN SCIENTIFIC COMPUTING, 3732:709-718, 2006
abstract, full text

Barreca, Maria Letizia; De Luca, Laura; Ferro, Stefania; Rao, Angela; Monforte, Anna-Maria; Chimirri, Alba
Computational and synthetic approaches for the discovery of HIV-1 integrase inhibitors
ARKIVOC, 7, 224-244, 2006
abstract, full text

Benitez, B.A.S.; Arora, K.; Schlick, T.
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism
BIOPHYSICAL JOURNAL, 90:42-56, JAN 2006
abstract, full text, DOI:10.1529/biophysj.105.071944

Modzelewska, Anna; Filipek, Slawomir; Palczewski, Krzysztof; Park, Paul S. -H.
Arrestin interaction with rhodopsin - Conceptual models
CELL BIOCHEMISTRY AND BIOPHYSICS, 46:1-15, 2006
abstract, full text, DOI:10.1385/CBB:46:1:1

Boghosian, Bruce; Coveney, Peter; Dong, Suchuan; Finn, Lucas; Jha, Shantenu; Karniadakis, George; Karonis, Nicholas
NEKTAR, SPICE and vortonics: Using federated grids for large scale scientific applications.
CHALLENGES OF LARGE APPLICATIONS IN DISTRIBUTED ENVIRONMENTS, PROCEEDINGS, 34-42, 2006
abstract, full text

Mulholland, Adrian J.
Modelling Biological Systems
CHEMICAL MODELLING: APPLICATIONS AND THEORY, VOL 4, 4:23-68, 2006
full text

Pedretti, A.; Vistoli, G.; Marconi, C.; Testa, B.
Muscarinic receptors: A comparative analysis of structural features and binding modes through homology modelling and molecular docking
CHEMISTRY & BIODIVERSITY, 3:481-501, 2006
abstract, full text, DOI:10.1002/cbdv.200690052

Sadiq, S. Kashif; Zasada, Stefan J.; Coveney, Peter V.
Grid assisted ensemble molecular dynamics simulations of HIV-1 proteases reveal novel conformations of the inhibitor saquinavir
COMPUTATIONAL LIFE SCIENCES II, PROCEEDINGS, 4216:150-161, 2006
abstract, full text

Fitch, Blake G.; Rayshubskiy, Aleksandr; Eleftheriou, Maria; Ward, T. J. Christopher; Giampapa, Mark; Zhestkov, Yuri; Pitman, Michael C.; Suits, Frank; Grossfield, Alan; Pitera, Jed; Swope, William; Zhou, Ruhong; Feller, Scott; Germain, Robert S.
Blue matter: Strong scaling of molecular dynamics on blue Gene/L
COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS, 3992:846-854, 2006
abstract, full text

Patny, Akshay; Desai, Prashant V.; Avery, Mitchell A.
Homology modeling of G-protein-coupled receptors and implications in drug design
CURRENT MEDICINAL CHEMISTRY, 13:1667-1691, 2006
abstract, full text, DOI:10.2174/092986706777442002

Kindratenko, Volodymyr; Pointer, David
A case study in porting a production scientific supercomputing application to a reconfigurable computer
FCCM 2006: 14TH ANNUAL IEEE SYMPOSIUM ON FIELD-PROGRAMMABLE CUSTOM COMPUTING MACHINES, PROCEEDINGS, 13-22, 2006
abstract, full text

Scrofano, Ronald; Gokhale, Maya; Trouw, Frans; Prasanna, Viktor K.
A hardware/software approach to molecular dynamics on reconfigurable computers
FCCM 2006: 14TH ANNUAL IEEE SYMPOSIUM ON FIELD-PROGRAMMABLE CUSTOM COMPUTING MACHINES, PROCEEDINGS, 23-32, 2006
abstract, full text

Patel, Arun; Madill, Christopher A.; Saldana, Manuel; Comis, Christopher; Pomes, Regis; Chow, Paul
A scalable FPGA-based multiprocessor
FCCM 2006: 14TH ANNUAL IEEE SYMPOSIUM ON FIELD-PROGRAMMABLE CUSTOM COMPUTING MACHINES, PROCEEDINGS, 111-120, 2006
abstract, full text

Cotallo-Aban, M.; Prada-Gracia, D.; Mazo, J. J.; Bruscolini, P.; Falo, F.; Sancho, J.
Analysis of apoflavodoxin folding behavior with elastic network models
FROM PHYSICS TO BIOLOGY: THE INTERFACE BETWEEN EXPERIMENT AND COMPUTATION, 851:135-149, 2006
abstract, full text

Yan, Liuming; Ma, Yuefei; Seminario, Jorge M.
Terahertz signal transmission in molecular systems
Frontiers in Electronics, 41:669-675, 2006
abstract, full text, DOI:10.1142/9789812773081_0042

Adrian, Png Eak Hock; Soo, Tan Tsu; Wah, Choo Keng
Large-scale simulation and prediction of HLA-epitope complex structures
GRID COMPUTING IN LIFE SCIENCES, 189-196, 2006
abstract, full text

Wei, Dawei; Guo, Wanlin
Molecular dynamics simulation of self-assembled carbon nanotubes
International Journal of Nanoscience, Vol 5, No 6, 5:835-839, 2006
abstract, full text, DOI:10.1142/S0219581X06005236

Li, A.Q.; Dowell, E.H.
Modal reduction of mathematical models of biological molecules
JOURNAL OF COMPUTATIONAL PHYSICS, 211:262-288, JAN 1 2006
abstract, full text, DOI:10.1016/j.jcp.2005.05.021

Plummer, M.; Hein, J.; Guest, M. F.; D'Mellow, K. J.; Bush, I. J.; Refson, K.; Pringle, G. J.; Smith, L.; Trew, A.
Terascale materials modelling on high performance system HPCx
JOURNAL OF MATERIALS CHEMISTRY, 16:1885-1893, 2006
abstract, full text, DOI:10.1039/b600182n

Miguet, Laurence; Zhang, Ziding; Grigorov, Martin G.
Computational studies of ligand-receptor interactions in bitter taste receptors
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 26:611-630, 2006
abstract, full text, DOI:10.1080/10799890600928210

Curini, Massimo; Epifano, Francesco; Genovese, Salvatore; Menghini, Luigi; Ricci, Donata; Fraternale, Daniele; Giamperi, Laura; Bucchini, Anahi; Bellacchio, Emanuele
Lipoxygenase inhibitory activity of boropinic acid, active principle of Boronia pinnata
NATURAL PRODUCT COMMUNICATIONS, 1:1141-1145, 2006
abstract, full text

Strahs, D.; Zhu, C.X.; Cheng, B.K.; Chen, J.; Tse-Dinh, Y.C.
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
NUCLEIC ACIDS RESEARCH, 34:1785-1797, 2006
abstract, full text, DOI:10.1093/nar/gkl109

Salsbury, F.R.; Clodfelter, J.E.; Gentry, M.B.; Hollis, T.; Scarpinato, K.D.
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response
NUCLEIC ACIDS RESEARCH, 34:2173-2185, 2006
abstract, full text, DOI:10.1093/nar/gkl238

Aluru, Srinivas; Amato, Nancy; Bader, David A.; Bhandarkar, Suchindra; Kale, Laxmikant; Marinescu, Dan C.
Parallel computational biology
PARALLEL PROCESSING FOR SCIENTIFIC COMPUTING, 357-378, 2006
full text, DOI:10.1137/1.9780898718133.ch19

Gao, Mu; Sotomayor, Marcos; Villa, Elizabeth; Lee, Eric H.; Schulten, Klaus
Molecular mechanisms of cellular mechanics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:3692-3706, 2006
abstract, full text, TCBG publications, DOI:10.1039/b606019f

Silva, Candida G.; Ostropytskyy, Vitaliy; Loureiro-Ferreira, Nuno; Berrar, Daniel; Dubitzky, Werner; Brito, Rui M. M.
P-found: The protein folding and unfolding simulation repository
PROCEEDINGS OF THE 2006 IEEE SYMPOSIUM ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 101-108, 2006
abstract, full text

Coveney, P. V.; Sadiq, S. K.; Saksena, R. S.; Thyveetil, Jm.; Zasada, S. J.; Mc Keown, M.; Pickles, S.
A lightweight application hosting environment for grid computing
Proceedings of the UK e-Science All Hands Meeting 2006, 217-224, 2006
abstract, full text

Coveney, P. V.; Sadiq, S. K.; Saksena, R. S.; Zasada, S. J.
Constructing chained molecular dynamics. Simulations of HIV-1 protease using the application hosting environment
Proceedings of the UK e-Science All Hands Meeting 2006, 428-431, 2006
abstract, full text

Correia, B.E.; Loureiro-Ferreira, N.; Rodrigues, J.R.; Brito, R.M.M.
A structural model of an amyloid protofilament of transthyretin
PROTEIN SCIENCE, 15:28-32, JAN 2006
abstract, full text, DOI:10.1110/ps.051787106

Wang, Y.L.; Arora, K.; Schlick, T.
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass
PROTEIN SCIENCE, 15:135-151, JAN 2006
abstract, full text, DOI:10.1110/ps.051726906

Park, S.; Saven, J.G.
Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin
PROTEIN SCIENCE, 15:200-207, JAN 2006
abstract, full text, DOI:10.1110/ps.051814306

Garg, Rajni; Bhhatarai, Barun
QSAR and molecular modeling studies of HIV protease inhibitors
QSAR AND MOLECULAR MODELING STUDIES IN HETEROCYCLIC DRUGS I, 3:181-271, 2006
abstract, full text

Sanbonmatsu, K. Y.; Tung, C. -S.
Large-scale simulations of the ribosome: a new landmark in computational biology
SciDAC 2006: Scientific Discovery Through Advanced Computing, 46:334-342, 2006
abstract, full text, DOI:10.1088/1742-6596/46/1/047

Gullingsrud, J.; Kim, C.; Taylor, S.S.; McCammon, J.A.
Dynamic binding of PKA regulatory subunit RI alpha
STRUCTURE, 14:141-149, JAN 2006
abstract, full text, DOI:10.1016/j.str.2005.09.019

Ma, Yuefei; Yan, Liuming; Semihario, Jorge M.
Molecular-based processing and transfer of information in the terahertz domain for military and security applications - art. no. 621204
Terahertz for Military and Security Applications IV, 6212:21204-21204, 2006
abstract, full text, DOI:10.1117/12.666888

Senapati, S.; Bui, J.M.; McCammon, J.A.
Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: A molecular dynamics study
JOURNAL OF MEDICINAL CHEMISTRY, 48:8155-8162, DEC 29 2005
abstract, full text, DOI:10.1021/jm050669m

Wang, P.; Yan, B.; Guo, J.T.; Hicks, C.; Xu, Y.
Structural genomics analysis of alternative splicing and application to isoform structure modeling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18920-18925, DEC 27 2005
abstract, full text, DOI:10.1073/pnas.0506770102

O'Donoghue, P.; Sethi, A.; Woese, C.R.; Luthey-Schulten, Z.A.
The evolutionary history of Cys-tRNA(Cys) formation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:19003-19008, DEC 27 2005
abstract, full text, DOI:10.1073/pnas.0509617102

Chipot, C.; Henin, J.
Exploring the free-energy landscape of a short peptide using an average force
JOURNAL OF CHEMICAL PHYSICS, 123 Art. No. 244906, DEC 22 2005
abstract, full text, DOI:10.1063/1.2138694

Sohn, R.; Parks, J.M.; Buhrman, G.; Brown, P.; Kristjansdottir, K.; Safi, A.; Edelsbrunner, H.; Yang, W.T.; Rudolph, J.
Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate
BIOCHEMISTRY, 44:16563-16573, DEC 20 2005
abstract, full text, DOI:10.1021/bi0516879

Cruz, L.; Urbanc, B.; Borreguero, J.M.; Lazo, N.D.; Teplow, D.B.; Stanley, H.E.
Solvent and mutation effects on the nucleation of amyloid beta-protein folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18258-18263, DEC 20 2005
abstract, full text, DOI:10.1073/pnas.0509276102

Espinoza-Fonseca, L.M.; Trujillo-Ferrara, J.G.
Identification of multiple allosteric sites on the M-1 muscarinic acetylcholine receptor
FEBS LETTERS, 579:6726-6732, DEC 19 2005
abstract, full text, DOI:10.1016/j.febslet.2005.10.069

Chung, S.H.; Corry, B.
Three computational methods for studying permeation, selectivity and dynamics in biological ion channels
SOFT MATTER, 1:417-427, DEC 14 2005
abstract, full text, DOI:10.1039/b512455g

Thomas, S.; Tanase, G.; Dale, L.K.; Moreira, J.M.; Rauchwerger, L.; Amato, N.M.
Parallel protein folding with STAPL
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1643-1656, DEC 10 2005
abstract, full text, DOI:10.1002/cpe.950

Wells, S.A.; Menor, S.; Hespenheide, B.; Thorpe, M.F.
Constrained geometric simulation of diffusive motion in proteins
PHYSICAL BIOLOGY, 2:S127-S136, DEC 2005
abstract, full text, DOI:10.1088/1478-3975/2/4/S07

Petersen, F.N.R.; Jensen, M.O.; Nielsen, C.H.
Interfacial tryptophan residues: A role for the cation-pi effect?
BIOPHYSICAL JOURNAL, 89:3985-3996, DEC 2005
abstract, full text, DOI:10.1059/biophysj.105.061804

Case, D.A.; Cheatham, T.E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K.M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R.J.
The Amber biomolecular simulation programs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1668-1688, DEC 2005
abstract, full text, DOI:10.1002/jcc.20290

Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K.
Scalable molecular dynamics with NAMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1781-1802, DEC 2005
abstract, full text, TCBG publications, DOI:10.1002/jcc.20289

Forbes, Jeffrey G.; Jin, Albert J.; Ma, Kan; Gutierrez-Cruz, Gustavo; Tsai, Wanxia L.; Wang, Kuan
Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, 26:291-301, DEC 2005
abstract, full text, DOI:10.1007/s10974-005-9035-4

Budi, A.; Legge, F.S.; Treutlein, H.; Yarovsky, I.
Electric field effects on insulin chain-B conformation
JOURNAL OF PHYSICAL CHEMISTRY B, 109:22641-22648, DEC 1 2005
abstract, full text, DOI:10.1021/jp052742q

Lue, Shouqin; Long, Mian
Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation
Molecular & Cellular Biomechanics, 2:161-177, DEC 2005
abstract, full text

Lim, R.Y.H.; Aebi, U.
In silico access to the nuclear pore complex
STRUCTURE, 13:1741-1743, DEC 2005
full text, DOI:10.1016/j.str.2005.11.002

Isgro, T.A.; Schulten, K.
Binding dynamics of isolated nucleoporin repeat regions to importin-beta
STRUCTURE, 13:1869-1879, DEC 2005
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.09.007

Jha, S.; Coveney, P.V.; Laughton, C.A.
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1617-1627, NOV 30 2005
abstract, full text, DOI:10.1002/jcc.20300

De Luca, L.; Vistoli, G.; Pedretti, A.; Barreca, M.L.; Chimirri, A.
Molecular dynamics studies of the full-length integrase-DNA complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 336:1010-1016, NOV 4 2005
abstract, full text, DOI:10.1016/j.bbrc.2005.08.211

Buchete, N.V.; Tycko, R.; Hummer, G.
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments
JOURNAL OF MOLECULAR BIOLOGY, 353:804-821, NOV 4 2005
abstract, full text, DOI:10.1016/j.jmb.2005.08.066

Vistoli, G.; Pedretti, A.; Villa, L.; Testa, B.
Solvent constraints on the property space of acetylcholine. 2. Ordered media
JOURNAL OF MEDICINAL CHEMISTRY, 48:6926-6935, NOV 3 2005
abstract, full text, DOI:10.1021/jm0580306

Seminario, J.M.; Yan, L.M.; Ma, Y.F.
Transmission of vibronic signals in molecular circuits
JOURNAL OF PHYSICAL CHEMISTRY A, 109:9712-9715, NOV 3 2005
abstract, full text, DOI:10.1021/jp054995p

Baudry, J.; Smith, J.C.
Can proteins and crystals self-catalyze methyl rotations?
JOURNAL OF PHYSICAL CHEMISTRY B, 109:20572-20578, NOV 3 2005
abstract, full text, DOI:10.1021/jp053111z

Katti, D.R.; Ghosh, P.; Schmidt, S.; Katti, K.S.
Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids
BIOMACROMOLECULES, 6:3276-3282, NOV-DEC 2005
abstract, full text, DOI:10.1021/bm0503219

Chipot, C.; Rozanska, X.; Dixit, S.B.
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:765-770, NOV 2005
abstract, full text, DOI:10.1007/s10822-005-9021-3

Zhang, D.Q.; McCammon, J.A.
The association of tetrameric acetylcholinesterase with CoIQ tail: A block normal mode analysis
PLOS COMPUTATIONAL BIOLOGY, 1:484-491, NOV 2005
abstract, full text, DOI:10.1371/journal.pcbi.0010062

Sanbonmatsu, K.Y.; Joseph, S.; Tung, C.S.
Simulating movement of tRNA into the ribosome during decoding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15854-15859, NOV 1 2005
abstract, full text, DOI:10.1073/pnas.0503456102

Liu, T.Y.; Jenwitheesuk, E.; Teller, D.C.; Samudrala, R.
Structural insights into the cellular retinaldehyde-binding protein (CRALBP)
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 61:412-422, NOV 1 2005
abstract, full text, DOI:10.1002/prot.20621

Wang, W.; Skeel, R.D.
Fast evaluation of polarizable forces
JOURNAL OF CHEMICAL PHYSICS, 123 Art. No. 164107, OCT 22 2005
abstract, full text, DOI:10.1063/1.2056544

Freites, J.A.; Tobias, D.J.; von Heijne, G.; White, S.H.
Interface connections of a transmembrane voltage sensor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15059-15064, OCT 18 2005
abstract, full text, DOI:10.1073/pnas.0507618102

Hosokawa, Y.; Maki, S.; Nagata, T.
Gold nanoparticles stabilized by tripod thioether oligomers: Synthesis and molecular dynamics studies
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 78:1773-1782, OCT 15 2005
abstract, full text, DOI:10.1246/bcsj.78.1773

Rai, B.K.; Prohofsky, E.W.; Durbin, S.M.
Single-atom test of all-atom empirical potentials: Fe in myoglobin
JOURNAL OF PHYSICAL CHEMISTRY B, 109:18983-18987, OCT 13 2005
abstract, full text, DOI:10.1021/jp052950i

Weinbach, Y.; Elber, R.
Revisiting and parallelizing SHAKE
JOURNAL OF COMPUTATIONAL PHYSICS, 209:193-206, OCT 10 2005
abstract, full text, DOI:10.1016/j.jcp.2005.03.015

Yonkunas, M.J.; Xu, Y.; Tang, P.
Anesthetic interaction with ketosteroid isomerase: Insights from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 89:2350-2356, OCT 2005
abstract, full text, DOI:10.1529/biophysj.105.063396

Pedersen, T.B.; Kaasgaard, T.; Jensen, M.O.; Frokjaer, S.; Mouritsen, O.G.; Jorgensen, K.
Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C-14-peptides
BIOPHYSICAL JOURNAL, 89:2494-2503, OCT 2005
abstract, full text, DOI:10.1529/biophysj.105.060756

Stagg, S.M.; Harvey, S.C.
Exploring the flexibility of ribosome recycling factor using molecular dynamics
BIOPHYSICAL JOURNAL, 89:2659-2666, OCT 2005
abstract, full text, DOI:10.1529/biophysj.104.052373

Seminario, J.M.; Yan, L.M.; Ma, Y.F.
Scenarios for molecular-level signal processing
PROCEEDINGS OF THE IEEE, 93:1753-1764, OCT 2005
abstract, full text, DOI:10.1109/JPROC.2005.853541

Gorfe, A.A.; Caflisch, A.
Functional plasticity in the substrate binding site of beta-secretase
STRUCTURE, 13:1487-1498, OCT 2005
abstract, full text, DOI:10.1016/j.str.2005.06.015

Jolley, C.; Ben-Shem, A.; Nelson, N.; Fromme, P.
Structure of plant photosystem I revealed by theoretical modeling
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:33627-33636, SEP 30 2005
abstract, full text, DOI:10.1074/jbc.M500937200

Coveney, P.V.; Fowler, P.W.
Modelling biological complexity: a physical scientist's perspective
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 2:267-280, SEP 22 2005
abstract, full text, DOI:10.1098/rsif.2005.0045

Franklin, J.; Doniach, S.
Adaptive time stepping in biomolecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 123 Art. No. 124909, SEP 22 2005
abstract, full text, DOI:10.1063/1.1997137

Myers, R.S.; Amaro, R.E.; Luthey-Schulten, Z.A.; Davisson, V.J.
Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase
BIOCHEMISTRY, 44:11974-11985, SEP 13 2005
abstract, full text, DOI:10.1021/bi050706b

Bae, E.; Phillips, G.N.
Identifying and engineering ion pairs in adenylate kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30943-30948, SEP 2 2005
abstract, full text, DOI:10.1074/jbc.M504216200

Paliwal, A.; Asthagiri, D.; Abras, D.; Lenhoff, A.M.; Paulaitis, M.E.
Light-scattering studies of protein solutions: Role of hydration in weak protein-protein interactions
BIOPHYSICAL JOURNAL, 89:1564-1573, SEP 2005
abstract, full text, DOI:10.1529/biophysj.105.065284

Filipek, S.
Organization of rhodopsin molecules in native membranes of rod cells - an old theoretical model compared to new experimental data
JOURNAL OF MOLECULAR MODELING, 11:385-391, SEP 2005
abstract, full text, DOI:10.1007/s00894-005-0268-3

Cohen, J.; Kim, K.; King, P.; Seibert, M.; Schulten, K.
Finding gas diffusion pathways in proteins: Application to O-2 and H-2 transport in Cpl [FeFe]-hydrogenase and the role of packing defects
STRUCTURE, 13:1321-1329, SEP 2005
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.05.013d

Mathe, J.; Aksimentiev, A.; Nelson, D.R.; Schulten, K.; Meller, A.
Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:12377-12382, AUG 30 2005
abstract, full text, TCBG publications, DOI:10.1073/pnas.0502947102

Dublet, B.; Ruello, A.; Pederzoli, M.; Hajjar, E.; Courbebaisse, M.; Canteloup, S.; Reuter, N.; Witko-Sarsat, V.
Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30242-30253, AUG 26 2005
abstract, full text, DOI:10.1074/jbc.M414609200

Ashworth, M.; Bush, I.J.; Guest, M.F.; Sunderland, A.G.; Booth, S.; Hein, J.; Smith, L.; Stratford, K.; Curioni, A.
HPCx: towards capability computing
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1329-1361, AUG 25 2005
abstract, full text, DOI:10.1002/cpe.895

Hemp, J.; Christian, C.; Barquera, B.; Gennis, R.B.; Martinez, T.J.
Helix switching of a key active-site residue in the cytochrome cbb(3) oxidases
BIOCHEMISTRY, 44:10766-10775, AUG 16 2005
abstract, full text, DOI:10.1021/bi050464f

Schmidt, S.R.; Katti, D.R.; Ghosh, P.; Katti, K.S.
Evolution of mechanical response of sodium montmorillonite interlayer with increasing hydration by molecular dynamics
LANGMUIR, 21:8069-8076, AUG 16 2005
abstract, full text, DOI:10.1021/la050615f

Pickles, S.M.; Haines, R.; Pinning, R.L.; Porter, A.R.
A practical toolkit for computational steering
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1843-1853, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1611

Kalawsky, R.S.; Nee, S.P.; Holmes, I.; Coveney, P.V.
A grid-enabled lightweight computational steering client: a .NET PDA implementation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1885-1894, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1617

Hein, J.I.; Reid, F.; Smith, L.; Bush, I.; Guest, M.; Sherwood, P.
On the performance of molecular dynamics applications on current high-end systems
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1987-1998, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1624

Fowler, P.W.; Jha, S.; Coveney, P.V.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1999-2015, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1625

Woods, C.J.; Ng, M.H.; Johnston, S.; Murdock, S.E.; Wu, B.; Tai, K.; Fangohr, H.; Jeffreys, P.; Cox, S.; Frey, J.G.; Sansom, M.S.P.; Essex, J.W.
Grid computing and biomolecular simulation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2017-2035, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1626

Wan, S.Z.; Coveney, P.V.; Flower, D.R.
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2037-2053, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1627

Giordanetto, F.; Fowler, P.W.; Saqi, M.; Coveney, P.V.
Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2055-2073, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1629

Rousay, E.R.; Fu, H.C.; Robinson, J.M.; Essex, J.W.; Frey, J.G.
Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2075-2095, AUG 15 2005
abstract, full text, DOI:10.1098/rsta.2005.1630

Damjanovic, A.; Garcia-Moreno, B.; Lattman, E.E.; Garcia, A.E.
Molecular dynamics study of water penetration in staphylococcal nuclease
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:433-449, AUG 15 2005
abstract, full text, DOI:10.1002/prot.20486

Park, S.; Saven, J.G.
Statistical and molecular dynamics studies of buried waters in globular proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:450-463, AUG 15 2005
abstract, full text, DOI:10.1002/prot.20511

Ota, N.; Agard, D.A.
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
JOURNAL OF MOLECULAR BIOLOGY, 351:345-354, AUG 12 2005
abstract, full text, DOI:10.1016/j.jmb.2005.05.043

de Brevern, A.G.; Wong, H.; Tournamille, C.; Colin, Y.; Van Kim, C.L.; Etchebest, C.
A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1724:288-306, AUG 5 2005
abstract, full text, DOI:10.1016/j.bbagen.2005.05.016

Carrillo-Tripp, M.; Feller, S.E.
Evidence for a mechanism by which omega-3 polyunsaturated lipids may affect membrane protein function
BIOCHEMISTRY, 44:10164-10169, AUG 2 2005
abstract, full text, DOI:10.1021/bi050822e

Mulkidjanian, A.Y.; Kozlova, M.A.; Cherepanov, D.A.
Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring
BIOCHEMICAL SOCIETY TRANSACTIONS, 33:845-850, AUG 2005
abstract, full text

Veluraja, K.; Margulis, C.J.
Conformational dynamics of sialyl Lewis(x) in aqueous solution and its interaction with selectinE. A study by molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:101-111, AUG 2005
abstract, full text

Wan, S.Z.; Coveney, P.V.; Flower, D.R.
Molecular basis of peptide recognition by the TCR: Affinity differences calculated using large scale computing
JOURNAL OF IMMUNOLOGY, 175:1715-1723, AUG 1 2005
abstract, full text

McGillivray, G.; Savarirayan, R.; Cox, T.C.; Stojkoski, C.; McNeil, R.; Bankier, A.; Bateman, J.F.; Roscioli, T.; Gardner, R.J.M.; Lamande, S.R.
Familial scaphocephaly syndrome caused by a novel mutation in the FGFR2 tyrosine kinase domain
JOURNAL OF MEDICAL GENETICS, 42:656-662, AUG 2005
full text, DOI:10.1136/jmg.2004.027888

Izaguirre, J.A.; Hampton, S.S.; Matthey, T.
Parallel multigrid summation for the N-body problem
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 65:949-962, AUG 2005
abstract, full text, DOI:10.1016/j.jpdc.2005.03.006

Makrodimitris, K.; Fernandez, E.J.; Woolf, T.B.; O'Connell, J.P.
ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes
MOLECULAR SIMULATION, 31:623-636, AUG 2005
abstract, full text, DOI:10.1080/08927020500108262

Wang, Y.; Schulten, K.; Tajkhorshid, E.
What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF
STRUCTURE, 13:1107-1118, AUG 2005
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.05.005

Crocker, M.S.; Hampton, S.S.; Matthey, T.; Izaguirre, J.A.
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1021-1031, JUL 30 2005
abstract, full text, DOI:10.1002/jcc.20240

Lynch, D.L.; Reggio, P.H.
Molecular dynamics simulations of the endocannabinoid N-arachidonoylethanolamine (Anandamide) in a phospholipid bilayer: Probing structure and dynamics
JOURNAL OF MEDICINAL CHEMISTRY, 48:4824-4833, JUL 28 2005
abstract, full text, DOI:10.1021/jm058185d

Borza, D.B.; Bondar, O.; Colon, S.; Todd, P.; Sado, Y.; Neilson, E.G.; Hudson, B.G.
Goodpasture autoantibodies unmask cryptic epitopes by selectively dissociating autoantigen complexes lacking structural reinforcement - Novel mechanisms for immune privilege and autoimmune pathogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:27147-27154, JUL 22 2005
abstract, full text, DOI:10.1074/jbc.M504050200

Roh, J.H.; Novikov, V.N.; Gregory, R.B.; Curtis, J.E.; Chowdhuri, Z.; Sokolov, A.P.
Onsets of anharmonicity in protein dynamics
PHYSICAL REVIEW LETTERS, 95 Art. No. 038101, JUL 15 2005
abstract, full text, DOI:10.1103/PhysRevLett.95.038101

Dittrich, M.; Freddolino, P.L.; Schulten, K.
When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii
JOURNAL OF PHYSICAL CHEMISTRY B, 109:13006-13013, JUL 7 2005
abstract, full text, TCBG publications, DOI:10.1021/jp050943o

Mezzenga, R.; Grigorov, M.; Zhang, Z.D.; Servais, C.; Sagalowicz, L.; Romoscanu, A.I.; Khanna, V.; Meyer, C.
Polysaccharide-induced order-to-order transitions in lyotropic liquid crystals
LANGMUIR, 21:6165-6169, JUL 5 2005
abstract, full text, DOI:10.1021/la050905w

Fernandez, L.E.; Perez, C.; Segovia, L.; Rodriguez, M.H.; Gill, S.S.; Bravo, A.; Soberon, M.
Cry11Aa toxin from Bacillus thuringiensis binds its receptor in Aedes aegypti mosquito larvae through loop alpha-8 of domain II
FEBS LETTERS, 579:3508-3514, JUL 4 2005
abstract, full text, DOI:10.1016/j.febslet.2005.05.032

Amaro, R.E.; Myers, R.S.; Davisson, V.J.; Luthey-Schulten, Z.A.
Structural elements in IGP synthase exclude water to optimize ammonia transfer
BIOPHYSICAL JOURNAL, 89:475-487, JUL 2005
abstract, full text, DOI:10.1529/biophysj.104.058651

Damjanovic, A.; Garcia-Moreno, B.; Lattman, E.E.; Garcia, A.E.
Molecular dynamics study of hydration of the protein interior
COMPUTER PHYSICS COMMUNICATIONS, 169:126-129, JUL 1 2005
abstract, full text, DOI:10.1016/j.cpc.2005.03.030

Engle, R.D.; Skeel, R.D.; Drees, M.
Monitoring energy drift with shadow Hamiltonians
JOURNAL OF COMPUTATIONAL PHYSICS, 206:432-452, JUL 1 2005
abstract, full text, DOI:10.1016/j.jcp.2004.12.009

Aldini, G.; Dalle-Donne, I.; Vistoli, G.; Facino, R.M.; Carini, M.
Covalent modification of actin by 4-hydroxy-trans-2-nonenal (HNE): LC-ESI-MS/MS evidence for Cys374 Michael adduction
JOURNAL OF MASS SPECTROMETRY, 40:946-954, JUL 2005
abstract, full text, DOI:10.1002/jms.872

Fleming, P.J.; Rose, G.D.
Do all backbone polar groups in proteins form hydrogen bonds?
PROTEIN SCIENCE, 14:1911-1917, JUL 2005
abstract, full text, DOI:10.1110/ps.051454805

Chao, S.D.; Kress, J.D.; Redondo, A.
Coarse-grained rigid blob model for soft matter simulations
JOURNAL OF CHEMICAL PHYSICS, 122 Art. No. 234912, JUN 15 2005
abstract, full text, DOI:10.1063/1.1938193

Henin, J.; Pohorille, A.; Chipot, C.
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:8478-8484, JUN 15 2005
abstract, full text, DOI:10.1021/ja050581y

Ortiz, V.; Nielsen, S.O.; Klein, M.L.; Discher, D.E.
Unfolding a linker between helical repeats
JOURNAL OF MOLECULAR BIOLOGY, 349:638-647, JUN 10 2005
abstract, full text, DOI:10.1016/j.jmb.2005.03.086

Aksimentiev, A.; Schulten, K.
Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
BIOPHYSICAL JOURNAL, 88:3745-3761, JUN 2005
abstract, full text, TCBG publications, DOI:10.1529/biophysj.104.058727

Liu, Z.W.; Xu, Y.; Tang, P.
Molecular dynamics Simulations of C2F6 effects on gramicidin A: Implications of the mechanisms of general anesthesia
BIOPHYSICAL JOURNAL, 88:3784-3791, JUN 2005
abstract, full text, DOI:10.1529/biophysj.104.055566

Tarek, M.
Membrane electroporation: A molecular dynamics simulation
BIOPHYSICAL JOURNAL, 88:4045-4053, JUN 2005
abstract, full text, DOI:10.1529/biophysj.104.050617

Zheng, G.B.; Wilmarth, T.; Jagadishprasad, P.; Kale, L.V.
Simulation-based performance prediction for large parallel machines
INTERNATIONAL JOURNAL OF PARALLEL PROGRAMMING, 33:183-207, JUN 2005
abstract, full text, DOI:10.1007/s10766-005-3582-6

Bishop, T.C.
Molecular dynamics simulations of a nucleosome and free DNA
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 22:673-685, JUN 2005
abstract, full text

Brigo, A.; Lee, K.W.; Fogolari, F.; Mustata, G.L.; Briggs, J.M.
Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:723-741, JUN 1 2005
abstract, full text, DOI:10.1002/prot.20447

Zhang, Q.M.; Lee, G.R.; Marszalek, P.E.
Atomic cranks and levers control sugar ring conformations
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1427-S1442, MAY 11 2005
abstract, full text, DOI:10.1088/0953-8984/17/18/001

Villa, E.; Balaeff, A.; Schulten, K.
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6783-6788, MAY 10 2005
abstract, full text, TCBG publications, DOI:10.1073/pnas.0409387102

Law, R.J.; Henchman, R.H.; McCammon, J.A.
A gating mechanism proposed from a simulation of a human alpha 7 nicotinic acetylcholine receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6813-6818, MAY 10 2005
abstract, full text, DOI:10.1073/pnas.0407739102

Brigo, A.; Lee, K.W.; Mustata, G.I.; Briggs, J.M.
Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain
BIOPHYSICAL JOURNAL, 88:3072-3082, MAY 2005
abstract, full text, DOI:10.1529/biophysj.104.050286

Asthagiri, D.; Paliwal, A.; Abras, D.; Lenhoff, A.M.; Paulaitis, M.E.
A consistent experimental and modeling approach to light-scattering studies of protein-protein interactions in solution
BIOPHYSICAL JOURNAL, 88:3300-3309, MAY 2005
abstract, full text, DOI:10.1529/biophysj.104.058859

Costantino, G.; Entrena-Guadix, A.; Macchiarulo, A.; Gioiello, A.; Pellicciari, R.
Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding
JOURNAL OF MEDICINAL CHEMISTRY, 48:3251-3259, MAY 5 2005
abstract, full text, DOI:10.1021/jm049182o

Chinta, S.J.; Kommaddi, R.P.; Turman, C.M.; Strobel, H.W.; Ravindranath, V.
Constitutive expression and localization of cytochrome P-450 1A1 in rat and human brain: presence of a splice variant form in human brain
JOURNAL OF NEUROCHEMISTRY, 93:724-736, MAY 2005
abstract, full text, DOI:10.1111/j.1471-4159.2005.03061.x

Kamath, S.A.; Buolamwini, J.K.
Asp746 to glycine change may have a greater influence than cys751 to serine change in accounting for ligand selectivity between EGFR and HER-2 at the ATP site
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:287-291, MAY 2005
abstract, full text, DOI:10.1007/s10822-005-5083-5

Bourgault, R.; Oakley, A.J.; Bewley, J.D.; Wilce, M.C.J.
Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit
PROTEIN SCIENCE, 14:1233-1241, MAY 2005
abstract, full text, DOI:10.1110/ps.041260905

Park, S.; Boder, E.T.; Saven, J.G.
Modulating the DNA affinity of Elk-1 with computationally selected mutations
JOURNAL OF MOLECULAR BIOLOGY, 348:75-83, APR 22 2005
abstract, full text, DOI:10.1016/j.jmb.2004.12.062

Adisa, B.; Bruce, D.A.
Molecular dynamics Simulations of helix-forming, amine-functionalized m-poly(phenyleneethynylene)s
JOURNAL OF PHYSICAL CHEMISTRY B, 109:7548-7556, APR 21 2005
abstract, full text, DOI:10.1021/jp0407122

Kahle, C.; Deubner, R.; Schollmayer, C.; Scheiber, J.; Baumann, K.; Holzgrabe, U.
NMR spectroscopic and molecular modelling studies on cyclodextrin-dipeptide inclusion complexes
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8, 1578-1589, APR 15 2005
abstract, full text, DOI:10.1002/ejoc.200400673

Alexopoulos, E.; Jares-Erijman, E.A.; Jovin, T.M.; Klement, R.; Machinek, R.; Sheldrick, G.M.; Uson, I.
Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 61:407-415, APR 2005
abstract, full text, DOI:10.1107/S090744490500082X

Henchman, R.H.; Wang, H.L.; Sine, S.M.; Taylor, P.; McCammon, J.A.
Ligand-induced conformational change in the alpha 7 nicotinic receptor ligand binding domain
BIOPHYSICAL JOURNAL, 88:2564-2576, APR 2005
abstract, full text, DOI:10.1529/biophysj.104.053934

Sokal, I.; Dupps, W.J.; Grassi, M.A.; Brown, J.; Affatigato, L.M.; Roychowdhury, N.; Yang, L.L.; Filipek, S.; Palczewski, K.; Stone, E.M.; Baehr, W.
A novel GCAP1 missense mutation (L151F) in a large family with autosomal dominant cone-rod dystrophy (adCORD)
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 46:1124-1132, APR 2005
abstract, full text, DOI:10.1167/iovs.04-1431

Sotomayor, M.; Corey, D.P.; Schulten, K.
In search of the hair-cell gating spring: Elastic properties of ankyrin and cadherin repeats
STRUCTURE, 13:669-682, APR 2005
abstract, full text, TCBG publications, DOI:10.1016/j.str.2005.03.001

Katti, D.R.; Schmidt, S.R.; Ghosh, P.; Katti, K.S.
Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics
CLAYS AND CLAY MINERALS, 53:171-178, APR 2005
abstract, full text, DOI:10.1346/CCMN.2005.0530207

Swain, M.D.; Benson, D.E.
Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:64-71, APR 1 2005
abstract, full text, DOI:10.1002/prot.20403

Jenwitheesuk, E.; Samudrala, R.
Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics
AIDS, 19:529-531, MAR 25 2005
abstract, full text, DOI:10.1097/01.aids.0000162343.96674.4c

Espinoza-Fonseca, L.M.; Trujillo-Ferrara, J.G.
Structural considerations for the rational design of selective anti-trypanosomal agents: The role of the aromatic clusters at the interface of triosephosphate isomerase dimer
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 328:922-928, MAR 25 2005
abstract, full text, DOI:10.1016/j.bbrc.2005.01.043

Vistoli, G.; Pedretti, A.; Villa, L.; Testa, B.
Solvent constraints on the property space of acetylcholine. I. Isotropic solvents
JOURNAL OF MEDICINAL CHEMISTRY, 48:1759-1767, MAR 24 2005
abstract, full text, DOI:10.1021/jm040823p

Sonne, J.; Hansen, F.Y.; Peters, G.H.
Methodological problems in pressure profile calculations for lipid bilayers
JOURNAL OF CHEMICAL PHYSICS, 122 Art. No. 124903, MAR 22 2005
abstract, full text, DOI:10.1063/1.1862624

Hollup, S.M.; Salensminde, G.; Reuter, N.
WEBnm@: a web application for normal mode analyses of proteins
BMC BIOINFORMATICS, 6 Art. No. 52, MAR 11 2005
abstract, full text, DOI:10.1186/1471-2105-6-52

Miller, F.; Kentsis, A.; Osman, R.; Pan, Z.Q.
Inactivation of VHL by tumorigenic mutations that disrupt dynamic coupling of the pVHL(.)hypoxia-inducible transcription factor-1 alpha complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:7985-7996, MAR 4 2005
abstract, full text, DOI:10.1074/jbc.M413160200

Delaforge, M.; Pruvost, A.; Perrin, L.; Andre, F.
Cytochrome P450-mediated oxidation of glucuronide derivatives: Example of estradiol-17 beta-glucuronide oxidation to 2-hydroxyestradiol-17 beta-glucuronide by CYP2C8
DRUG METABOLISM AND DISPOSITION, 33:466-473, MAR 2005
abstract, full text, DOI:10.1124/dmd.104.002097

Germain, R.S.; Zhestkov, Y.; Eleftheriou, M.; Rayshubskiy, A.; Suits, F.; Ward, T.J.C.; Fitch, B.G.
Early performance data on the Blue Matter molecular simulation framework
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 49:447-455, MAR-MAY 2005
abstract, full text

Cozmuta, I.; O'Keeffe, J.T.; Bose, D.; Stolc, V.
Hybrid MD-Nernst Planck model of alpha-hemolysin conductance properties
MOLECULAR SIMULATION, 31:79-93, FEB 15 2005
abstract, full text, DOI:10.1080/08927020412331308467

Roman, C.; Ciontu, F.; Courtois, B.
Nanoscopic modeling of a carbon nanotube force-measuring biosensor
MOLECULAR SIMULATION, 31:123-133, FEB 15 2005
abstract, full text, DOI:10.1080/08927020412331308511

Cohen, J.; Kim, K.; Posewitz, M.; Ghirardi, M.L.; Schulten, K.; Seibert, M.; King, P.
Molecular dynamics and experimental investigation of H-2 and O-2 diffusion in [Fe]-hydrogenase
BIOCHEMICAL SOCIETY TRANSACTIONS, 33:80-82, FEB 2005
abstract, full text, TCBG publications

Benz, R.W.; Castro-Roman, F.; Tobias, D.J.; White, S.H.
Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach
BIOPHYSICAL JOURNAL, 88:805-817, FEB 2005
abstract, full text, DOI:10.1529/biophysj.104.046821

Saladino, A.C.; Xu, Y.; Tang, P.
Homology Modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor
BIOPHYSICAL JOURNAL, 88:1009-1017, FEB 2005
abstract, full text, DOI:10.1529/biophysj.104.053421

Moran, O.; Galietta, L.J.V.; Zegarra-Moran, O.
Binding site of activators of the cystic fibrosis transmembrane conductance regulator in the nucleotide binding domains
CELLULAR AND MOLECULAR LIFE SCIENCES, 62:446-460, FEB 2005
abstract, full text, DOI:10.1007/s00018-004-4422-3

Meineke, M.A.; Vardeman, C.F.; Lin, T.; Fennell, C.J.; Gezelter, J.D.
OOPSE: An object-oriented parallel simulation engine for molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:252-271, FEB 2005
abstract, full text, DOI:10.1002/jcc.20161

Cojocaru, V.; Nottrott, S.; Klement, R.; Jovin, T.M.
The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study
RNA-A PUBLICATION OF THE RNA SOCIETY, 11:197-209, FEB 2005
abstract, full text, DOI:10.1261/rna.7149605

Molnar, F.; Rieger, J.
"Like-charge attraction" between anionic polyelectrolytes: Molecular dynamics simulations
LANGMUIR, 21:786-789, JAN 18 2005
abstract, full text, DOI:10.1021/la048057c

Williams, E.T.; Turman, C.M.; Strobel, H.W.
NAMD-LP: Filtering and translating NAMD-generated files
MOLECULAR SIMULATION, 31:67-68, JAN 15 2005
full text, DOI:10.1080/08927020512331325774

Hourai, Y.; Nishida, A.; Oyanagi, Y.
Network-aware data mapping on parallel molecular dynamics
11th International Conference on Parallel and Distributed Systems, Vol I, Proceedings, 126-132, 2005
abstract, full text

Stahl, F.; Berrar, D.; Silva, C.; Rodrigues, J.R.; Brito, R.M.M.; Dubitzky, W.
Grid warehousing of molecular dynamics protein unfolding data
2005 IEEE International Symposium on Cluster Computing and the Grid, Vols 1 and 2, 496-503, 2005
abstract, full text

Shivam, Piyush; Babu, Shivnath; Chase, Jeffrey S.
Learning application models for utility resource planning
3rd International Conference on Autonomic Computing, Proceedings, 255-264, 2005
abstract, full text

Zhang, Q.M.; Jaroniec, J.; Lee, G.; Marszalek, P.E.
Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:2723-2727, 2005
full text, DOI:10.1002/anie.200462067

Choi, S.; Clements, D.J.; Pophristic, V.; Ivanov, I.; Vemparala, S.; Bennett, J.S.; Klein, M.L.; Winkler, J.D.; DeGrado, W.E.
The design and evaluation of heparin-binding foldamers
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:6685-6689, 2005
full text, DOI:10.1002/anie.200501279

Witheesuk, E.J.; Samudrala, R.
Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach
ANTIVIRAL THERAPY, 10:157-166, 2005
abstract, full text

Tajkhorshid, Emad; Cohen, Jordi; Aksimentiev, Aleksij; Sotomayor, Marcos; Schulten, Klaus
Towards an Understanding of Membrane Channels
Bacterial Ion Channels: And Their Eukaryotic Homologs, 153-190, 2005
full text, TCBG publications

Azevedo, P.J.; Silva, C.G.; Rodrigues, J.R.; Loureiro-Ferreira, N.; Brito, R.M.M.
Detection of hydrophobic clusters in molecular dynamics protein unfolding simulations using association rules
BIOLOGICAL AND MEDICAL DATA ANALYSIS, PROCEEDINGS, 3745:329-337, 2005
abstract, full text

Bolhuis, P.G.
Kinetic pathways of beta-hairpin (Un)folding in explicit solvent
BIOPHYSICAL JOURNAL, 88:50-61, JAN 2005
abstract, full text, DOI:10.1529/biophysj.104.048744

Goodyear, D.J.; Sharpe, S.; Grant, C.W.M.; Morrow, M.R.
Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations
BIOPHYSICAL JOURNAL, 88:105-117, JAN 2005
abstract, full text, DOI:10.1529/biophysj.104.047506

Shih, A.Y.; Denisov, I.G.; Phillips, J.C.; Sligar, S.G.; Schulten, K.
Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins
BIOPHYSICAL JOURNAL, 88:548-556, JAN 2005
abstract, full text, TCBG publications, DOI:10.1529/biophysj.104.046896

Nowak, Wieslaw; Marszalek, Piotr E.
Molecular Dynamics Simulations of Single Molecule Atomic Force Microscope Experiments
COMPUTATIONAL CHEMISTRY: REVIEWS OF CURRENT TRENDS, VOL 9, 9:47-83, 2005
abstract, full text, DOI:10.1142/9789812701305_0002

Scott, L.R.; Clark, T.; Bagheri, B.
Education and research challenges in parallel computing
COMPUTATIONAL SCIENCE - ICCS 2005, PT 2, 3515:44-51, 2005
abstract, full text

Jenkins, J.; Sengupta, D.; Sundaram, S.
Characterization of a solid state DNA nanopore sequencer using multi-scale (nano-to-device) modeling
COMPUTATIONAL SCIENCE - ICCS 2005, PT 3, 3516:309-316, 2005
abstract, full text

Debnath, A.K.
Application of 3D-QSAR techniques in anti-HIV-1 drug design - An overview
CURRENT PHARMACEUTICAL DESIGN, 11:3091-3110, 2005
abstract, full text, DOI:10.2174/1381612054864902

Zhou, Z.W.; Wang, F.; Todd, B.D.
Development of chemistry portal for grid-enabled molecular science
First International Conference on e-Science and Grid Computing, Proceedings, 48-55, 2005
abstract, full text

Wiley, A.P.; Swain, M.T.; Phillips, S.C.; Essex, J.W.; Edge, C.M.
Parametrization of reversible digitally filtered molecular dynamics simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1:24-35, JAN-FEB 2005
abstract, full text, DOI:10.1021/ct049970t

Katti, D.R.; Ghosh, P.; Katti, K.
Evaluation of deformation mechanisms at mineral-protein composite interface using steered molecular dynamics simulations
Mechanical Properties of Bioinspired and Biological Materials, 844:201-206, 2005
abstract, full text

Ghosh, P.; Katti, D.R.; Katti, K.
Influence of protein structures on mechanical response
Mechanical Properties of Bioinspired and Biological Materials, 844:243-248, 2005
abstract, full text

Sidiqi, M.; Wilce, J.A.; Vivian, J.P.; Porter, C.J.; Barker, A.; Leedman, P.J.; Wilce, M.C.J.
Structure and RNA binding of the third KH domain of poly(C)-binding protein 1
NUCLEIC ACIDS RESEARCH, 33:1213-1221, 2005
abstract, full text, DOI:10.1093/nar/gki265

Lemke, K.; Wojciechowski, M.; Laine, W.; Bailly, C.; Colson, P.; Baginski, M.; Larsen, A.K.; Skladanowski, A.
Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities
NUCLEIC ACIDS RESEARCH, 33:6034-6047, 2005
abstract, full text, DOI:10.1093/nar/gki904

Li, Aiqin; Dowell, Earl H.
Modal reduction of mathematical models of biological molecules
Proceedings of the ASME International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, Vol 1, Pts A-C, 1801-1815, 2005
abstract, full text

Filipek, S.; Modzelewska, A.; Krzysko, K.A.
Functional oligomers of rhodopsin - a G protein-coupled receptor template
Proceedings of the Joint Meeting on Medicinal Chemistry, 5-10, 2005
abstract, full text

Lu, B.Z.; Wong, C.F.; Mccammon, J.A.
Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study
PROTEIN SCIENCE, 14:159-168, JAN 2005
abstract, full text, DOI:10.1110/ps.04894605

Ma, Y.F.; Yan, L.M.; Seminario, J.M.
Terahertz molecular electronics devices and systems
TERAHERTZ FOR MILITARY AND SECURITY APPLICATIONS III, 5790:206-218, 2005
abstract, full text, DOI:10.1117/12.603650

Espinoza-Fonseca, L. Michel
Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer
THEORETICAL BIOLOGY AND MEDICAL MODELLING, 2 Art. No. 38, 2005
abstract, full text, DOI:10.1186/1742-4682-2-38

Autenrieth, F.; Tajkhorshid, E.; Schulten, K.; Luthey-Schulten, Z.
Role of water in transient cytochrome c(2) docking
JOURNAL OF PHYSICAL CHEMISTRY B, 108:20376-20387, DEC 30 2004
abstract, full text, TCBG publications, DOI:10.1021/jp047994q

Amaro, R.; Luthey-Schulten, Z.
Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein
CHEMICAL PHYSICS, 307:147-155, DEC 27 2004
abstract, full text, DOI:10.1016/j.chemphys.2004.05.019

De Fabritiis, G.; Delgado-Buscalioni, R.; Coveney, P.V.
Energy controlled insertion of polar molecules in dense fluids
JOURNAL OF CHEMICAL PHYSICS, 121:12139-12142, DEC 22 2004
abstract, full text, DOI:10.1063/1.1835957

Pedesseau, L.; Jouanna, P.
Phases, periphases, and interphases equilibrium by molecular modeling. I. Mass equilibrium by the semianalytical stochastic perturbations method and application to a solution between (120) gypsum faces
JOURNAL OF CHEMICAL PHYSICS, 121:12511-12522, DEC 22 2004
abstract, full text, DOI:10.1063/1.1821491

Grabe, M.; Lecar, H.; Jan, Y.N.; Jan, L.Y.
A quantitative assessment of models for voltage-dependent gating of ion channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:17640-17645, DEC 21 2004
abstract, full text, DOI:10.1073/pnas.0408116101

Tang, D.M.; Li, A.Q.; Attar, P.; Dowell, E.H.
Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope
JOURNAL OF COMPUTATIONAL PHYSICS, 201:723-752, DEC 10 2004
abstract, full text, DOI:10.1016/j.jcp.2004.06.016

Scott, L.R.
Bioinformatics
PERSPECTIVES IN BIOLOGY AND MEDICINE, 47:135-139, WIN 2004
full text, DOI:10.1353/pbm.2004.0015

Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Collective diffusion model for water permeation through microscopic channels
PHYSICAL REVIEW LETTERS, 93 Art. No. 224501, NOV 26 2004
abstract, full text, TCBG publications, DOI:10.1103/PhysRevLett.93.224501

Saladino, A.C.; Tang, P.
Optimization of structures and LJ parameters of 1-chloro-1,2,2-trifluorocyclobutane and 1,2-dichlorohexafluorocyclobutane
JOURNAL OF PHYSICAL CHEMISTRY A, 108:10560-10564, NOV 25 2004
abstract, full text, DOI:10.1021/jp046662i

Mitra, A.; Sept, D.
Localization of the antimitotic peptide and depsipeptide binding site on beta-tubulin
BIOCHEMISTRY, 43:13955-13962, NOV 9 2004
abstract, full text, DOI:10.1021/bi0487387

Jensen, M.O.; Mouritsen, O.G.
Lipids do influence protein function - the hydrophobic matching hypothesis revisited
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1666:205-226, NOV 3 2004
abstract, full text, DOI:10.1016/j.bbamem.2004.06.009

Bertola, D.R.; Pereira, A.C.; de Oliveira, P.S.L.; Kim, C.A.; Krieger, J.E.
Clinical variability in a Noonan syndrome family with a new PTPN11 gene mutation
AMERICAN JOURNAL OF MEDICAL GENETICS PART A, 130A:378-383, NOV 1 2004
abstract, full text, DOI:10.1002/ajmg.a.30270

Sotomayor, M.; Schulten, K.
Molecular dynamics study of Gating in the mechanosensitive channel of small conductance MscS
BIOPHYSICAL JOURNAL, 87:3050-3065, NOV 2004
abstract, full text, TCBG publications, DOI:10.1529/biophysj.104.046045

Paliwal, A.; Asthagiri, D.; Bossev, D.P.; Paulaitis, M.E.
Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation
BIOPHYSICAL JOURNAL, 87:3479-3492, NOV 2004
abstract, full text, DOI:10.1529/biophysj.104.050526

Zhang, D.Q.; Konecny, R.; Baker, N.A.; McCammon, J.A.
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach
BIOPOLYMERS, 75:325-337, NOV 2004
abstract, full text, DOI:10.1002/bip.20120

Turjanski, A.G.; Estrin, D.A.; Rosenstein, R.E.; McCormick, J.E.; Martin, S.R.; Pastore, A.; Biekofsky, R.R.; Martorana, V.
NMR and molecular dynamics studies of the interaction of melatonin with calmodulin
PROTEIN SCIENCE, 13:2925-2938, NOV 2004
abstract, full text, DOI:10.1110/ps.04611404

Craig, D.; Gao, M.; Schulten, K.; Vogel, V.
Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force
STRUCTURE, 12:2049-2058, NOV 2004
abstract, full text, TCBG publications, DOI:10.1016/j.str.2004.09.009

Espinoza-Fonseca, L.M.
Molecular docking of four beta-amyloid(1-42) fragments on the alpha 7 nicotinic receptor: delineating the binding site of the A beta peptides
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 323:1191-1196, OCT 29 2004
abstract, full text, DOI:10.1016/j.bbrc.2004.08.218

Dima, R.I.; Thirumalai, D.
Probing the instabilities in the dynamics of helical fragments from mouse PrPc
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:15335-15340, OCT 26 2004
abstract, full text, DOI:10.1073/pnas.0404235101

Tanaka, T.; Yada, R.Y.
Redesign of catalytic center of an enzyme: aspartic to serine proteinase
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 323:947-953, OCT 22 2004
abstract, full text, DOI:10.1016/j.bbrc.2004.08.191

Saccani, J.; Castano, S.; Beaurain, F.; Laguerre, M.; Desbat, B.
Stabilization of phospholipid multilayers at the air-water interface by compression beyond the collapse: A BAM, PM-IRRAS, and molecular dynamics study
LANGMUIR, 20:9190-9197, OCT 12 2004
abstract, full text, DOI:10.1021/la0489920

Treptow, W.; Maigret, B.; Chipot, C.; Tarek, M.
Coupled motions between pore and voltage-sensor domains: A model for Shaker B, a voltage-gated potassium channel
BIOPHYSICAL JOURNAL, 87:2365-2379, OCT 2004
abstract, full text, DOI:10.1529/biophysj.104.039628

Tung, C.S.; Sanbonmatsu, K.Y.
Atomic model of the Thermus thermophilus 70S ribosome developed in silico
BIOPHYSICAL JOURNAL, 87:2714-2722, OCT 2004
abstract, full text, DOI:10.1529/biophysj.104.040162

Muller, M.; Gumbiowski, K.; Cherepanov, D.A.; Winkler, S.; Junge, W.; Engelbrecht, S.; Panke, O.
Rotary F-1-ATPase - Is the C-terminus of subunit gamma fixed or mobile?
EUROPEAN JOURNAL OF BIOCHEMISTRY, 271:3914-3922, OCT 2004
abstract, full text, DOI:10.1111/j.1432-1033.2004.04328.x

Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E.
UCSF chimera - A visualization system for exploratory research and analysis
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:1605-1612, OCT 2004
abstract, full text, DOI:10.1002/jcc.20084

Autenrieth, F.; Tajkhorshid, E.; Baudry, J.; Luthey-Schulten, Z.
Classical force field parameters for the heme prosthetic group of cytochrome c
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:1613-1622, OCT 2004
abstract, full text, DOI:10.1002/jcc20079

Kalsotra, A.; Turman, C.M.; Kikuta, Y.; Strobel, H.W.
Expression and characterization of human cytochrome P450 4F11: Putative role in the metabolism of therapeutic drugs and eicosanoids
TOXICOLOGY AND APPLIED PHARMACOLOGY, 199:295-304, SEP 15 2004
abstract, full text, DOI:10.1016/j.taap.2003.12.033

Chiarini, R.; Moran, O.; Revoltella, R.P.
Identification of an antigenic domain near the C terminus of human granulocyte-macrophage colony-stimulating factor and its spatial localization
JOURNAL OF BIOLOGICAL CHEMISTRY, 279:37908-37917, SEP 3 2004
abstract, full text, DOI:10.1074/jbc.M404663200

Matthey, T.; Cickovski, T.; Hampton, S.; Ko, A.; Ma, Q.; Nyerges, M.; Raeder, T.; Slabach, T.; Izaguirre, J.A.
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE, 30:237-265, SEP 2004
abstract, full text, DOI:10.1145/1024074.1024075

Pedersen, A.K.; Peters, G.H.; Moller, K.B.; Iversen, L.F.; Kastrup, J.S.
Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 60:1527-1534, SEP 2004
abstract, full text, DOI:10.1107/S0907444904015094

Lee, G.; Nowak, W.; Jaroniec, J.; Zhang, Q.M.; Marszalek, P.E.
Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides
BIOPHYSICAL JOURNAL, 87:1456-1465, SEP 2004
abstract, full text, DOI:10.1529/biophysj.104.042879

Aksimentiev, A.; Heng, J.B.; Timp, G.; Schulten, K.
Microscopic kinetics of DNA translocation through synthetic nanopores
BIOPHYSICAL JOURNAL, 87:2086-2097, SEP 2004
abstract, full text, TCBG publications, DOI:10.1529/biophysj.104.042960

Yeh, I.C.; Hummer, G.
Nucleic acid transport through carbon nanotube membranes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:12177-12182, AUG 17 2004
abstract, full text, DOI:10.1073/pnas.0402699101

Henin, J.; Chipot, C.
Overcoming free energy barriers using unconstrained molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 121:2904-2914, AUG 15 2004
abstract, full text, DOI:10.1063/1.1773132

Glykos, N.M.; Kokkindis, M.
Structural polymorphism of a marginally stable 4-alpha-helical bundle. Images of a trapped molten globule?
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 56:420-425, AUG 15 2004
full text, DOI:10.1002/prot.20167

Lee, O.S.; Saven, J.G.
Simulation studies of a helical m-phenylene ethynylene foldamer
JOURNAL OF PHYSICAL CHEMISTRY B, 108:11988-11994, AUG 12 2004
abstract, full text, DOI:10.1021/jp048642m

Braun, R.; Engelman, D.M.; Schulten, K.
Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices
BIOPHYSICAL JOURNAL, 87:754-763, AUG 2004
abstract, full text, TCBG publications, DOI:10.1529/biophysj.104.040279

Sutherland, J.J.; O'Brien, L.A.; Lillicrap, D.; Weaver, D.F.
Molecular modeling of the von Willebrand factor A2 domain and the effects of associated type 2A von Willebrand disease mutations
JOURNAL OF MOLECULAR MODELING, 10:259-270, AUG 2004
abstract, full text, DOI:10.1007/s00894-004-0194-9

Roux, B.; Schulten, K.
Computational studies of membrane channels
STRUCTURE, 12:1343-1351, AUG 2004
abstract, full text, TCBG publications, DOI:10.1016/j.str.2004.06.013

Espinoza-Fonseca, L.M.
Base docking model of the homomeric alpha 7 nicotinic receptor-beta-amyloid(1-42) complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 320:587-591, JUL 23 2004
abstract, full text, DOI:10.1016/j.bbrc.2004.05.207

Pogorelov, T.V.; Luthey-Schulten, Z.
Variations in the fast folding rates of the lambda-repressor: A hybrid molecular dynamics study
BIOPHYSICAL JOURNAL, 87:207-214, JUL 2004
abstract, full text, DOI:10.1529/biophysj.104.042861

O'Brien, L.A.; Sutherland, J.J.; Hegadorn, C.; Benford, K.; Racz, H.; Rapson, D.; Hough, C.; Lillicrap, D.
A novel type 2A (Group II) von Willebrand disease mutation (L1503Q) associated with loss of the highest molecular weight von Willebrand factor multimers
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 2:1135-1142, JUL 2004
abstract, full text, DOI:10.1111/j.1538-7836.2004.00732.x

Ouellet, J.; Perreault, J.P.
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate
RNA-A PUBLICATION OF THE RNA SOCIETY, 10:1059-1072, JUL 2004
abstract, full text, DOI:10.1261/rna.7230604

Pedretti, A.; Silva, M.E.; Villa, L.; Vistoli, G.
Binding site analysis of full-length alpha(1a) adrenergic receptor using homology modeling and molecular docking
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 319:493-500, JUN 25 2004
abstract, full text, DOI:10.1016/j.bbrc.2004.04.149

Larios, E.; Li, J.S.; Schulten, K.; Kihara, H.; Gruebele, M.
Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin
JOURNAL OF MOLECULAR BIOLOGY, 340:115-125, JUN 25 2004
abstract, full text, TCBG publications, DOI:10.1016/j.jmb.2004.04.048

Espinoza-Fonseca, L.M.; Trujillo-Ferrara, J.G.
Exploring the possible binding sites at the interface of triosephosphate isomerase dimer as a potential target for anti-tripanosomal drug design
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 14:3151-3154, JUN 21 2004
abstract, full text, DOI:10.1016/j.bmcl.2004.04.013

Gullingsrud, J.; Schulten, K.
Lipid bilayer pressure profiles and mechanosensitive channel gating
BIOPHYSICAL JOURNAL, 86:3496-3509, JUN 2004
abstract, full text, TCBG publications, DOI:10.1529/biophysj.103.034322

Jensen, M.O.; Mouritsen, O.G.; Peters, G.H.
Simulations of a membrane-anchored peptide: Structure, dynamics, and influence on bilayer properties
BIOPHYSICAL JOURNAL, 86:3556-3575, JUN 2004
abstract, full text, DOI:10.1529/biophysj.103.029140

Ala-Laurila, P.; Donner, K.; Koskelainen, A.
Thermal activation and photoactivation of visual pigments
BIOPHYSICAL JOURNAL, 86:3653-3662, JUN 2004
abstract, full text, DOI:10.1529/biophysj.103.035626

Kasson, P.M.; Pande, V.S.
Molecular dynamics simulation of lipid reorientation at bilayer edges
BIOPHYSICAL JOURNAL, 86:3744-3749, JUN 2004
abstract, full text, DOI:10.1529/biophysj.103.029652

Zhu, H.B.; Chun, T.K.Y.; Wang, L.Z.; Cai, W.T.; See, S.
A prototype of distributed molecular visualization on computational grids
FUTURE GENERATION COMPUTER SYSTEMS, 20:727-737, JUN 2004
abstract, full text, DOI:10.1016/j.future.2003.11.023

Deng, Y.; Glimm, J.; Davenport, J.W.; Cai, X.; Santos, E.
Performance models on QCDOC for molecular dynamics with Coulomb potentials
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 18:183-195, SUM 2004
abstract, full text, DOI:10.1177/1094342004044010

Garofoli, S.; Falconi, M.; Desideri, A.
Thermophilicity of wild type and mutant cold shock proteins by molecular dynamics simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 21:771-779, JUN 2004
abstract, full text

Sternal, K.; Czub, J.; Baginski, M.
Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies
JOURNAL OF MOLECULAR MODELING, 10:223-232, JUN 2004
abstract, full text, DOI:10.1007/s00894-004-0190-0

Brito, R.M.M.; Dubitzky, W.; Rodrigues, J.R.
Protein folding and unfolding simulations: A new challenge for data mining
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 8:153-166, SUM 2004
abstract, full text, DOI:10.1089/1536231041388311

Jensen, M.O.; Mouritsen, O.G.; Peters, G.H.
The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces
JOURNAL OF CHEMICAL PHYSICS, 120:9729-9744, MAY 22 2004
abstract, full text, DOI:10.1063/1.1697379

Boulet, P.; Covency, P.V.; Stackhouse, S.
Simulation of hydrated Li+-, Na+- and K+-montmorillonite/polymer nanocomposites using large-scale molecular dynamics
CHEMICAL PHYSICS LETTERS, 389:261-267, MAY 11 2004
abstract, full text, DOI:10.1016/j.cplett.2004.03.084

Anishkin, A.; Sukharev, S.
Water dynamics and dewetting transitions in the small mechanosensitive channel MscS
BIOPHYSICAL JOURNAL, 86:2883-2895, MAY 2004
abstract, full text, DOI:10.1016/S0006-3495(04)74340-4

Cadena, C.; Anthony, J.L.; Shah, J.K.; Morrow, T.I.; Brennecke, J.F.; Maginn, E.J.
Why is CO2 so soluble in imidazolium-based ionic liquids?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126:5300-5308, APR 28 2004
abstract, full text, DOI:10.1021/ja039615x

Nielsen, S.O.; Lopez, C.F.; Srinivas, G.; Klein, M.L.
Coarse grain models and the computer simulation of soft materials
JOURNAL OF PHYSICS-CONDENSED MATTER, 16:R481-R512, APR 21 2004
abstract, full text, DOI:10.1088/0953-8984/16/15/R03

Rousseau, R.; Kleinschmidt, V.; Schmitt, U.W.; Marx, D.
Modeling protonated water networks in bacteriorhodopsin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 6:1848-1859, APR 21 2004
abstract, full text, DOI:10.1039/b313220j

Gronwald, W.; Kalbitzer, H.R.
Automated structure determination of proteins by NMR spectroscopy
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 44:33-96, APR 16 2004
full text, DOI:10.1016/j.pnmrs.2003.12.002

Hoyrup, P.; Callisen, T.H.; Jensen, M.O.; Halperin, A.; Mouritsen, O.G.
Lipid protrusions, membrane softness, and enzymatic activity
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 6:1608-1615, APR 7 2004
abstract, full text, DOI:10.1039/b314146b

Linke, S.; Stojkoski, C.; Kewley, R.J.; Booker, G.W.; Whitelaw, M.L.; Peet, D.J.
Substrate requirements of the oxygen-sensing asparaginyl hydroxylase factor-inhibiting hypoxia-inducible factor
JOURNAL OF BIOLOGICAL CHEMISTRY, 279:14391-14397, APR 2 2004
abstract, full text, DOI:10.1074/jbc.M313614200

Huber, T.; Botelho, A.V.; Beyer, K.; Brown, M.F.
Membrane model for the G-protein-coupled receptor rhodopsin: Hydrophobic interface and dynamical structure
BIOPHYSICAL JOURNAL, 86:2078-2100, APR 2004
abstract, full text

Budi, A.; Legge, S.; Treutlein, H.; Yarovsky, I.
Effect of external stresses on protein conformation: a computer modelling study
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 33:121-129, APR 2004
abstract, full text, DOI:10.1007/s00249-003-0359-y

Park, S.; Schulten, K.
Calculating potentials of mean force from steered molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 120:5946-5961, APR 1 2004
abstract, full text, TCBG publications, DOI:10.1063/1.1651473

Dromey, J.A.; Weenink, S.M.; Peters, G.H.; Endl, J.; Tighe, P.J.; Todd, I.; Christie, M.R.
Mapping of epitopes for autoantibodies to the type 1 diabetes autoantigen IA-2 by peptide phage display and molecular modeling: Overlap of antibody and T cell determinants
JOURNAL OF IMMUNOLOGY, 172:4084-4090, APR 1 2004
abstract, full text

Gursoy, A.; Kale, L.V.
Performance and modularity benefits of message-driven execution
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 64:461-480, APR 2004
abstract, full text, DOI:10.1016/j.jpdc.2004.03.006

Morrissette, N.S.; Mitra, A.; Sept, D.; Sibley, L.D.
Dinitroanilines bind alpha-tubulin to disrupt microtubules
MOLECULAR BIOLOGY OF THE CELL, 15:1960-1968, APR 2004
abstract, full text, DOI:10.1091/mbc.E03-07-0530

Morrow, T.I.; Maginn, E.J.
Density, local composition and diffusivity of aqueous choline chloride solutions: a molecular dynamics study
FLUID PHASE EQUILIBRIA, 217:97-104, MAR 10 2004
abstract, full text, DOI:10.1016/j.fluid.2003.08.020

Aksimentiev, A.; Balabin, I.A.; Fillingame, R.H.; Schulten, K.
Insights into the molecular mechanism of rotation in the F-o sector of ATP synthase
BIOPHYSICAL JOURNAL, 86:1332-1344, MAR 2004
abstract, full text, TCBG publications, DOI:10.1016/S0006-3495(04)74205-8

Tan, M.L.; Balabin, I.; Onuchic, J.N.
Dynamics of electron transfer pathways in cytochrome c oxidase
BIOPHYSICAL JOURNAL, 86:1813-1819, MAR 2004
abstract, full text, DOI:10.1016/S0006-3495(04)74248-4

Zhang, L.L.; Ruan, Q.; Zhou, L.X.
Nonlinear indices analyzing method for molecular dynamics of protein dynamical transition
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 15:351-361, MAR 2004
abstract, full text, DOI:10.1142/S0129183104005759

Ikeguchi, M.
Partial rigid-body dynamics in NPT, NPAT and NP gamma T ensembles for proteins and membranes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:529-541, MAR 2004
abstract, full text, DOI:10.1002/jcc.10402

Pedretti, A.; Villa, L.; Vistoli, G.
VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 18:167-173, MAR 2004
abstract, full text, DOI:10.1023/B:JCAM.0000035186.90683.f2

Mustata, G.; Briggs, J.M.
Cluster analysis of water molecules in alanine racemase and their putative structural role
PROTEIN ENGINEERING DESIGN & SELECTION, 17:223-234, MAR 2004
abstract, full text, DOI:10.1093/protein/gzh033

Liu, Z.W.; Xu, Y.; Saladino, A.C.; Wymore, T.; Tang, P.
Parametrization of 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) and hexafluoroethane for nonbonded interactions
JOURNAL OF PHYSICAL CHEMISTRY A, 108:781-786, FEB 5 2004
abstract, full text, DOI:10.1021/jp0368482

Yeh, I.C.; Hummer, G.
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 86:681-689, FEB 2004
abstract, full text

Cohen, J.; Schulten, K.
Mechanism of anionic conduction across ClC
BIOPHYSICAL JOURNAL, 86:836-845, FEB 2004
abstract, full text, TCBG publications

Tindbaek, N.; Svendsen, A.; Oestergaard, P.R.; Draborg, H.
Engineering a substrate-specific cold-adapted subtilisin
PROTEIN ENGINEERING DESIGN & SELECTION, 17:149-156, FEB 2004
abstract, full text, DOI:10.1093/protein/gzh019

Bishop, T.C.; Cortez, R.; Zhmudsky, O.O.
Investigation of bend and shear waves in a geometrically exact elastic rod model
JOURNAL OF COMPUTATIONAL PHYSICS, 193:642-665, JAN 20 2004
abstract, full text, DOI:10.1016/j.jcp.2003.08.028

Buchete, N.V.; Straub, J.E.; Thirumalai, D.
Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases
POLYMER, 45:597-608, JAN 15 2004
abstract, full text, DOI:10.1016/j.polymer.2003.10.093

Mursinna, R.S.; Lee, K.W.; Briggs, J.M.; Martinis, S.A.
Molecular dissection of a critical specificity determinant within the amino acid editing domain of leucyl-tRNA synthetase
BIOCHEMISTRY, 43:155-165, JAN 13 2004
abstract, full text, DOI:10.1021/bi034919h

Wang, P.; Su, Z.C.; Guo, J.T.; Xu, Y.
Structural analysis of FGFR1 kinase activation through molecular dynamics simulation
2004 IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE, PROCEEDINGS, 700-701, 2004
abstract, full text

Nomoto, A.; Kaneko, W.; Terada, T.; Nakamura, S.; Shimizu, K.
Programming environment based on distributed shared arrays for high-performance scientific computing
2004 INTERNATIONAL SYMPOSIUM ON APPLICATIONS AND THE INTERNET WORKSHOPS, PROCEEDINGS, 630-636, 2004
abstract, full text, DOI:10.1109/SAINTW.2004.1268699

Gao, H.J.; Kong, Y.
Simulation of DNA-nanotube interactions
ANNUAL REVIEW OF MATERIALS RESEARCH, 34:123-150, 2004
abstract, full text, DOI:10.1146/annurev.matsci.34.040203.120402

Madina, D.; Ikegami, T.
Cellular dynamics in a 3D molecular dynamics system with chemistry
Artificial Life IX, 461-465, 2004
abstract, full text

Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Theory and simulation of water permeation in aquaporin-1
BIOPHYSICAL JOURNAL, 86:50-57, JAN 2004
abstract, full text, TCBG publications, DOI:10.1016/S0006-3495(04)74082-5

Lu, S.Q.; Long, M.
Forced extension of P-selectin construct using steered molecular dynamics
CHINESE SCIENCE BULLETIN, 49:10-17, JAN 2004
abstract, full text, DOI:10.1360/03ww0164

Katti, D.R.; Katti, K.S.; Ghosh, P.; Schmidt, S.
Exploring mineral biopolymer interactions to model mechanical response of interfaces in bio-nanocomposite, nacre
Computational Mechanics, Proceedings, 807-812, 2004
abstract, full text

Villa, E.; Balaeff, A.; Mahadevan, L.; Schulten, K.
Multiscale method for simulating protein-DNA complexes
MULTISCALE MODELING & SIMULATION, 2:527-553, 2004
abstract, full text, TCBG publications, DOI:10.1137/040604789

Wypychowski, J.; Pytlinski, J.; Skorwider, L.; Nazaruk, M.; Benedyczak, K.; Wronski, M.; Bala, P.
Life sciences grid in EUROGRID and GRIP projects
NEW GENERATION COMPUTING, 22:147-156, 2004
abstract, full text

Watanabe, T.; Kawata, M.; Nagashima, U.
Molecular simulation of DNA microarrays - an application of 2D particle mesh Ewald algorithm
NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS, 88-90, 2004
abstract, full text

Cozmuta, I.; O'Keeffe, J.T.; Stolc, V.
Hybrid MD-PNP simulations of the alpha-hemolysin open channel ionic current
NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS, 143-146, 2004
abstract, full text

Roman, C.; Ciontu, F.; Courtois, B.
A carbon nanotube-based sensor for measuring forces at the cellular scale
NSTI NANOTECH 2004, VOL 3, TECHNICAL PROCEEDINGS, 95-98, 2004
abstract, full text

Yu, J.; Ha, T.J.; Schulten, K.
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
NUCLEIC ACIDS RESEARCH, 32:6683-6695, 2004
abstract, full text, TCBG publications, DOI:10.1093/nar/gkh1006

Schleif, R.
Modeling and studying proteins with molecular dynamics
NUMERICAL COMPUTER METHODS, PT D, 383:28-47, 2004
full text

Tai, K.S.; Murdock, S.; Wu, B.; Ng, M.H.; Johnston, S.; Fangohr, H.; Cox, S.J.; Jeffreys, P.; Essex, J.W.; Sansom, M.S.P.
BioSimGrid: towards a worldwide repository for biomolecular simulations
ORGANIC & BIOMOLECULAR CHEMISTRY, 2:3219-3221, 2004
abstract, full text, DOI:10.1039/b411352g

Cao, X.L.; Mo, Z.Y.
A new scalable parallel method for molecular dynamics based on cell-block data structure
PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS, PROCEEDINGS, 3358:757-764, 2004
abstract, full text

Collins, Lee A.; Mazevet, Stephane; Kress, Joel D.; Schneider, Barry I.; Feder, David L.
Time-dependent simulations of large-scale quantum dynamics
PHYSICA SCRIPTA, T110:408-412, 2004
abstract, full text, DOI:10.1238/Physica.Topical.110a00408

Yang, W.Y.; Larios, E.; Gruebele, M.
On the extended beta-conformation propensity of polypeptides at high temperature
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 125:16220-16227, DEC 31 2003
abstract, full text, DOI:10.1021/ja0360081

Hoseki, J.; Okamoto, A.; Takada, N.; Suenaga, A.; Futatsugi, N.; Konagaya, A.; Taiji, M.; Yano, T.; Kuramitsu, S.; Kagamiyama, H.
Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution
BIOCHEMISTRY, 42:14469-14475, DEC 16 2003
abstract, full text, DOI:10.1021/bi034776z

Gao, M.; Craig, D.; Lequin, O.; Campbell, I.D.; Vogel, V.; Schulten, K.
Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:14784-14789, DEC 9 2003
abstract, full text, TCBG publications, DOI:10.1073/pnas.2334390100

Jenwitheesuk, E.; Samudrala, R.
Identifying inhibitors of the SARS coronavirus proteinase
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 13:3989-3992, NOV 17 2003
abstract, full text, DOI:10.1016/j.bmcl.2003.08.066

Jensen, M.O.; Tajkhorshid, E.; Schulten, K.
Electrostatic tuning of permeation and selectivity in aquaporin water channels
BIOPHYSICAL JOURNAL, 85:2884-2899, NOV 1 2003
abstract, full text, TCBG publications

Lu, D.Y.; Grayson, P.; Schulten, K.
Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF
BIOPHYSICAL JOURNAL, 85:2977-2987, NOV 1 2003
abstract, full text, TCBG publications

Bolhuis, P.G.
Transition-path sampling of beta-hairpin folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:12129-12134, OCT 14 2003
abstract, full text, DOI:10.1073/pnas.1534924100

Gullingsrud, J.; Schulten, K.
Gating of MscL studied by steered molecular dynamics
BIOPHYSICAL JOURNAL, 85:2087-2099, OCT 2003
abstract, full text, TCBG publications, DOI:10.1016/S0006-3495(03)74637-2

Dittrich, M.; Hayashi, S.; Schulten, K.
On the mechanism of ATP hydrolysis in F(1)-ATPase
BIOPHYSICAL JOURNAL, 85:2253-2266, OCT 2003
abstract, full text, TCBG publications, DOI:10.1016/S0006-3495(03)74650-5

Tarek, M.; Maigret, B.; Chipot, C.
Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers
BIOPHYSICAL JOURNAL, 85:2287-2298, OCT 2003
abstract, full text, DOI:10.1016/S0006-3495(03)74653-0

Mustata, G.I.; Soares, T.A.; Briggs, J.M.
Molecular dynamics studies of alanine racemase: A structural model for drug design
BIOPOLYMERS, 70:186-200, OCT 2003
abstract, full text, DOI:10.1002/bip.10425

Frank, M.; Gutbrod, P.; Hassayoun, C.; von der Lieth, C.W.
Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts
JOURNAL OF MOLECULAR MODELING, 9:308-315, OCT 2003
abstract, full text, DOI:10.1007/s00894-003-0144-y

Likic, V.A.; Strehler, E.E.; Gooley, P.R.
Dynamics of Ca2+-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations
PROTEIN SCIENCE, 12:2215-2229, OCT 2003
abstract, full text, DOI:10.1110/ps.0377803

Niccolai, N.; Spiga, O.; Bernini, A.; Scarselli, M.; Ciutti, A.; Fiaschi, I.; Chiellini, S.; Molinari, H.; Temussi, P.A.
NMR studies of protein hydration and TEMPOL accessibility
JOURNAL OF MOLECULAR BIOLOGY, 332:437-447, SEP 12 2003
abstract, full text, DOI:10.1016/S0022-2836(03)00852-0

Lamb, H.K.; Leslie, K.; Dodds, A.L.; Nutley, M.; Cooper, A.; Johnson, C.; Thompson, P.; Stammers, D.K.; Hawkins, A.R.
The negative transcriptional regulator NmrA discriminates between oxidized and reduced dinucleotides
JOURNAL OF BIOLOGICAL CHEMISTRY, 278:32107-32114, AUG 22 2003
abstract, full text, DOI:10.1074/jbc.M304104200

Park, S.; Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K.
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 119:3559-3566, AUG 8 2003
abstract, full text, TCBG publications, DOI:10.1063/1.1590311

Asthagiri, D.; Pratt, L.R.; Ashbaugh, H.S.
Absolute hydration free energies of ions, ion-water clusters, and quasichemical theory
JOURNAL OF CHEMICAL PHYSICS, 119:2702-2708, AUG 1 2003
abstract, full text, DOI:10.1063/1.1587122

O'Brien, L.A.; James, P.D.; Othman, M.; Berber, E.; Cameron, C.; Notley, C.R.P.; Hegadorn, C.A.; Sutherland, J.J.; Hough, C.; Rivard, G.E.; O'Shaunessey, D.; Lillicarp, D.
Founder von Willebrand factor haplotype associated with type 1 von Willebrand disease
BLOOD, 102:549-557, JUL 15 2003
abstract, full text, DOI:10.1182/blood-2002-12-3693

Bird, L.E.; Ren, J.; Wright, A.; Leslie, K.D.; Degreve, B.; Balzarini, J.; Stammers, D.K.
Crystal structure of varicella zoster virus thymidine kinase
JOURNAL OF BIOLOGICAL CHEMISTRY, 278:24680-24687, JUL 4 2003
abstract, full text, DOI:10.1074/jbc.M302025200

Grayson, P.; Tajkhorshid, E.; Schulten, K.
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics
BIOPHYSICAL JOURNAL, 85:36-48, JUL 2003
abstract, full text, TCBG publications

Zhu, F.Q.; Schulten, K.
Water and proton conduction through carbon nanotubes as models for biological channels
BIOPHYSICAL JOURNAL, 85:236-244, JUL 2003
abstract, full text, TCBG publications

Mozziconacci, J.; Victor, J.M.
Nucleosome gaping supports a functional structure for the 30nm chromatin fiber
JOURNAL OF STRUCTURAL BIOLOGY, 143:72-76, JUL 2003
abstract, full text, DOI:10.1016/S1047-8477(03)00102-3

Amaro, R.; Tajkhorshid, E.; Luthey-Schulten, Z.
Developing an energy landscape for the novel function of a (beta/alpha)(8) barrel: Ammonia conduction through HisF
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:7599-7604, JUN 24 2003
abstract, full text, DOI:10.1073/pnas.1331150100

Phillips, S.C.; Gledhill, R.J.; Essex, J.W.; Edge, C.M.
Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 107:4869-4876, JUN 19 2003
abstract, full text, DOI:10.1021/jp0261758

Costantino, G.; Macchiarulo, A.; Entrena-Guadix, A.; Camaioni, E.; Pellicciari, R.
Binding mode of 6ECDCA, a potent bile acid agonist of the Farnesoid X Receptor (FXR)
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 13:1865-1868, JUN 2 2003
abstract, full text, DOI:10.1016/S0960-894X(03)00281-6

Abdali, S.; Jensen, M.O.; Bohr, H.
Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations
JOURNAL OF PHYSICS-CONDENSED MATTER, 15:S1853-S1860, MAY 14 2003
abstract, full text, DOI:10.1088/0953-8984/15/18/316

Moran, O.; Traverso, S.; Elia, L.; Pusch, M.
Molecular Modeling of p-chlorophenoxyacetic acid binding to the CLC-0 channels
BIOCHEMISTRY, 42:5176-5185, MAY 13 2003
abstract, full text, DOI:10.1021/bi027368o

Lesyng, B.; Bala, P.; Erwin, D.
EUROGRID - European computational grid testbed
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 63:590-596, MAY 2003
abstract, full text, DOI:10.1016/S0743-7315(03)00005-4

Bayas, M.V.; Schulten, K.; Leckband, D.
Forced detachment of the CD2-CD58 complex
BIOPHYSICAL JOURNAL, 84:2223-2233, APR 2003
abstract, full text, TCBG publications, DOI:10.1016/S0006-3495(03)75028-0

Phillips, S.C.; Swain, M.T.; Wiley, A.P.; Essex, J.W.; Edge, C.M.
Reversible digitally filtered molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 107:2098-2110, MAR 6 2003
abstract, full text, DOI:10.1021/jp026456f

Anishkin, A.; Gendel, V.; Sharifi, N.A.; Chiang, C.S.; Shirinian, L.; Guy, H.R.; Sukharev, S.
On the conformation of the COOH-terminal domain of the large mechanosensitive channel MscL
JOURNAL OF GENERAL PHYSIOLOGY, 121:227-244, MAR 2003
abstract, full text, DOI:10.1085/jgp.20028768

Jensen, T.R.; Jensen, M.O.; Reitzel, N.; Balashev, K.; Peters, G.H.; Kjaer, K.; Bjornholm, T.
Water in contact with extended hydrophobic surfaces: Direct evidence of weak dewetting
PHYSICAL REVIEW LETTERS, 90 Art. No. 086101, FEB 28 2003
abstract, full text, DOI:10.1103/PhysRevLett.90.086101

Barash, D.; Yang, L.J.; Qian, X.L.; Schlick, T.
Inherent speedup limitations in multiple time step/Particle Mesh Ewald algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 24:77-88, JAN 15 2003
abstract, full text, DOI:10.1002/jcc.10196

Wong, T.C.
Membrane structure of the human immunodeficiency virus gp41 fusion peptide by molecular dynamics simulation II. The glycine mutants
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1609:45-54, JAN 10 2003
abstract, full text, DOI:10.1016/S0005-2736(02)00652-1

Cozmuta, I.; O'Keeffe, J.; Stolc, V.
Towards an MD simulation of ion currents in the alpha hemolysin channel
2003 THIRD IEEE CONFERENCE ON NANOTECHNOLOGY, VOLS ONE AND TWO, PROCEEDINGS, 187-190, 2003
abstract, full text

Nielsen, B.G.; Jensen, M.O.; Bohr, H.G.
The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to mu and delta opiate receptors
BIOPOLYMERS, 71:577-592, 2003
abstract, full text, DOI:10.1002/bip.10539

Pytlinski, J.; Skorwider, L.; Benedyczak, K.; Wronski, M.; Bala, P.; Huber, V.
Uniform access to the distributed resources for the computational chemistry using UNICORE
COMPUTATIONAL SCIENCE - ICCS 2003, PT II, PROCEEDINGS, 2658:307-315, 2003
abstract, full text

DeSouza, J.; Kale, L.V.
Jade: A parallel message-driven Java
COMPUTATIONAL SCIENCE - ICCS 2003, PT III, PROCEEDINGS, 2659:760-769, 2003
abstract, full text

Kale, L.V.; Kumar, S.; Zheng, G.B.; Lee, C.W.
Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study
COMPUTATIONAL SCIENCE - ICCS 2003, PT IV, PROCEEDINGS, 2660:23-32, 2003
abstract, full text

Matthey, T.; Ko, A.; Izaguirre, J.A.
PROTOMOL: A molecular dynamics research framework for algorithmic development
COMPUTATIONAL SICENCE - ICCS 2003, PT III, PROCEEDINGS, 2659:50-59, 2003
abstract, full text

Kaneko, W.; Nomoto, A.; Watanabe, Y.; Nakamura, S.; Shimizu, K.
Design and implementation of a parallel programming environment based on distributed shared arrays
HIGH PERFORMANCE COMPUTING, 2858:402-411, 2003
abstract, full text

Ashworth, M.; Bush, I.J.; Guest, M.F.; Plummer, M.; Sunderland, A.G.; Booth, S.; Henty, D.S.; Smith, L.; Stratford, K.
HPCx: A new resource for UK computational science
HIGH PERFORMANCE COMPUTING SYSTEMS AND APPLICATIONS, 141-152, 2003
abstract, full text

Teodoro, M.L.; Phillips, G.N.; Kavraki, L.E.
Understanding protein flexibility through dimensionality reduction
JOURNAL OF COMPUTATIONAL BIOLOGY, 10:617-634, 2003
abstract, full text, DOI:10.1089/10665270360688228

Bhandarkar, M.; Kale, L.V.
An interface model for parallel components
LANGUAGES AND COMPILERS FOR PARALLEL COMPUTING, 2624:209-222, 2003
abstract, full text, DOI:10.1007/3-540-35767-X_14

Ma, Q.; Izaguirre, J.A.
Targeted mollified impulse: A multiscale stochastic integrator for long molecular dynamics simulations
MULTISCALE MODELING & SIMULATION, 2:1-21, 2003
abstract, full text, DOI:10.1137/S1540345903423567

Ito, M.; Nishikawa, T.; Nagashima, U.
Replica exchange molecular dynamics toolkit for drug-receptor docking
NANOTECH 2003, VOL 1, 36-39, 2003
abstract, full text

Beaurain, F.; Laguerre, M.
MD studies of the DIS/DIS kissing complex solution and x-ray structures
OLIGONUCLEOTIDES, 13:501-514, 2003
abstract, full text, DOI:10.1089/154545703322860816

Tajkhorshid, E.; Aksimentiev, A.; Balabin, I.; Gao, M.; Isralewitz, B.; Phillips, J.C.; Zhu, F.Q.; Schulten, K.
Large scale simulation of protein mechanics and function
PROTEIN SIMULATIONS, 66:195-+, 2003
full text, TCBG publications

Ma, Q.; Izaguirre, J.A.; Skeel, R.D.
Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 24:1951-1973, 2003
abstract, full text, DOI:10.1137/S1064827501399833

Skeel, R.D.; Izaguirre, J.A.
An impulse integrator for Langevin dynamics
MOLECULAR PHYSICS, 100:3885-3891, DEC 20 2002
abstract, full text, DOI:10.1080/0020897021000018321

Morrow, T.I.; Maginn, E.J.
Molecular dynamics study of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate
JOURNAL OF PHYSICAL CHEMISTRY B, 106:12807-12813, DEC 12 2002
abstract, full text, DOI:10.1021/jp0267003

Tang, P.; Xu, Y.
Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: The implication of molecular mechanisms of general anesthesia
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:16035-16040, DEC 10 2002
abstract, full text, DOI:10.1073/pnas.252522299

Saam, J.; Tajkhorshid, E.; Hayashi, S.; Schulten, K.
Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin
BIOPHYSICAL JOURNAL, 83:3097-3112, DEC 2002
abstract, full text, TCBG publications

Gao, M.; Wilmanns, M.; Schulten, K.
Steered molecular dynamics studies of titin I1 domain unfolding
BIOPHYSICAL JOURNAL, 83:3435-3445, DEC 2002
abstract, full text, TCBG publications

Zhang, L.L.; Zhang, J.H.; Zhou, L.X.
Dynamical transition of myoglobin and Cu/Zn superoxide dismutase revealed by molecular dynamics simulation
CHINESE PHYSICS LETTERS, 19:1788-1791, DEC 2002
abstract, full text

Mustata, G.I.; Briggs, J.M.
A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 16:935-953, DEC 2002
abstract, full text, DOI:10.1023/A:1023875514454

Gao, M.; Craig, D.; Vogel, V.; Schulten, K.
Identifying unfolding intermediates of FN-III10 by steered molecular dynamics
JOURNAL OF MOLECULAR BIOLOGY, 323:939-950, NOV 8 2002
abstract, full text, TCBG publications, DOI:10.1016/S0022-2836(02)01001-X

Lupo, J.A.; Wang, Z.Q.; McKenney, A.M.; Pachter, R.; Mattson, W.
A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and application
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 21:89-99, OCT 2002
abstract, full text, DOI:10.1016/S1093-3263(02)00125-0

Rothbard, J.B.; Kreider, E.; Vandeusen, C.L.; Wright, L.; Wylie, B.L.; Wender, P.A.
Arginine-rich molecular transporters for drug delivery: Role of backbone spacing in cellular uptake
JOURNAL OF MEDICINAL CHEMISTRY, 45:3612-3618, AUG 15 2002
abstract, full text, DOI:10.1021/jm0105676

Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Pressure-induced water transport in membrane channels studied by molecular dynamics
BIOPHYSICAL JOURNAL, 83:154-160, JUL 2002
abstract, full text, TCBG publications

Thomas, W.E.; Trintchina, E.; Forero, M.; Vogel, V.; Sokurenko, E.V.
Bacterial adhesion to target cells enhanced by shear force
CELL, 109:913-923, JUN 28 2002
abstract, full text, DOI:10.1016/S0092-8674(02)00796-1

Yeh, I.C.; Hummer, G.
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 124:6563-6568, JUN 12 2002
abstract, full text, DOI:10.1021/ja025789n

Jensen, M.O.; Park, S.; Tajkhorshid, E.; Schulten, K.
Energetics of glycerol conduction through aquaglyceroporin GlpF
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:6731-6736, MAY 14 2002
abstract, full text, TCBG publications, DOI:10.1073/pnas.102649299

Skeel, R.D.; Tezcan, I.; Hardy, D.J.
Multiple grid methods for classical molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 23:673-684, APR 30 2002
abstract, full text, DOI:10.1002/jcc.10072

Tajkhorshid, E.; Nollert, P.; Jensen, M.O.; Miercke, L.J.W.; O'Connell, J.; Stroud, R.M.; Schulten, K.
Control of the selectivity of the aquaporin water channel family by global orientational tuning
SCIENCE, 296:525-530, APR 19 2002
abstract, full text, TCBG publications, DOI:10.1126/science.1067778

Lakshminarasimhulu, P.; Madura, J.D.
A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape
COMPUTER PHYSICS COMMUNICATIONS, 144:141-153, APR 1 2002
abstract, full text, DOI:10.1016/S0010-4655(02)00157-1

Kosztin, I.; Bruinsma, R.; O'Lague, P.; Schulten, K.
Mechanical force generation by G proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:3575-3580, MAR 19 2002
abstract, full text, TCBG publications, DOI:10.1073/pnas.052209199

Krammer, A.; Craig, D.; Thomas, W.E.; Schulten, K.; Vogel, V.
A structural model for force regulated integrin binding to fibronectin's RGD-synergy site
MATRIX BIOLOGY, 21:139-147, MAR 2002
abstract, full text, TCBG publications, DOI:10.1016/S0945-053X(01)00197-4

Damjanovic, A.; Kosztin, I.; Kleinekathofer, U.; Schulten, K.
Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study
PHYSICAL REVIEW E, 65 Art. No. 031919, MAR 2002
abstract, full text, TCBG publications, DOI:10.1103/PhysRevE.65.031919

Mazevet, S.; Collins, L.A.; Kress, J.D.
Evolution of ultracold neutral plasmas
PHYSICAL REVIEW LETTERS, 88 Art. No. 055001, FEB 4 2002
abstract, full text, DOI:10.1103/PhysRevLett.88.055001

Huber, T.; Rajamoorthi, K.; Kurze, V.F.; Beyer, K.; Brown, M.F.
Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by H-2 NMR and molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 124:298-309, JAN 16 2002
abstract, full text, DOI:10.1021/ja011383j

Mann, G.; Yun, R.H.; Nyland, L.; Prins, J.; Board, J.; Hermans, J.
The sigma MD program and a generic interface applicable to multi-functional programs with complex, hierarchical command structure
COMPUTATIONAL METHODS FOR MACROMOLECULES: CHALLENGES AND APPLICATIONS, 24:129-145, 2002
abstract, full text

Izaguirre, J.A.; Qun, M.; Matthey, T.; Willcock, J.; Slabach, T.; Moore, B.; Viamontes, G.
Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
COMPUTATIONAL METHODS FOR MACROMOLECULES: CHALLENGES AND APPLICATIONS, 24:146-174, 2002
abstract, full text

Bokhari, S.H.; Glaser, M.A.; Jordan, H.F.
Parallelizing a DNA simulation code for the Cray MTA-2
CSB2002: IEEE COMPUTER SOCIETY BIOINFORMATICS CONFERENCE, 291-302, 2002
abstract, full text

Braun, R.; Sarikaya, M.; Schulten, K.
Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics
JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION, 13:747-757, 2002
abstract, full text, TCBG publications, DOI:10.1163/156856202760197384

Gao, M.; Lu, H.; Schulten, K.
Unfolding of titin domains studied by molecular dynamics simulations
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, 23:513-521, 2002
abstract, full text, TCBG publications, DOI:10.1023/A:1023466608163

Skeel, R.D.; Hardy, D.J.
Practical construction of modified Hamiltonians
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 23:1172-1188, DEC 18 2001
abstract, full text, DOI:10.1137/S106482750138318X

Gumbiowski, K.; Cherepanov, D.; Muller, M.; Panke, O.; Promto, P.; Winkler, S.; Junge, W.; Engelbrecht, S.
F-ATPase: Forced full rotation of the rotor despite covalent cross-link with the stator
JOURNAL OF BIOLOGICAL CHEMISTRY, 276:42287-42292, NOV 9 2001
abstract, full text, DOI:10.1074/jbc.M106884200

Jensen, M.O.; Tajkhorshid, E.; Schulten, K.
The mechanism of glycerol conduction in aquaglyceroporins
STRUCTURE, 9:1083-1093, NOV 2001
abstract, full text, TCBG publications, DOI:10.1016/S0969-2126(01)00668-2

Dixit, S.B.; Chipot, C.
Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited
JOURNAL OF PHYSICAL CHEMISTRY A, 105:9795-9799, OCT 25 2001
abstract, full text, DOI:10.1021/jp011878v

Gao, M.; Lu, H.; Schulten, K.
Simulated refolding of stretched titin immunoglobulin domains
BIOPHYSICAL JOURNAL, 81:2268-2277, OCT 2001
abstract, full text, TCBG publications

Koumanov, A.; Karshikoff, A.; Friis, E.P.; Borchert, T.V.
Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 105:9339-9344, SEP 27 2001
abstract, full text, DOI:10.1021/jp010949n

Zhu, F.Q.; Tajkhorshid, E.; Schulten, K.
Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer
FEBS LETTERS, 504:212-218, AUG 31 2001
abstract, full text, TCBG publications, DOI:10.1016/S0014-5793(01)02749-1

Cherepanov, D.A.; Mulkidjanian, A.Y.
Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1505:179-184, JUN 1 2001
abstract, full text, DOI:10.1016/S0005-2728(01)00162-1

Gullingsrud, J.; Kosztin, D.; Schulten, K.
Structural determinants of MscL gating studied by molecular dynamics simulations
BIOPHYSICAL JOURNAL, 80:2074-2081, MAY 2001
abstract, full text, TCBG publications

Baudry, J.; Tajkhorshid, E.; Molnar, F.; Phillips, J.; Schulten, K.
Molecular dynamics study of bacteriorhodopsin and the purple membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 105:905-918, FEB 8 2001
abstract, full text, TCBG publications, DOI:10.1021/jp000898e

Izaguirre, J.A.; Catarello, D.P.; Wozniak, J.M.; Skeel, R.D.
Langevin stabilization of molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 114:2090-2098, FEB 1 2001
abstract, full text, DOI:10.1063/1.1332996

Elmer, S.; Pande, V.S.
A new twist on the helix-coil transition: A non-biological helix with protein-like intermediates and traps
JOURNAL OF PHYSICAL CHEMISTRY B, 105:482-485, JAN 18 2001
abstract, full text, DOI:10.1021/jp0019761

Wang, Z.Q.; Lupo, J.A.; Patnaik, S.; Pachter, R.
Large scale molecular dynamics simulations of a 4-n-pentyl-4 '-cyanobiphenyl (5CB) liquid crystalline model in the bulk and as a droplet
COMPUTATIONAL AND THEORETICAL POLYMER SCIENCE, 11:375-387, 2001
abstract, full text, DOI:10.1016/S1089-3156(01)00017-4

Bhandarkar, M.; Kale, L.V.; de Sturler, E.; Hoeflinger, J.
Adaptive load balancing for MPI programs
COMPUTATIONAL SCIENCE -- ICCS 200, PROCEEDINGS PT 2, 2074:108-117, 2001
abstract, full text

Bhandarkar, M.A.; Kale, L.V.
A parallel framework for explicit FEM
HIGH PERFORMANCE COMPUTING - HIPC 2000, PROCEEDINGS, 1970:385-394, 2001
abstract, full text

Straatsma, T.P.; McCammon, J.A.
Load balancing of molecular dynamics simulation with NWChem
IBM SYSTEMS JOURNAL, 40:328-341, 2001
abstract, full text

Isralewitz, B.; Baudry, J.; Gullingsrud, J.; Kosztin, D.; Schulten, K.
Steered molecular dynamics investigations of protein function
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 19:13-25, 2001
abstract, full text, TCBG publications, DOI:10.1016/S1093-3263(00)00133-9

Izaguirre, J.A.
Langevin stabilization of multiscale mollified molecular dynamics
MULTISCALE COMPUTATIONAL METHODS IN CHEMISTRY AND PHYSICS, 177:34-47, 2001
abstract, full text

Medeiros, P.D.; Cunha, J.C.
Using groups to support the interconnection of parallel applications
NINTH EUROMICRO WORKSHOP ON PARALLEL AND DISTRIBUTED PROCESSING, PROCEEDINGS, 89-96, 2001
abstract, full text

Xu, Dong; Xu, Ying; Uberbacher, Edward C.
Computational Tools For Protein Modeling
CURRENT PROTEIN & PEPTIDE SCIENCE, 1:1-21, JUL 2000
abstract, full text, DOI:10.2174/1389203003381469

Heffelfinger, G.S.
Parallel atomistic simulations
COMPUTER PHYSICS COMMUNICATIONS, 128:219-237, JUN 2000
abstract, full text, DOI:10.1016/S0010-4655(00)00050-3

Heath, M.T.; Dick, W.A.
Virtual prototyping of solid propellant rockets
COMPUTING IN SCIENCE & ENGINEERING, 2:21-32, MAR-APR 2000
abstract, full text, DOI:10.1109/5992.825746

Bryant, Z.; Pande, V.S.; Rokhsar, D.S.
Mechanical unfolding of a beta-hairpin using molecular dynamics
BIOPHYSICAL JOURNAL, 78:584-589, FEB 2000
abstract, full text

Brunner, R.K.; Kale, L.V.
Handling application-induced load imbalance using parallel objects
PARALLEL AND DISTRIBUTED COMPUTING FOR SYMBOLIC AND IRREGULAR APPLICATIONS, 167-181, 2000
abstract, full text

Schlick, T.; Skeel, R.D.; Brunger, A.T.; Kale, L.V.; Board, J.A.; Hermans, J.; Schulten, K.
Algorithmic challenges in computational molecular biophysics
JOURNAL OF COMPUTATIONAL PHYSICS, 151:9-48, MAY 1 1999
abstract, full text, TCBG publications, DOI:10.1006/jcph.1998.6182