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, 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

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, 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.
conference

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.
Computational 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

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

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. Kalé.
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. Kalé.
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 Kalé, 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 Kalé, 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 Kalé, 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. Kalé, 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 Kalé, 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 Kalé, 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 Kalé, 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.

4847 citations found April 28, 2014.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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. UNSP 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

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

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

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

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

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

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

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

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

Ban, Ehsan; Picu, Catalin R.
Strength of DNA Sticky End Links
BIOMACROMOLECULES, 15:143-149, JAN 2014
abstract, full text, DOI:10.1021/bm401425k

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

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

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

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

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

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

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

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

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

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

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/jp40882231

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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/bi30009517

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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/ct3004000x

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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