Discrete molecular dynamics
Overview
Elizabeth A. Proctor, Feng Ding, Nikolay V. Dokholyan
Published Online: Jan 21 2011
DOI:10.1002/wcms.4
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Molecular and Statistical Mechanics
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Classical molecular dynamics on graphics processing unit architectures
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Hybrid discrete‐continuum solvation methods
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Modeling of ribonucleic acid–ligand interactions
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Christin Rakers, Marcel Bermudez, Bettina G. Keller, Jérémie Mortier, Gerhard Wolber
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GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
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Polarizable force fields for molecular dynamics simulations of biomolecules
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Christopher M. Baker
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Multiresolution calculation of ionic liquids
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Recent successes in coarse‐grained modeling of DNA
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Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian
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Coarse‐grained models of water
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Leonardo Darré, Matías R. Machado, Sergio Pantano
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Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins
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Ludovico Sutto, Simone Marsili, Francesco Luigi Gervasio
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Essential dynamics: foundation and applications
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Isabella Daidone, Andrea Amadei
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Carbohydrate force fields
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B. Lachele Foley, Matthew B. Tessier, Robert J. Woods
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Next challenges in protein–protein docking: from proteome to interactome and beyond
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Adrien S.J. Melquiond, Ezgi Karaca, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin
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Recent developments and applications of the CHARMM force fields
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Selected features of the polarizable continuum model for the representation of solvation
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Umbrella sampling
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The COSMO and COSMO‐RS solvation models
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Andreas Klamt
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Proline‐derived organocatalysis and synergism between theory and experiments
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Raghavan B. Sunoj
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Cation–π and anion–π interactions
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Antonio Frontera, David Quiñonero, Pere M. Deyà
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Cooperative dynamics of proteins unraveled by network models
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Eran Eyal, Anindita Dutta, Ivet Bahar
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Receptor flexibility in small‐molecule docking calculations
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Metadynamics
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Michele Parrinello, Massimiliano Bonomi, Alessandro Barducci
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Polarization effects in molecular interactions
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F. Javier Luque, François Dehez, Christophe Chipot, Modesto Orozco
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Algorithm improvements for molecular dynamics simulations
Advanced Review
Per Larsson, Berk Hess, Erik Lindahl
Published Online: Jan 21 2011
DOI:10.1002/wcms.3