Concepedia

Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR

Yvonne Westermaier, Sergio Ruiz‐Carmona, Isabelle Théret, Françoise Perron‐Sierra, Guillaume Poissonnet, Catherine Dacquet, Jean A. Boutin, Pierre Ducrot, Xavier Barril

Journal of Computer-Aided Molecular Design · 2017 · 45 citations · 38 references

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38

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations

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Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems

Tom Darden, Darrin M. York, Lee G. Pedersen · The Journal of Chemical Physics · 1993 · 30.7K citations · Full text

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PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe, Thomas E. Cheatham · Journal of Chemical Theory and Computation · 2013 · 7.6K citations

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

Gareth Jones, Peter Willett, Robert C. Glen et al. · Journal of Molecular Biology · 1997 · 6.7K citations

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Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Kresten Lindorff‐Larsen, Stefano Piana, Kim Palmö et al. · Proteins Structure Function and Bioinformatics · 2010 · 6.3K citations · Full text

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