Vijay Pande
Title
Cited by
Cited by
Year
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
J Lee, X Cheng, JM Swails, MS Yeom, PK Eastman, JA Lemkul, S Wei, ...
Journal of chemical theory and computation 12 (1), 405-413, 2016
12792016
Current status of the AMOEBA polarizable force field
JW Ponder, C Wu, P Ren, VS Pande, JD Chodera, MJ Schnieders, ...
The journal of physical chemistry B 114 (8), 2549-2564, 2010
10942010
MDTraj: a modern open library for the analysis of molecular dynamics trajectories
RT McGibbon, KA Beauchamp, MP Harrigan, C Klein, JM Swails, ...
Biophysical journal 109 (8), 1528-1532, 2015
9012015
Molecular graph convolutions: moving beyond fingerprints
S Kearnes, K McCloskey, M Berndl, V Pande, P Riley
Journal of computer-aided molecular design 30 (8), 595-608, 2016
9002016
MoleculeNet: a benchmark for molecular machine learning
Z Wu, B Ramsundar, EN Feinberg, J Gomes, C Geniesse, AS Pappu, ...
Chemical science 9 (2), 513-530, 2018
8602018
Absolute comparison of simulated and experimental protein-folding dynamics
CD Snow, H Nguyen, VS Pande, M Gruebele
nature 420 (6911), 102-106, 2002
7692002
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
EJ Sorin, VS Pande
Biophysical journal 88 (4), 2472-2493, 2005
7462005
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
P Eastman, J Swails, JD Chodera, RT McGibbon, Y Zhao, KA Beauchamp, ...
PLoS computational biology 13 (7), e1005659, 2017
7092017
Random-coil behavior and the dimensions of chemically unfolded proteins
JE Kohn, IS Millett, J Jacob, B Zagrovic, TM Dillon, N Cingel, RS Dothager, ...
Proceedings of the National Academy of Sciences 101 (34), 12491-12496, 2004
6952004
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
MR Shirts, JW Pitera, WC Swope, VS Pande
The Journal of chemical physics 119 (11), 5740-5761, 2003
6872003
Screen savers of the world unite!
M Shirts, VS Pande
Science 290 (5498), 1903-1904, 2000
6742000
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
JD Chodera, N Singhal, VS Pande, KA Dill, WC Swope
The Journal of chemical physics 126 (15), 04B616, 2007
6562007
Accelerating molecular dynamic simulation on graphics processing units
MS Friedrichs, P Eastman, V Vaidyanathan, M Houston, S Legrand, ...
Journal of computational chemistry 30 (6), 864-872, 2009
6152009
Everything you wanted to know about Markov State Models but were afraid to ask
VS Pande, K Beauchamp, GR Bowman
Methods 52 (1), 99-105, 2010
5832010
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
VA Voelz, GR Bowman, K Beauchamp, VS Pande
Journal of the American Chemical Society 132 (5), 1526-1528, 2010
5522010
OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation
P Eastman, MS Friedrichs, JD Chodera, RJ Radmer, CM Bruns, JP Ku, ...
Journal of chemical theory and computation 9 (1), 461-469, 2013
5382013
On the transition coordinate for protein folding
R Du, VS Pande, AY Grosberg, T Tanaka, ES Shakhnovich
The Journal of chemical physics 108 (1), 334-350, 1998
5191998
Alchemical free energy methods for drug discovery: progress and challenges
JD Chodera, DL Mobley, MR Shirts, RW Dixon, K Branson, VS Pande
Current opinion in structural biology 21 (2), 150-160, 2011
4752011
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
VS Pande, I Baker, J Chapman, SP Elmer, S Khaliq, SM Larson, YM Rhee, ...
Biopolymers: Original Research on Biomolecules 68 (1), 91-109, 2003
4722003
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
MR Shirts, E Bair, G Hooker, VS Pande
Physical review letters 91 (14), 140601, 2003
4622003
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Articles 1–20