Vijay Pande
Title
Cited by
Cited by
Year
Statistical physics of macromolecules
AR Khokhlov
Amer Inst of Physics, 1994
28001994
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
10222010
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
9812016
Absolute comparison of simulated and experimental protein-folding dynamics
CD Snow, H Nguyen, VS Pande, M Gruebele
nature 420 (6911), 102-106, 2002
7582002
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
7392015
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
EJ Sorin, VS Pande
Biophysical journal 88 (4), 2472-2493, 2005
7232005
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
7092016
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
6742004
Screen savers of the world unite!
M Shirts, VS Pande
Science 290 (5498), 1903-1904, 2000
6522000
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
6442003
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
6312018
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
6312007
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
5972009
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
5382010
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
5242010
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
5172017
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
5042013
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
4971998
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
4562003
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
MR Shirts, VS Pande
The Journal of chemical physics 122 (13), 134508, 2005
4452005
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Articles 1–20