Articles with public access mandates - Vijay PandeLearn more
Not available anywhere: 7
tICA-metadynamics: accelerating metadynamics by using kinetically selected collective variables
M M. Sultan, VS Pande
Journal of chemical theory and computation 13 (6), 2440-2447, 2017
Mandates: US National Science Foundation, US National Institutes of Health
Ward clustering improves cross-validated Markov state models of protein folding
BE Husic, VS Pande
Journal of chemical theory and computation 13 (3), 963-967, 2017
Mandates: US National Institutes of Health
Solvent viscosity dependence of the protein folding dynamics
YM Rhee, VS Pande
The Journal of Physical Chemistry B 112 (19), 6221-6227, 2008
Mandates: US National Institutes of Health
Bayesian single-exponential kinetics in single-molecule experiments and simulations
DL Ensign, VS Pande
The Journal of Physical Chemistry B 113 (36), 12410-12423, 2009
Mandates: US National Institutes of Health
A minimum variance clustering approach produces robust and interpretable coarse-grained models
BE Husic, KA McKiernan, HK Wayment-Steele, MM Sultan, VS Pande
Journal of chemical theory and computation 14 (2), 1071-1082, 2018
Mandates: US National Science Foundation, US National Institutes of Health
Simulated dynamics of glycans on ligand-binding domain of NMDA receptors reveals strong dynamic coupling between glycans and protein core
AV Sinitskiy, VS Pande
Journal of Chemical Theory and Computation 13 (11), 5496-5505, 2017
Mandates: US National Institutes of Health
Potential-based dynamical reweighting for Markov state models of protein dynamics
JK Weber, VS Pande
Journal of Chemical Theory and Computation 11 (6), 2412-2420, 2015
Mandates: US National Institutes of Health
Available somewhere: 204
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
J Lee, X Cheng, S Jo, AD MacKerell, JB Klauda, W Im
Biophysical journal 110 (3), 641a, 2016
Mandates: US National Science Foundation, US Department of Energy, US National …
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
Mandates: US National Institutes of Health
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: US National Institutes of Health
Molecular graph convolutions: moving beyond fingerprints
S Kearnes, K McCloskey, M Berndl, V Pande, P Riley
Journal of computer-aided molecular design 30, 595-608, 2016
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
Graph convolutional policy network for goal-directed molecular graph generation
J You, B Liu, Z Ying, V Pande, J Leskovec
Advances in neural information processing systems 31, 2018
Mandates: US Department of Defense, US National Institutes of Health
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
Mandates: US National Institutes of Health
Markov state models: From an art to a science
BE Husic, VS Pande
Journal of the American Chemical Society 140 (7), 2386-2396, 2018
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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