Vijay Pande

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	All	Since 2016
Citations	42895	20139
h-index	105	72
i10-index	315	232

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Co-authors

Gregory R. BowmanAssociate Professor, Washington University in St LouisVerified email at biochem.wustl.edu
Kyle A. BeauchampBiophysics Program, Stanford UniversityVerified email at stanford.edu
Christopher D. SnowAssociate Professor of Chemical and Biological Engineering, Colorado State UniversityVerified email at colostate.edu
Michael R. ShirtsAssociate Professor of Chemical and Biological Engineering, University of Colorado BoulderVerified email at colorado.edu
Alexander Y GrosbergProfessor of Physics, New York UniversityVerified email at nyu.edu
Lee-Ping WangDepartment of Chemistry, UC DavisVerified email at ucdavis.edu
John D. ChoderaMemorial Sloan-Kettering Cancer CenterVerified email at mskcc.org
Diwakar ShuklaAssistant Professor, University of Illinois at Urbana-ChampaignVerified email at illinois.edu
Robert T. McGibbonD.E. Shaw ResearchVerified email at DEShawResearch.com
Young Min RheeKorea Advanced Institute of Science and TechnologyVerified email at kaist.ac.kr
TJ LaneGroup Leader, DESYVerified email at desy.de
Bharath RamsundarDeepChem, previously Computable, previously StanfordVerified email at stanford.edu
Peter KassonAssociate Professor, University of Virginia and Uppsala UniversityVerified email at virginia.edu
Christian SchwantesPreviously: Stanford UniversityVerified email at stanford.edu
Imran S HaqueRecursion PharmaceuticalsVerified email at cs.stanford.edu
Todd J MartinezStanford UniversityVerified email at stanford.edu
Vincent VoelzAssociate Professor of Chemistry, Temple UniversityVerified email at temple.edu
Xuhui HuangProfessor of Chemistry at Hong Kong University of Science and TechnologyVerified email at ust.hk
Michael J. SchniedersAssociate Professor of Biomedical Engineering and Biochemistry, The University of IowaVerified email at uiowa.edu
Steven KearnesGoogleVerified email at google.com

Vijay Pande

Professor of Chemistry, Stanford University

Verified email at stanford.edu - Homepage

Biophysics statistical mechanics protein folding computational biology deep learning


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Statistical physics of macromolecules AR Khokhlov Amer Inst of Physics, 1994	2800	1994
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	1022	2010
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	981	2016
Absolute comparison of simulated and experimental protein-folding dynamics CD Snow, H Nguyen, VS Pande, M Gruebele nature 420 (6911), 102-106, 2002	758	2002
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	739	2015
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations EJ Sorin, VS Pande Biophysical journal 88 (4), 2472-2493, 2005	723	2005
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	709	2016
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	674	2004
Screen savers of the world unite! M Shirts, VS Pande Science 290 (5498), 1903-1904, 2000	652	2000
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	644	2003
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	631	2018
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	631	2007
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	597	2009
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	538	2010
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	524	2010
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	517	2017
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	504	2013
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	497	1998
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	456	2003
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	445	2005

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