| Statistical physics of macromolecules AR Khokhlov, AY Grosberg, VS Pande AIP press, 1994 | 3082 | 1994 |
| 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 | 2850 | 2016 |
| 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 | 2365 | 2018 |
| 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 | 1924 | 2017 |
| Statistically optimal analysis of samples from multiple equilibrium states MR Shirts, JD Chodera The Journal of chemical physics 129 (12), 2008 | 1765 | 2008 |
| 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 | 1728 | 2015 |
| 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 | 1670 | 2016 |
| 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 | 1445 | 2010 |
| Markov models of molecular kinetics: Generation and validation JH Prinz, H Wu, M Sarich, B Keller, M Senne, M Held, JD Chodera, ... The Journal of chemical physics 134 (17), 2011 | 1247 | 2011 |
| Strategies for pre-training graph neural networks W Hu, B Liu, J Gomes, M Zitnik, P Liang, V Pande, J Leskovec arXiv preprint arXiv:1905.12265, 2019 | 1204 | 2019 |
| 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 | 997 | 2018 |
| Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro KT Choy, AYL Wong, P Kaewpreedee, SF Sia, D Chen, KPY Hui, ... Antiviral research 178, 104786, 2020 | 973 | 2020 |
| GROMACS user manual version 3.2 D van der Spoel, E Lindahl, B Hess, AR van Buuren, E Apol, ... Nijenborgh 4, 9747, 2004 | 882 | 2004 |
| Low data drug discovery with one-shot learning H Altae-Tran, B Ramsundar, AS Pappu, V Pande ACS central science 3 (4), 283-293, 2017 | 829 | 2017 |
| Absolute comparison of simulated and experimental protein-folding dynamics CD Snow, H Nguyen, VS Pande, M Gruebele nature 420 (6911), 102-106, 2002 | 822 | 2002 |
| 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 | 808 | 2004 |
| Exploring the helix-coil transition via all-atom equilibrium ensemble simulations EJ Sorin, VS Pande Biophysical journal 88 (4), 2472-2493, 2005 | 802 | 2005 |
| 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 | 760 | 2010 |
| 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 | 749 | 2003 |
| 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), 2007 | 741 | 2007 |
