| 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 | 2265 | 2017 |
| Statistically optimal analysis of samples from multiple equilibrium states MR Shirts, JD Chodera The Journal of chemical physics 129, 124105, 2008 | 1897 | 2008 |
| 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 | 1501 | 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, 174105, 2011 | 1325 | 2011 |
| Markov state models of biomolecular conformational dynamics JD Chodera, F Noé Current opinion in structural biology 25, 135-144, 2014 | 785 | 2014 |
| 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, 155101, 2007 | 753 | 2007 |
| 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 | 722 | 2013 |
| 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, 2011 | 631 | 2011 |
| Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity EC Thomson, LE Rosen, JG Shepherd, R Spreafico, A da Silva Filipe, ... Cell 184 (5), 1171-1187. e20, 2021 | 585 | 2021 |
| Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design JD Chodera, DL Mobley Annual review of biophysics 42 (1), 121-142, 2013 | 567 | 2013 |
| Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations JD Chodera, WC Swope, JW Pitera, C Seok, KA Dill Journal of Chemical Theory and Computation 3 (1), 26-41, 2007 | 550 | 2007 |
| Hypoxia induces production of L-2-hydroxyglutarate AM Intlekofer, RG Dematteo, S Venneti, LWS Finley, C Lu, AR Judkins, ... Cell metabolism 22 (2), 304-311, 2015 | 491 | 2015 |
| Ensemble docking in drug discovery RE Amaro, J Baudry, J Chodera, Ö Demir, JA McCammon, Y Miao, ... Biophysical journal 114 (10), 2271-2278, 2018 | 434 | 2018 |
| SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape TN Starr, N Czudnochowski, Z Liu, F Zatta, YJ Park, A Addetia, D Pinto, ... Nature 597 (7874), 97-102, 2021 | 433 | 2021 |
| Systematic improvement of a classical molecular model of water LP Wang, T Head-Gordon, JW Ponder, P Ren, JD Chodera, PK Eastman, ... The Journal of Physical Chemistry B 117 (34), 9956-9972, 2013 | 367 | 2013 |
| The protein folding problem: when will it be solved? KA Dill, SB Ozkan, TR Weikl, JD Chodera, VA Voelz Current opinion in structural biology 17 (3), 342-346, 2007 | 358 | 2007 |
| Predicting absolute ligand binding free energies to a simple model site DL Mobley, AP Graves, JD Chodera, AC McReynolds, BK Shoichet, ... Journal of molecular biology 371 (4), 1118-1134, 2007 | 350 | 2007 |
| The ribosome modulates nascent protein folding CM Kaiser, DH Goldman, JD Chodera, I Tinoco Jr, C Bustamante Science 334 (6063), 1723-1727, 2011 | 341 | 2011 |
| On the use of orientational restraints and symmetry corrections in alchemical free energy calculations DL Mobley, JD Chodera, KA Dill The Journal of chemical physics 125, 084902, 2006 | 337 | 2006 |
| Predicting small-molecule solvation free energies: an informal blind test for computational chemistry A Nicholls, DL Mobley, JP Guthrie, JD Chodera, CI Bayly, MD Cooper, ... Journal of medicinal chemistry 51 (4), 769-779, 2008 | 331 | 2008 |
David MobleyProfessor, University of California, IrvineVerified email at uci.edu