| 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 | 2521 | 2017 |
| Statistically optimal analysis of samples from multiple equilibrium states MR Shirts, JD Chodera The Journal of chemical physics 129, 124105, 2008 | 1968 | 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 | 1578 | 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 | 1370 | 2011 |
| Markov state models of biomolecular conformational dynamics JD Chodera, F Noé Current opinion in structural biology 25, 135-144, 2014 | 805 | 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 | 758 | 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 | 746 | 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 | 652 | 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 | 614 | 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 | 588 | 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 | 555 | 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 | 515 | 2015 |
| 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 | 475 | 2021 |
| Ensemble docking in drug discovery RE Amaro, J Baudry, J Chodera, Ö Demir, JA McCammon, Y Miao, ... Biophysical journal 114 (10), 2271-2278, 2018 | 464 | 2018 |
| 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 | 379 | 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 | 364 | 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 | 357 | 2007 |
| The ribosome modulates nascent protein folding CM Kaiser, DH Goldman, JD Chodera, I Tinoco Jr, C Bustamante Science 334 (6063), 1723-1727, 2011 | 351 | 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 | 344 | 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 | 338 | 2008 |
David MobleyProfessor, University of California, IrvineVerified email at uci.edu
Michael R. ShirtsProfessor of Chemical and Biological Engineering, University of Colorado BoulderVerified email at colorado.edu
Vijay PandeAndreessen Horowitz, Stanford UniversityVerified email at stanford.edu
Ken A. DillDirector of Laufer Center, Stony Brook UniversityVerified email at laufercenter.orgNoe FrankMicrosoft ResearchVerified email at microsoft.com
William SwopeIBM Almaden Research CenterVerified email at gene.com
David MinhIllinois Institute of TechnologyVerified email at iit.edu
Carlos Jose BustamanteUniversity of California, BerkeleyVerified email at alice.berkeley.edu
Jay PonderDepartment of Chemistry, Washington UniversityVerified email at dasher.wustl.edu
Pengyu RenDepartment of Biomedical Engineering, The University of Texas at AustinVerified email at mail.utexas.edu
Gavin E. CrooksNormal ComputingVerified email at berkeley.edu
Bettina G. KellerProfessor of Theoretical Chemistry, Freie Universität BerlinVerified email at fu-berlin.de
Imran S HaqueKimia TherapeuticsVerified email at cs.stanford.edu
Michael J. SchniedersProfessor of Biomedical Engineering and Biochemistry, The University of IowaVerified email at uiowa.edu
