| A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0] AT Bogetti, B Mostofian, A Dickson, AJ Pratt, AS Saglam, PO Harrison, ... Living journal of computational molecular science 1 (2), 2019 | 857 | 2019 |
| Quantifying uncertainty and sampling quality in biomolecular simulations A Grossfield, DM Zuckerman Annual reports in computational chemistry 5, 23-48, 2009 | 363 | 2009 |
| Weighted ensemble simulation: review of methodology, applications, and software DM Zuckerman, LT Chong Annual review of biophysics 46 (1), 43-57, 2017 | 327 | 2017 |
| Equilibrium sampling in biomolecular simulations DM Zuckerman Annual review of biophysics 40 (1), 41-62, 2011 | 276 | 2011 |
| The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures BW Zhang, D Jasnow, DM Zuckerman The Journal of chemical physics 132 (5), 2010 | 242 | 2010 |
| Resolution exchange simulation E Lyman, FM Ytreberg, DM Zuckerman Physical review letters 96 (2), 028105, 2006 | 240 | 2006 |
| Theory of a systematic computational error in free energy differences DM Zuckerman, TB Woolf Physical Review Letters 89 (18), 180602, 2002 | 200 | 2002 |
| Best practices for quantification of uncertainty and sampling quality in molecular simulations [Article v1. 0] A Grossfield, PN Patrone, DR Roe, AJ Schultz, DW Siderius, ... Living journal of computational molecular science 1 (1), 5067, 2018 | 186 | 2018 |
| WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis MC Zwier, JL Adelman, JW Kaus, AJ Pratt, KF Wong, NB Rego, E Suárez, ... Journal of chemical theory and computation 11 (2), 800-809, 2015 | 166 | 2015 |
| Comparison of free energy methods for molecular systems FM Ytreberg, RH Swendsen, DM Zuckerman The Journal of chemical physics 125 (18), 2006 | 165 | 2006 |
| Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin BW Zhang, D Jasnow, DM Zuckerman Proceedings of the National Academy of sciences 104 (46), 18043-18048, 2007 | 159 | 2007 |
| Statistical physics of biomolecules: an introduction DM Zuckerman CRC press, 2010 | 152 | 2010 |
| Ensemble-based convergence analysis of biomolecular trajectories E Lyman, DM Zuckerman Biophysical journal 91 (1), 164-172, 2006 | 149 | 2006 |
| Steady-state simulations using weighted ensemble path sampling D Bhatt, BW Zhang, DM Zuckerman The Journal of chemical physics 133 (1), 2010 | 143 | 2010 |
| Structure of native lens connexin 46/50 intercellular channels by cryo-EM JB Myers, BG Haddad, SE O’Neill, DS Chorev, CC Yoshioka, ... Nature 564 (7736), 372-377, 2018 | 140 | 2018 |
| Transition-event durations in one-dimensional activated processes BW Zhang, D Jasnow, DM Zuckerman The Journal of chemical physics 126 (7), 2007 | 123 | 2007 |
| A second look at canonical sampling of biomolecules using replica exchange simulation DM Zuckerman, E Lyman Journal of chemical theory and computation 2 (4), 1200-1202, 2006 | 123 | 2006 |
| Single-ensemble nonequilibrium path-sampling estimates of free energy differences FM Ytreberg, DM Zuckerman arXiv preprint physics/0403093, 2004 | 122 | 2004 |
| Path-sampling strategies for simulating rare events in biomolecular systems LT Chong, AS Saglam, DM Zuckerman Current opinion in structural biology 43, 88-94, 2017 | 120 | 2017 |
| Dynamic reaction paths and rates through importance-sampled stochastic dynamics DM Zuckerman, TB Woolf The Journal of chemical physics 111 (21), 9475-9484, 1999 | 110 | 1999 |
