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Daniel M. Zuckerman
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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
7202019
Quantifying uncertainty and sampling quality in biomolecular simulations
A Grossfield, DM Zuckerman
Annual reports in computational chemistry 5, 23-48, 2009
3522009
Weighted ensemble simulation: review of methodology, applications, and software
DM Zuckerman, LT Chong
Annual review of biophysics 46 (1), 43-57, 2017
2782017
Equilibrium sampling in biomolecular simulations
DM Zuckerman
Annual review of biophysics 40 (1), 41-62, 2011
2622011
Resolution exchange simulation
E Lyman, FM Ytreberg, DM Zuckerman
Physical review letters 96 (2), 028105, 2006
2352006
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
2192010
Theory of a systematic computational error in free energy differences
DM Zuckerman, TB Woolf
Physical Review Letters 89 (18), 180602, 2002
1972002
Comparison of free energy methods for molecular systems
FM Ytreberg, RH Swendsen, DM Zuckerman
The Journal of chemical physics 125 (18), 2006
1642006
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), 2018
1632018
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
1542007
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
1482015
Ensemble-based convergence analysis of biomolecular trajectories
E Lyman, DM Zuckerman
Biophysical journal 91 (1), 164-172, 2006
1422006
Statistical physics of biomolecules: an introduction
DM Zuckerman
CRC press, 2010
1392010
Steady-state simulations using weighted ensemble path sampling
D Bhatt, BW Zhang, DM Zuckerman
The Journal of chemical physics 133 (1), 2010
1272010
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
1212018
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
1212006
Single-ensemble nonequilibrium path-sampling estimates of free energy differences
FM Ytreberg, DM Zuckerman
The Journal of chemical physics 120 (23), 10876-10879, 2004
1212004
Transition-event durations in one-dimensional activated processes
BW Zhang, D Jasnow, DM Zuckerman
The Journal of chemical physics 126 (7), 2007
1152007
Dynamic reaction paths and rates through importance-sampled stochastic dynamics
DM Zuckerman, TB Woolf
The Journal of chemical physics 111 (21), 9475-9484, 1999
1081999
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
1062017
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Articles 1–20