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Journal of Computational Chemistry|November 29, 2011
Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" modelsSteven Lettieri, Daniel M ZuckermanAnnual Reports in Computational Chemistry|May 11, 2010
Quantifying uncertainty and sampling quality in biomolecular simulationsAlan Grossfield, Daniel M ZuckermanThe Journal of Chemical Physics|January 3, 2016
Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunitsJustin Spiriti, Daniel M ZuckermanThe Journal of Physical Chemistry. B|February 19, 2024
From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian AnalysisAugust George, Daniel M ZuckermanThe Journal of Chemical Physics|March 5, 2009
Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocolEdward Lyman, Daniel M ZuckermanThe Journal of Physical Chemistry. B|October 16, 2007
On the structural convergence of biomolecular simulations by determination of the effective sample sizeEdward Lyman, Daniel M ZuckermanJournal of Chemical Theory and Computation|December 2, 2008
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange SimulationDaniel M Zuckerman, Edward LymanJournal of Chemical Theory and Computation|September 29, 2020
Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" AnalysisJeremy Copperman, Daniel M ZuckermanJournal of Chemical Theory and Computation|April 20, 2019
Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian BootstrappingBarmak Mostofian, Daniel M ZuckermanJournal of Chemical Theory and Computation|June 11, 2011
Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinaseDivesh Bhatt, Daniel M ZuckermanPageof 12