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Journal of Chemical Theory and Computation|December 2, 2008
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange SimulationDaniel M Zuckerman, Edward LymanThe Journal of Physical Chemistry. B|April 8, 2014
Evaluating the strength of salt bridges: a comparison of current biomolecular force fieldsKarl T Debiec, Angela M Gronenborn, Lillian T ChongJournal 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 ZuckermanJournal of Chemical Theory and Computation|November 18, 2014
Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange SimulationsJustin Spiriti, Daniel M ZuckermanBiophysical Journal|April 18, 2006
Ensemble-based convergence analysis of biomolecular trajectoriesEdward Lyman, Daniel M ZuckermanPlos One|March 21, 2017
Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratioRamu Anandakrishnan, Daniel M ZuckermanThe Journal of Chemical Physics|December 9, 2009
Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth methodDivesh Bhatt, Daniel M ZuckermanThe Journal of Chemical Physics|August 21, 2007
Annealed importance sampling of peptidesEdward Lyman, Daniel M ZuckermanPageof 15