List of works - Daniel M Zuckerman

A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]

scientific article published on 01 November 2006

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

scientific article published on January 2006

A black-box re-weighting analysis can correct flawed simulation data

scientific article

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

scientific article published on 02 July 2020

Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method

scientific article published on December 2009

Absolute free energies estimated by combining precalculated molecular fragment libraries

scientific article

Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models

scientific article published on 25 November 2011

Annealed importance sampling of peptides

scientific article published in August 2007

Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds

scientific article published on 21 June 2001

Automated sampling assessment for molecular simulations using the effective sample size

scientific article published on September 2010

Best Practices for Foundations in Molecular Simulations [Article v1.0]

scientific article published on 29 November 2018

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]

scientific article published on 27 October 2018

Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?

scientific article published on August 2011

Comparison of free energy methods for molecular systems

scientific article published on November 2006

Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

scientific article published on 28 August 2020

Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model

scientific article published on 01 September 2007

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

scholarly article

Efficient dynamic importance sampling of rare events in one dimension

scientific article published on 27 December 2000

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo

scientific article

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

scientific article published on September 2013

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems

scientific article published in November 2004

EmrE reminds us to expect the unexpected in membrane transport

scientific article published on 01 January 2020

Equilibrium Sampling in Biomolecular Simulations ⬇️

scientific article published on January 1, 2011

Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space

scientific article

General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models

scientific article published in August 2009

Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase

scientific article

High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking

scientific article published on 01 November 2019

On the structural convergence of biomolecular simulations by determination of the effective sample size

scientific article published on 13 October 2007

Peptide conformational equilibria computed via a single-stage shifting protocol

scientific article published on 01 May 2005

Quantifying uncertainty and sampling quality in biomolecular simulations

scientific article published on January 2009

Rapid sampling of all-atom peptides using a library-based polymer-growth approach

scientific article

Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol

scientific article published on February 2009

Resolution Exchange Simulation with Incremental Coarsening

scientific article published in May 2006

Resolution exchange simulation

scientific article published on 18 January 2006

Simple estimation of absolute free energies for biomolecules

scientific article published in March 2006

Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1 ⬇️

scientific article published on November 15, 2011

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories

scientific article published on 3 March 2014

Single-ensemble nonequilibrium path-sampling estimates of free energy differences

scientific article published on 01 June 2004

Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping

scientific article published on 07 May 2019

Statistical mechanics of membrane adhesion by reversible molecular bonds

scientific article published on 01 May 1995

Steady-state simulations using weighted ensemble path sampling

scientific article published on July 2010

The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.

scientific article

Theory of a systematic computational error in free energy differences

scientific article published on 15 October 2002

Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

scientific article

Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture

scientific article published on 01 November 2019

Transition-event durations in one-dimensional activated processes

scientific article published in February 2007

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

scientific article published on 9 October 2014

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.

scientific article

WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications

scientific article published on 19 January 2022

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

scientific article published on 28 April 2021

Why We Need the Living Journal of Computational Molecular Science

scientific article published on 21 August 2017

List of works by Daniel M Zuckerman

A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

A black-box re-weighting analysis can correct flawed simulation data

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method

Absolute free energies estimated by combining precalculated molecular fragment libraries

Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models

Annealed importance sampling of peptides

Asymmetric primitive-model electrolytes: Debye-Hückel theory, criticality, and energy bounds

Automated sampling assessment for molecular simulations using the effective sample size

Best Practices for Foundations in Molecular Simulations [Article v1.0]

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations [Article v1.0]

Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?

Comparison of free energy methods for molecular systems

Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

Demonstrated Convergence of the Equilibrium Ensemble for a Fast United-Residue Protein Model

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

Efficient dynamic importance sampling of rare events in one dimension

Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems

EmrE reminds us to expect the unexpected in membrane transport

Equilibrium Sampling in Biomolecular Simulations ⬇️

Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space

General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models

Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase

High-throughput, single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking

On the structural convergence of biomolecular simulations by determination of the effective sample size

Peptide conformational equilibria computed via a single-stage shifting protocol

Quantifying uncertainty and sampling quality in biomolecular simulations

Rapid sampling of all-atom peptides using a library-based polymer-growth approach

Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol

Resolution Exchange Simulation with Incremental Coarsening

Resolution exchange simulation

Simple estimation of absolute free energies for biomolecules

Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1 ⬇️

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories

Single-ensemble nonequilibrium path-sampling estimates of free energy differences

Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping

Statistical mechanics of membrane adhesion by reversible molecular bonds

Steady-state simulations using weighted ensemble path sampling

The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.

Theory of a systematic computational error in free energy differences

Thermal motions of the E. coli glucose-galactose binding protein studied using well-sampled, semi-atomistic simulations.

Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture

Transition-event durations in one-dimensional activated processes

Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.

WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

Why We Need the Living Journal of Computational Molecular Science