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Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

Annual review of biophysics, 2017-05, Vol.46 (1), p.43-57

2017

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Equilibrium Sampling in Biomolecular Simulations

Annual review of biophysics, 2011-06, Vol.40 (1), p.41-62

Zuckerman, Daniel M

2011

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Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

PLoS computational biology, 2023-04, Vol.19 (4), p.e1011059

2023

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

Nature communications, 2020-08, Vol.11 (1), p.4331-4331, Article 4331

2020

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Computational Estimation of Microsecond to Second Atomistic Folding Times

Journal of the American Chemical Society, 2019-04, Vol.141 (16), p.6519-6526

2019

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Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.3473-3481

2016

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

The Journal of chemical physics, 2010-02, Vol.132 (5), p.054107-054107

2010

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Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio

PloS one, 2017-03, Vol.12 (3), p.e0173500-e0173500

2017

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

PLoS computational biology, 2020-07, Vol.16 (7), p.e1007884-e1007884

2020

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A kinetic mechanism for enhanced selectivity of membrane transport

PLoS computational biology, 2020-07, Vol.16 (7), p.e1007789

2020

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Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein–Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide

The journal of physical chemistry letters, 2016-09, Vol.7 (17), p.3440-3445

2016

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Steady-state simulations using weighted ensemble path sampling

The Journal of chemical physics, 2010-07, Vol.133 (1), p.014110-014110-12

2010

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WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

Journal of chemical theory and computation, 2015-02, Vol.11 (2), p.800-809

2015

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Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

PloS one, 2019-04, Vol.14 (4), p.e0215694-e0215694

2019

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Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1

Biophysical journal, 2011-11, Vol.101 (10), p.2399-2407

2011

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

Journal of chemical theory and computation, 2014-07, Vol.10 (7), p.2658-2667

2014

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Supramolecular self assembly of nanodrill-like structures for intracellular delivery

Journal of controlled release, 2018-07, Vol.282, p.76-89

2018

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Efficient and Verified Simulation of a Path Ensemble for Conformational Change in a United-Residue Model of Calmodulin

Proceedings of the National Academy of Sciences - PNAS, 2007-11, Vol.104 (46), p.18043-18048

2007

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Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian “Microbin” Analysis

Journal of chemical theory and computation, 2020-11, Vol.16 (11), p.6763-6775

2020

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Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

PLoS computational biology, 2016-02, Vol.12 (2), p.e1004611-e1004611

2016

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From Average Transient Transporter Currents to Microscopic MechanismA Bayesian Analysis

The journal of physical chemistry. B, 2024-02, Vol.128 (8), p.1830-1842

2024

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Morphodynamical cell state description via live-cell imaging trajectory embedding

Communications biology, 2023-05, Vol.6 (1), p.484-484, Article 484

2023

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Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo

Journal of chemical theory and computation, 2024-04, Vol.20 (8), p.2971-2984

2024

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Transition-event durations in one-dimensional activated processes

The Journal of chemical physics, 2007-02, Vol.126 (7), p.074504-074504-18

2007

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How precisely can transporter mechanisms be determined from electrophysiology data? A Bayesian investigation

Biophysical journal, 2023-02, Vol.122 (3), p.284a-284a

2023

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Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

Equilibrium Sampling in Biomolecular Simulations

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

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

Computational Estimation of Microsecond to Second Atomistic Folding Times

Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models

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

Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio

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

A kinetic mechanism for enhanced selectivity of membrane transport

Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein–Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide

Steady-state simulations using weighted ensemble path sampling

WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1

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

Supramolecular self assembly of nanodrill-like structures for intracellular delivery

Efficient and Verified Simulation of a Path Ensemble for Conformational Change in a United-Residue Model of Calmodulin

Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian “Microbin” Analysis

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

From Average Transient Transporter Currents to Microscopic MechanismA Bayesian Analysis

Morphodynamical cell state description via live-cell imaging trajectory embedding

Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo

Transition-event durations in one-dimensional activated processes

How precisely can transporter mechanisms be determined from electrophysiology data? A Bayesian investigation

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