Weighted ensemble simulation: review of methodology, applications, and software
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel
simulations run with intermittent communication that can enhance sampling of rare events …
simulations run with intermittent communication that can enhance sampling of rare events …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …
generating pathways and rate constants for rare events such as protein folding and protein …
Protein folding kinetics and thermodynamics from atomistic simulation
Advances in simulation techniques and computing hardware have created a substantial
overlap between the timescales accessible to atomic-level simulations and those on which …
overlap between the timescales accessible to atomic-level simulations and those on which …
WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis
MC Zwier, JL Adelman, JW Kaus, AJ Pratt… - Journal of chemical …, 2015 - ACS Publications
The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel
calculations with intermittent communication to enhance the sampling of rare events, such …
calculations with intermittent communication to enhance the sampling of rare events, such …
The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
The “weighted ensemble” method, introduced by Huber and Kim [Biophys. J. 70, 97 (1996)],
is one of a handful of rigorous approaches to path sampling of rare events. Expanding …
is one of a handful of rigorous approaches to path sampling of rare events. Expanding …
Molecular modeling investigations of sorption and diffusion of small molecules in Glassy polymers
With a wide range of applications, from energy and environmental engineering, such as in
gas separations and water purification, to biomedical engineering and packaging, glassy …
gas separations and water purification, to biomedical engineering and packaging, glassy …
Reaching biological timescales with all-atom molecular dynamics simulations
Molecular dynamics (MD) simulations can provide atomically detailed views of protein
motions, sampling multiple timescales ranging from femtoseconds to nanoseconds on …
motions, sampling multiple timescales ranging from femtoseconds to nanoseconds on …
Efficient atomistic simulation of pathways and calculation of rate constants for a protein–peptide binding process: Application to the MDM2 protein and an intrinsically …
MC Zwier, AJ Pratt, JL Adelman, JW Kaus… - The journal of …, 2016 - ACS Publications
The characterization of protein binding processes with all of the key conformational
changes has been a grand challenge in the field of biophysics. Here, we have used the …
changes has been a grand challenge in the field of biophysics. Here, we have used the …
Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations
A grand challenge in the field of biophysics has been the complete characterization of
protein–protein binding processes at atomic resolution. This characterization requires the …
protein–protein binding processes at atomic resolution. This characterization requires the …