(Q36069631)

12 August 2017

WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis (English)

1 reference

12 August 2017

0 references

0 references

1 reference

Matthew C Zwier

1

1 reference

12 August 2017

Joshua L Adelman

2

1 reference

12 August 2017

Joseph W Kaus

3

1 reference

12 August 2017

Adam J Pratt

4

1 reference

12 August 2017

Kim F Wong

5

1 reference

12 August 2017

Nicholas B Rego

6

1 reference

12 August 2017

Ernesto Suárez

7

1 reference

12 August 2017

Steven Lettieri

8

1 reference

12 August 2017

David W Wang

9

1 reference

12 August 2017

Michael Grabe

10

1 reference

12 August 2017

Daniel M Zuckerman

11

1 reference

12 August 2017

Lillian T Chong

12

1 reference

12 August 2017

1 February 2015

1 reference

Journal of Chemical Theory and Computation

12 August 2017

1 reference

12 August 2017

11

1 reference

12 August 2017

2

1 reference

12 August 2017

800-809

1 reference

EMMA: A Software Package for Markov Model Building and Analysis.

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Best practices for scientific computing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Enhanced modeling via network theory: Adaptive sampling of Markov state models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Simulating rare events using a weighted ensemble-based string method

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Simulations of the alternating access mechanism of the sodium symporter Mhp1.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

CHARMM: the biomolecular simulation program

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Scalable molecular dynamics with NAMD

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

The Amber biomolecular simulation programs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Weighted-ensemble Brownian dynamics simulations for protein association reactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Steady-state simulations using weighted ensemble path sampling

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Transition-event durations in one-dimensional activated processes.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Computing time scales from reaction coordinates by milestoning.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4573570

Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26392815

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sampling Rare Switching Events in Biochemical Networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26392815

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26392815

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT5010615

1 reference

12 August 2017

1 reference

12 August 2017

PubMed publication ID

26392815

1 reference