A comparison of weighted ensemble and Markov state model methodologies

Feng, Haoyun; Costaouec, Ronan; Darve, Eric; Izaguirre, Jesús A.

doi:10.1063/1.4921890

Title: A comparison of weighted ensemble and Markov state model methodologies

Authors:

^[1]; Costaouec, Ronan ^[2]; Darve, Eric ^[2]; Izaguirre, Jesús A. ^[1]

Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
Mechanical Engineering Department, Stanford University, Stanford, California 94035, USA

Publication Date:: Fri Jun 05 00:00:00 EDT 2015

Sponsoring Org.:: USDOE

OSTI Identifier:: 1228629

Grant/Contract Number:: SC0006770

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: The Journal of Chemical Physics

Additional Journal Information:: Journal Name: The Journal of Chemical Physics Journal Volume: 142 Journal Issue: 21; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

Citation Formats


                    Feng, Haoyun, Costaouec, Ronan, Darve, Eric, and Izaguirre, Jesús A. A comparison of weighted ensemble and Markov state model methodologies.  United States: N. p., 2015. 
Web.  doi:10.1063/1.4921890.

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                    Feng, Haoyun, Costaouec, Ronan, Darve, Eric, & Izaguirre, Jesús A. A comparison of weighted ensemble and Markov state model methodologies.  United States.  https://doi.org/10.1063/1.4921890

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                    Feng, Haoyun, Costaouec, Ronan, Darve, Eric, and Izaguirre, Jesús A. Fri .  
"A comparison of weighted ensemble and Markov state model methodologies".  United States.  https://doi.org/10.1063/1.4921890.

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@article{osti_1228629,

  title        = {A comparison of weighted ensemble and Markov state model methodologies},

  author       = {Feng, Haoyun and Costaouec, Ronan and Darve, Eric and Izaguirre, Jesús A.},

  abstractNote = {},

  doi          = {10.1063/1.4921890},

  journal      = {The Journal of Chemical Physics},

  number       = 21,

  volume       = 142,

  place        = {United States},

  year         = {Fri Jun 05 00:00:00 EDT 2015},

  month        = {Fri Jun 05 00:00:00 EDT 2015}

}

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Works referenced in this record:

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Title: A comparison of weighted ensemble and Markov state model methodologies

Citation Formats

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures journal, February 2010

Towards a Theory of Transition Paths journal, May 2006

Using generalized ensemble simulations and Markov state models to identify conformational states journal, October 2009

Non-Markovian Analyses for Extracting Long-Time Behavior from Molecular Simulation Trajectories journal, January 2015

Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory † journal, May 2004

Transition Path Theory for Markov Jump Processes journal, January 2009

Error analysis and efficient sampling in Markovian state models for molecular dynamics journal, November 2005

Estimating the Eigenvalue Error of Markov State Models journal, January 2012

Computing Reaction Rates in Bio-molecular Systems Using Discrete Macro-states book, May 2012

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics journal, June 2011

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal, February 2008

Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin journal, November 2007

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale journal, August 2011

Hypoelliptic Estimates and Spectral Theory for Fokker-Planck Operators and Witten Laplacians book, January 2005

Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones? journal, July 2008

Everything you wanted to know about Markov State Models but were afraid to ask journal, September 2010

AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble journal, September 2014

Steady-state simulations using weighted ensemble path sampling journal, July 2010

Error estimates on averages of correlated data journal, July 1989

Heterogeneous Path Ensembles for Conformational Transitions in Semiatomistic Models of Adenylate Kinase journal, October 2010

On the Approximation Quality of Markov State Models journal, January 2010

Weighted-ensemble Brownian dynamics simulations for protein association reactions journal, January 1996

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures
journal, February 2010

Towards a Theory of Transition Paths
journal, May 2006

Using generalized ensemble simulations and Markov state models to identify conformational states
journal, October 2009

Non-Markovian Analyses for Extracting Long-Time Behavior from Molecular Simulation Trajectories
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory ^†
journal, May 2004

Transition Path Theory for Markov Jump Processes
journal, January 2009

Error analysis and efficient sampling in Markovian state models for molecular dynamics
journal, November 2005

Estimating the Eigenvalue Error of Markov State Models
journal, January 2012

Computing Reaction Rates in Bio-molecular Systems Using Discrete Macro-states
book, May 2012

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics
journal, June 2011

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
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MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
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Hypoelliptic Estimates and Spectral Theory for Fokker-Planck Operators and Witten Laplacians
book, January 2005

Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?
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Everything you wanted to know about Markov State Models but were afraid to ask
journal, September 2010

AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
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Error estimates on averages of correlated data
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Heterogeneous Path Ensembles for Conformational Transitions in Semiatomistic Models of Adenylate Kinase
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On the Approximation Quality of Markov State Models
journal, January 2010

Weighted-ensemble Brownian dynamics simulations for protein association reactions
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