(Q36335364)

13 August 2017

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty (English)

1 reference

13 August 2017

0 references

Gregory R Bowman

1

1 reference

PMC publication ID

3477182

13 August 2017

language of work or name

English

0 references

publication date

1 October 2012

1 reference

Journal of Chemical Physics

13 August 2017

1 reference

13 August 2017

137

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13 August 2017

13

1 reference

13 August 2017

134111

1 reference

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

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Identifying Metastable States of Folding Proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Protein folded states are kinetic hubs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Network models for molecular kinetics and their initial applications to human health

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Comparing geometric and kinetic cluster algorithms for molecular simulation data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Functional versus folding landscapes: the same yet different

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Using generalized ensemble simulations and Markov state models to identify conformational states

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

COMPUTING: Screen Savers of the World Unite!

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Exploring protein native states and large-scale conformational changes with a modified generalized born model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Markov models of molecular kinetics: generation and validation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

A Bayesian method for construction of Markov models to describe dynamics on various time-scales

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Probability distributions of molecular observables computed from Markov models.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Coarse master equations for peptide folding dynamics.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3477182

On Information and Sufficiency

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4755751

Divergence measures based on the Shannon entropy

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.4755751

21 January 2018

Identifiers

DOI

10.1063/1.4755751

1 reference

13 August 2017

1 reference

1 reference

PMC publication ID

3477182

13 August 2017

PubMed publication ID

23039589

1 reference

PMC publication ID

3477182