Building Markov state models along pathways to determine free energies and rates of transitions (Q37172338)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18715051%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

title

Building Markov state models along pathways to determine free energies and rates of transitions (English)

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12 January 2020

1

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12 January 2020

author name string

Benoît Roux

series ordinal

2

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12 January 2020

language of work or name

English

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publication date

1 August 2008

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18715051%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Physics

12 January 2020

published in

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12 January 2020

volume

129

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12 January 2020

issue

6

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12 January 2020

page(s)

064107

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Finding transition pathways using the string method with swarms of trajectories

12 January 2020

cites work

1 reference

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Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics

6 September 2017

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Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations

6 September 2017

1 reference

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Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

6 September 2017

1 reference

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Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water

6 September 2017

1 reference

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Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2674374

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

6 September 2017

1 reference

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Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix

6 September 2017

1 reference

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Computing time scales from reaction coordinates by milestoning.

27 June 2018

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Peptide folding kinetics from replica exchange molecular dynamics.

21 January 2018

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Conformational sampling via a self-regulating effective energy surface.

21 January 2018

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

21 January 2018

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Foldamer dynamics expressed via Markov state models. II. State space decomposition

21 January 2018

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Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

21 January 2018

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String method in collective variables: minimum free energy paths and isocommittor surfaces.

21 January 2018

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Error analysis and efficient sampling in Markovian state models for molecular dynamics.

21 January 2018

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

21 January 2018

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

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

21 January 2018

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Finite temperature string method for the study of rare events.

21 January 2018

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String method for the study of rare events

21 January 2018

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Rate constants for diffusive processes by partial path sampling.

21 January 2018

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Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

21 January 2018

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On the transition coordinate for protein folding

21 January 2018

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Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

21 January 2018

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Two-state allosteric behavior in a single-domain signaling protein

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18715051

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.2959573

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18715051%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

1 reference

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12 January 2020

PubMed publication ID

18715051

1 reference