(Q33948378)

30 July 2017

title

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics (English)

1 reference

30 July 2017

Jeremy C Smith

5

0 references

Vijay Pande

3

object named as

Vijay S Pande

1 reference

30 July 2017

Jan-Hendrik Prinz

1

1 reference

30 July 2017

John D Chodera

2

1 reference

30 July 2017

William C Swope

4

1 reference

30 July 2017

Frank Noé

6

1 reference

30 July 2017

language of work or name

English

0 references

publication date

1 June 2011

1 reference

Journal of Chemical Physics

30 July 2017

published in

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30 July 2017

volume

134

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30 July 2017

issue

24

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30 July 2017

page(s)

244108

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

30 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Parallel tempering: theory, applications, and new perspectives

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Statistically optimal analysis of samples from multiple equilibrium states

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Intrinsic dynamics of an enzyme underlies catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Observation of a Power-Law Memory Kernel for Fluctuations within a Single Protein Molecule

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

A protein folding pathway with multiple folding intermediates at atomic resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

5 July 2018

Single-molecule folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Enzyme dynamics during catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Generalized-ensemble algorithms for molecular simulations of biopolymers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Multiple pathways on a protein-folding energy landscape: kinetic evidence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

Fast and slow tracks in lysozyme folding: insight into the role of domains in the folding process

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3139503

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics

5 July 2018

1 reference

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

Coarse master equations for peptide folding dynamics.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Peptide folding kinetics from replica exchange molecular dynamics.

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Temperature weighted histogram analysis method, replica exchange, and transition paths.

21 January 2018

1 reference

Analyzing biased Monte Carlo and molecular dynamics simulations

21 January 2018

1 reference

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

Probability distributions of molecular observables computed from Markov models.

21 January 2018

1 reference

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

The folding mechanism of a beta-sheet: the WW domain

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21721613

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Optimized Monte Carlo data analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21721613

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.3592153

1 reference

30 July 2017

1 reference

30 July 2017

1 reference