Simulating replica exchange simulations of protein folding with a kinetic network model (Q36024022)

11 August 2017

Simulating replica exchange simulations of protein folding with a kinetic network model (English)

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11 August 2017

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Weihua Zheng

1

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11 August 2017

Michael Andrec

series ordinal

2

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11 August 2017

Emilio Gallicchio

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3

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11 August 2017

Ronald M Levy

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4

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11 August 2017

language of work or name

English

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publication date

18 September 2007

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Proceedings of the National Academy of Sciences of the United States of America

11 August 2017

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11 August 2017

104

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11 August 2017

39

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11 August 2017

15340-15345

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11 August 2017

Serial replica exchange

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Free energy landscapes for amyloidogenic tetrapeptides dimerization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Multiplexed-replica exchange molecular dynamics method for protein folding 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=2000486

Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Folding dynamics and mechanism of beta-hairpin formation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Negative activation enthalpies in the kinetics of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Exploring the energy landscape of protein folding using replica-exchange and conventional 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=2000486

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Replica Monte Carlo simulation of spin glasses.

11 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Equation of State Calculations by Fast Computing Machines

21 January 2018

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https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Atomic simulations of protein folding, using the replica exchange algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

The incomplete beta function law for parallel tempering sampling of classical canonical systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

On the efficiency of exchange in parallel tempering monte carlo simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Optimized parallel tempering simulations of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Rate-temperature relationships in lambda-repressor fragment lambda 6-85 folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Optimal allocation of replicas in parallel tempering simulations.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2000486

Parallel simulated tempering dynamics of ligand–protein binding with ensembles of protein conformations

23 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0704418104

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

21 January 2018

1 reference

12 December 2020

Selection of temperature intervals for parallel-tempering simulations

1 reference

12 December 2020

A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]

1 reference

12 December 2020

Characterization of the transition state of lysozyme unfolding. I. Effect of protein-solvent interactions on the transition state

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0704418104

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11 August 2017

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11 August 2017

PubMed publication ID

17878309

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