Simple continuous and discrete models for simulating replica exchange simulations of protein folding. (Q34296935)

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2 January 2020

title

Simple continuous and discrete models for simulating replica exchange simulations of protein folding (English)

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2 January 2020

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1

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2 January 2020

Emilio Gallicchio

series ordinal

3

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2 January 2020

author name string

Michael Andrec

series ordinal

2

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2 January 2020

Ronald M Levy

series ordinal

4

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2 January 2020

language of work or name

English

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publication date

6 February 2008

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Journal of Physical Chemistry B

2 January 2020

published in

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2 January 2020

volume

112

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2 January 2020

page(s)

6083-6093

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2 January 2020

issue

19

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

2 January 2020

cites work

1 reference

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

6 July 2018

1 reference

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Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations

6 July 2018

1 reference

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Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

6 July 2018

1 reference

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

6 July 2018

1 reference

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Free energy landscapes for amyloidogenic tetrapeptides dimerization

6 July 2018

1 reference

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

6 July 2018

1 reference

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Protein folding pathways from replica exchange simulations and a kinetic network model

6 July 2018

1 reference

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Multiplexed-replica exchange molecular dynamics method for protein folding simulation

6 July 2018

1 reference

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Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

6 July 2018

1 reference

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Entropic barriers, transition states, funnels, and exponential protein folding kinetics: a simple model

6 July 2018

1 reference

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Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

6 July 2018

1 reference

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Negative activation enthalpies in the kinetics of protein folding

6 July 2018

1 reference

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

6 July 2018

1 reference

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

On the efficiency of exchange in parallel tempering monte carlo simulations

28 October 2018

1 reference

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Protein folding kinetics and thermodynamics from atomistic simulations.

28 October 2018

1 reference

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Optimized parallel tempering simulations of proteins.

28 October 2018

1 reference

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Validation of Markov state models using Shannon's entropy.

28 October 2018

1 reference

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Convergence of replica exchange molecular dynamics.

28 October 2018

1 reference

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Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

28 October 2018

1 reference

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Efficient sampling of protein structures by model hopping.

28 October 2018

1 reference

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Optimal allocation of replicas in parallel tempering simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

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

28 October 2018

1 reference

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

28 October 2018

1 reference

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Replica Monte Carlo simulation of spin glasses.

28 October 2018

1 reference

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Replica exchange molecular dynamics simulations of amyloid peptide aggregation

28 October 2018

1 reference

12 December 2020

Selection of temperature intervals for parallel-tempering simulations

1 reference

12 December 2020

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

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

Identifiers

DOI

10.1021/JP076377+

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

1 reference