(Q34718562)

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The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system

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scholarly article

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Europe PubMed Central

PubMed publication ID

4 August 2017

The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system (English)

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Europe PubMed Central

PubMed publication ID

4 August 2017

author name string

Xianfeng Li

1

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Europe PubMed Central

PubMed publication ID

4 August 2017

Robert A Latour

2

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Europe PubMed Central

PubMed publication ID

4 August 2017

publication date

14 October 2010

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Europe PubMed Central

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4 August 2017

language of work or name

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Journal of Computational Chemistry

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Europe PubMed Central

PubMed publication ID

4 August 2017

32

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Europe PubMed Central

PubMed publication ID

4 August 2017

6

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

1091-1100

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

TIGER2: an improved algorithm for temperature intervals with global exchange of replicas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

The free energy landscape for β hairpin folding in explicit water

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Understanding beta-hairpin formation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

7 July 2018

Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21689

21 January 2018

Folding landscapes of the Alzheimer amyloid-beta(12-28) peptide.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21689

21 January 2018

Equation of State Calculations by Fast Computing Machines

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21689

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21689

21 January 2018

Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21689

21 January 2018

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3064076

26 October 2018

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

https://pubmed.ncbi.nlm.nih.gov/20949510

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An improved replica-exchange sampling method: temperature intervals with global energy reassignment

1 reference

https://pubmed.ncbi.nlm.nih.gov/20949510

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/JCC.21689

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

DBLP publication ID

journals/jcc/LiL11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

4 August 2017

ResearchGate publication ID

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