Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics (Q33740100)

29 July 2017

title

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics (English)

1 reference

29 July 2017

Eric Vanden-Eijnden

1 reference

29 July 2017

Cameron F Abrams

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29 July 2017

language of work or name

English

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publication date

1 March 2010

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

29 July 2017

published in

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29 July 2017

volume

107

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29 July 2017

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29 July 2017

page(s)

4961-4966

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

29 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=2841907

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Self-guided Langevin dynamics study of regulatory interactions in NtrC.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

The structural biology of HIV assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Structural definition of a conserved neutralization epitope on HIV-1 gp120

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Broad-spectrum anti-human immunodeficiency virus (HIV) potential of a peptide HIV type 1 entry inhibitor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Dynamics of allosteric transitions in GroEL.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Crystal structure of wild-type chaperonin GroEL.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Scalable molecular dynamics with NAMD

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Broadly cross-reactive HIV neutralizing human monoclonal antibody Fab selected by sequential antigen panning of a phage display library

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Escaping free-energy minima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

A dynamic model for the allosteric mechanism of GroEL

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Collective protein dynamics in relation to function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

HIV-1: fifteen proteins and an RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Structural mechanisms for domain movements in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Structural and Functional Aspects of Domain Motions in Proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2841907

Collective variable description of native protein dynamics

21 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Single-sweep methods for free energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

The blind search for the closed states of hinge-bending proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Structural mimicry of CD4 by a cross-reactive HIV-1 neutralizing antibody with CDR-H2 and H3 containing unique motifs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0914540107

Some recent techniques for free energy calculations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20194785

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure and function in GroEL-mediated protein folding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20194785

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0914540107

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference