(Q31029932)

15 November 2017

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations (English)

1 reference

molecular dynamics simulation

15 November 2017

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author name string

Viktor Hornak

1

1 reference

15 November 2017

Asim Okur

2

1 reference

15 November 2017

Robert C Rizzo

3

1 reference

15 November 2017

Carlos Simmerling

4

1 reference

15 November 2017

language of work or name

English

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publication date

17 January 2006

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15 November 2017

6

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

inferred from page(s)

published in

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15 November 2017

103

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15 November 2017

915-920

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15 November 2017

4

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The Amber biomolecular simulation programs

15 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Development and testing of a general amber force field

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate 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=1347991

Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Molecular dynamics and NMR spin relaxation 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=1347991

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Inhibitors of HIV-1 protease: a major success of structure-assisted drug design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Domain communication in the dynamical structure of human immunodeficiency virus 1 protease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

HIVdb: a database of the structures of human immunodeficiency virus protease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Flexibility and function in HIV-1 protease

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1347991

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

25 November 2018

1 reference

12 December 2020

Anisotropic rotational diffusion of perdeuterated HIV protease from 15N NMR relaxation measurements at two magnetic fields

1 reference

12 December 2020

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

1 reference

12 December 2020

Solvation influences flap collapse in HIV-1 protease

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0508452103

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15 November 2017

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15 November 2017

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