(Q30479516)

10 August 2017

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics (English)

1 reference

molecular dynamics simulation

10 August 2017

0 references

1

Joanna Trylska

1 reference

10 August 2017

Valentina Tozzini

2

0 references

J. Andrew McCammon

series ordinal

4

object named as

J Andrew McCammon

1 reference

10 August 2017

Chia-en A Chang

3

1 reference

PMC publication ID

1877780

10 August 2017

language of work or name

English

0 references

publication date

23 March 2007

1 reference

10 August 2017

1 reference

10 August 2017

92

1 reference

10 August 2017

12

1 reference

10 August 2017

4179-4187

1 reference

The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

"Wide-open" 1.3 A structure of a multidrug-resistant HIV-1 protease as a drug target

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

HIV-1 protease inhibitors: a comparative QSAR analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

New anti-HIV agents and targets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Rational approach to AIDS drug design through structural biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Effect of substrate residues on the P2' preference of retroviral proteinases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Computer simulation of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Closing of the flaps of HIV-1 protease induced by substrate binding: a model of a flap closing mechanism in retroviral aspartic proteases

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Flap opening mechanism of HIV-1 protease

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Interactive essential dynamics

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Flexibility and function in HIV-1 protease

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1877780

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17384072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17384072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17384072

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1529/BIOPHYSJ.106.100560

1 reference

10 August 2017

1 reference

PMC publication ID

1877780

10 August 2017

PubMed publication ID

17384072

1 reference

PMC publication ID

1877780