(Q24654012)

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Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations

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scholarly article

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Europe PubMed Central

PubMed publication ID

22 June 2017

Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations (English)

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

molecular dynamics simulation

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J. Andrew McCammon

2

object named as

J Andrew McCammon

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

author name string

Anthony Ivetac

1

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Europe PubMed Central

PubMed publication ID

22 June 2017

language of work or name

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publication date

24 March 2009

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Europe PubMed Central

PubMed publication ID

22 June 2017

Journal of Molecular Biology

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Europe PubMed Central

PubMed publication ID

22 June 2017

388

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

3

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

644-658

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

The RNA polymerase "switch region" is a target for inhibitors

1 reference

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7 April 2017

Projections of global mortality and burden of disease from 2002 to 2030

1 reference

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7 April 2017

Binding of the second generation non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding

1 reference

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7 April 2017

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution

1 reference

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7 April 2017

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant

1 reference

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7 April 2017

Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors

1 reference

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7 April 2017

High resolution structures of HIV-1 RT from four RT-inhibitor complexes

1 reference

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7 April 2017

The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1

1 reference

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7 April 2017

GROMACS: fast, flexible, and free

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

VMD: visual molecular dynamics

1 reference

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7 April 2017

The design of drugs for HIV and HCV

1 reference

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7 April 2017

Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

Canonical dynamics: Equilibrium phase-space distributions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

Essential dynamics of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

7 April 2017

Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei

1 reference

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28 September 2017

Rilpivirine, a non-nucleoside reverse transcriptase inhibitor for the treatment of HIV infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Etravirine for the treatment of HIV infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Non-nucleoside reverse transcriptase inhibitors (NNRTIs): past, present, and future

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Mitochondria are sensors for HIV drugs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

HIV reverse transcriptase structures: designing new inhibitors and understanding mechanisms of drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

New non-nucleoside reverse transcriptase inhibitors (NNRTIs) in development for the treatment of HIV infections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Steered molecular dynamics simulation on the binding of NNRTI to HIV-1 RT.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors: past, present, and future perspectives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

1 reference

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28 September 2017

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

1 reference

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28 September 2017

Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies.

1 reference

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28 September 2017

Human immunodeficiency virus reverse transcriptase substrate-induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 September 2017

Protein dynamics derived from clusters of crystal structures

1 reference

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30 May 2018

Strained template under the thumbs. How reverse transcriptase of human immunodeficiency virus type 1 moves along its template

1 reference

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30 May 2018

An efficient method for sampling the essential subspace of proteins.

1 reference

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30 May 2018

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1 reference

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30 May 2018

Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

19 June 2018

Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

28 November 2018

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

1 reference

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28 November 2018

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 V

1 reference

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Twenty years of therapy for HIV-1 infection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2744402

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1 reference

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28 November 2018

Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase

1 reference

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Computational drug design accommodating receptor flexibility: the relaxed complex scheme

1 reference

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1 reference

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28 November 2018

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

1 reference

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28 November 2018

Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates.

1 reference

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1 reference

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1 reference

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New developments in anti-HIV chemotherapy

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19324058

12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19324058

12 December 2020

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Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324058

12 December 2020

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19324058

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19324058

12 December 2020

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LINCS: A linear constraint solver for molecular simulations

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

7 January 2021

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GROMACS 3.0: a package for molecular simulation and trajectory analysis

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

7 January 2021

based on heuristic

inferred from DOI database lookup

GROMACS: A message-passing parallel molecular dynamics implementation

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

7 January 2021

based on heuristic

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Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

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based on heuristic

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The GROMOS Biomolecular Simulation Program Package

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

7 January 2021

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Polymorphic transitions in single crystals: A new molecular dynamics method

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2009.03.037

7 January 2021

based on heuristic

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Molecular dynamics with coupling to an external bath

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1 reference

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A molecular dynamics method for simulations in the canonical ensemble

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Identifiers

10.1016/J.JMB.2009.03.037

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

22 June 2017

ResearchGate publication ID

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