(Q30355077)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

title

Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

molecular dynamics simulation

28 February 2020

main subject

0 references

author

Kalyan Das

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

2

Eddy Arnold

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

author name string

R S K Vijayan

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

language of work or name

English

0 references

publication date

22 November 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

volume

82

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

page(s)

815-829

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

28 February 2020

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

cites work

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3 June 2018

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3 June 2018

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3 June 2018

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Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase

3 June 2018

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Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase.

3 June 2018

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HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism

3 June 2018

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3 June 2018

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3 June 2018

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Allosteric suppression of HIV-1 reverse transcriptase structural dynamics upon inhibitor binding

3 June 2018

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Cytoscape 2.8: new features for data integration and network visualization

3 June 2018

1 reference

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The N348I mutation at the connection subdomain of HIV-1 reverse transcriptase decreases binding to nevirapine.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Structural basis of HIV-1 resistance to AZT by excision

3 June 2018

1 reference

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N348I in HIV-1 reverse transcriptase can counteract the nevirapine-mediated bias toward RNase H cleavage during plus-strand initiation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

A novel molecular mechanism of dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors.

3 June 2018

1 reference

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Combinations of mutations in the connection domain of human immunodeficiency virus type 1 reverse transcriptase: assessing the impact on nucleoside and nonnucleoside reverse transcriptase inhibitor resistance

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Hidden alternative structures of proline isomerase essential for catalysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Solution structural dynamics of HIV-1 reverse transcriptase heterodimer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Connection domain mutations N348I and A360V in HIV-1 reverse transcriptase enhance resistance to 3'-azido-3'-deoxythymidine through both RNase H-dependent and -independent mechanisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Dynamic binding orientations direct activity of HIV reverse transcriptase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Allostery: absence of a change in shape does not imply that allostery is not at play

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

N348I in the connection domain of HIV-1 reverse transcriptase confers zidovudine and nevirapine resistance

3 June 2018

1 reference

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Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase

3 June 2018

1 reference

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Selection of mutations in the connection and RNase H domains of human immunodeficiency virus type 1 reverse transcriptase that increase resistance to 3'-azido-3'-dideoxythymidine.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.

3 June 2018

1 reference

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Dynamically driven protein allostery.

3 June 2018

1 reference

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Automatic atom type and bond type perception in molecular mechanical calculations

3 June 2018

1 reference

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Oligomeric protein structure networks: insights into protein-protein interactions

3 June 2018

1 reference

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GROMACS: fast, flexible, and free

3 June 2018

1 reference

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A network representation of protein structures: implications for protein stability.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Uncovering the overlapping community structure of complex networks in nature and society

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Is allostery an intrinsic property of all dynamic proteins?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

UCSF Chimera--a visualization system for exploratory research and analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Development and testing of a general amber force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Role of residues in the tryptophan repeat motif for HIV-1 reverse transcriptase dimerization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Nonnucleoside reverse transcriptase inhibitors are chemical enhancers of dimerization of the HIV type 1 reverse transcriptase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Folding funnels and binding mechanisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Identification of side-chain clusters in protein structures by a graph spectral method.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

DNA polymerases: structural diversity and common mechanisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Phenotypic mechanism of HIV-1 resistance to 3'-azido-3'-deoxythymidine (AZT): increased polymerization processivity and enhanced sensitivity to pyrophosphate of the mutant viral reverse transcriptase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Unblocking of chain-terminated primer by HIV-1 reverse transcriptase through a nucleotide-dependent mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Essential dynamics of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Navigating the folding routes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Nevirapine alters the cleavage specificity of ribonuclease H of human immunodeficiency virus 1 reverse transcriptase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Ligand binding and internal equilibiums in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

Human immunodeficiency virus type 1 reverse transcriptase: spatial and temporal relationship between the polymerase and RNase H activities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

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

3 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

A method for the analysis of domain movements in large biomolecular complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Bio3d: an R package for the comparative analysis of protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

A note on two problems in connexion with graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Thermodynamics of HIV-1 reverse transcriptase in action elucidates the mechanism of action of non-nucleoside inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Convergence of sampling in protein simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Local motions in a benchmark of allosteric proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24460

The amino acid Asn136 in HIV-1 reverse transcriptase (RT) maintains efficient association of both RT subunits and enables the rational design of novel RT inhibitors

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502926

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24174331

12 December 2020

inferred from PubMed ID database lookup

High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24174331

12 December 2020

inferred from PubMed ID database lookup

Small-world network approach to identify key residues in protein-protein interaction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24174331

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/PROT.24460

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24174331%20AND%20SRC:MED&resulttype=core&format=json

28 February 2020

1 reference