The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study. (Q39195267)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27835934%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

title

The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study (English)

1 reference

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Sangeetha Balasubramanian

27 March 2020

author

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27 March 2020

Muthukumaran Rajagopalan

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27 March 2020

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27 March 2020

Anna Marie Skalka

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27 March 2020

Ravi Shankar Bojja

1 reference

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27 March 2020

Mark D Andrake

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27 March 2020

language of work or name

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28 November 2016

1 reference

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Journal of Biomolecular Structure and Dynamics

27 March 2020

published in

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27 March 2020

volume

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27 March 2020

issue

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27 March 2020

page(s)

3469-3485

1 reference

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Crystal structure of the Rous sarcoma virus intasome

27 March 2020

cites work

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The dynamics of interconverting D- and E-forms of the HIV-1 integrase N-terminal domain

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On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study.

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Architecture and assembly of HIV integrase multimers in the absence of DNA substrates

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Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis

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Steered molecular dynamics simulation of the binding of the β2 and β3 regions in domain-swapped human cystatin C dimer

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Structural dynamics of HIV-1 envelope Gp120 outer domain with V3 loop

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Structural dynamics of full-length retroviral integrase: a molecular dynamics analysis.

15 September 2018

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Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines

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Diffusion and association processes in biological systems: theory, computation and experiment

15 September 2018

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Pharmacophore Development and Docking Studies of the HIV‐1 Integrase Inhibitors Derived from N‐methylpyrimidones, Dihydroxypyrimidines, and Bicyclic Pyrimidinones

15 September 2018

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Architecture of a Full-length Retroviral Integrase Monomer and Dimer, Revealed by Small Angle X-ray Scattering and Chemical Cross-linking

15 September 2018

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Design and synthesis of novel N-hydroxy-dihydronaphthyridinones as potent and orally bioavailable HIV-1 integrase inhibitors

15 September 2018

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Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors

15 September 2018

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

15 September 2018

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Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation.

15 September 2018

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Azaindole N-methyl hydroxamic acids as HIV-1 integrase inhibitors-II. The impact of physicochemical properties on ADME and PK

15 September 2018

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Structure-based modeling of the functional HIV-1 intasome and its inhibition

15 September 2018

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Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation

15 September 2018

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15 September 2018

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The impact of viral RNA on the association rates of capsid protein assembly: bacteriophage MS2 as a case study

15 September 2018

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QSAR study of carboxylic acid derivatives as HIV-1 Integrase inhibitors

15 September 2018

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A computational analysis of the binding model of MDM2 with inhibitors

15 September 2018

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The future of antiretroviral therapy: challenges and needs

15 September 2018

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15 September 2018

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15 September 2018

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15 September 2018

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15 September 2018

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15 September 2018

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Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

15 September 2018

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Piecing together the structure of retroviral integrase, an important target in AIDS therapy

15 September 2018

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Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs

15 September 2018

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Characterization and structural analysis of HIV-1 integrase conservation

15 September 2018

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Raltegravir, elvitegravir, and metoogravir: the birth of "me-too" HIV-1 integrase inhibitors

15 September 2018

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Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution

15 September 2018

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Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase inhibitor for the treatment of HIV-AIDS infection

15 September 2018

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Subgroup and resistance analyses of raltegravir for resistant HIV-1 infection

15 September 2018

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Molecular motions of human HIV-1 gp120 envelope glycoproteins

15 September 2018

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Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.

15 September 2018

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Structure-based maximal affinity model predicts small-molecule druggability.

15 September 2018

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Calculation of protein-ligand binding affinities.

15 September 2018

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

15 September 2018

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Relationship between the oligomeric status of HIV-1 integrase on DNA and enzymatic activity

15 September 2018

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Retroviral DNA integration: reaction pathway and critical intermediates

15 September 2018

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

15 September 2018

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Diffusional encounter of barnase and barstar

15 September 2018

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A three-dimensional model of the human immunodeficiency virus type 1 integration complex

15 September 2018

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Processing of viral DNA ends channels the HIV-1 integration reaction to concerted integration.

15 September 2018

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15 September 2018

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Modeling HIV-1 integrase complexes based on their hydrodynamic properties

15 September 2018

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Functional oligomeric state of avian sarcoma virus integrase

15 September 2018

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Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein

15 September 2018

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Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding

15 September 2018

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Electrostatics of nanosystems: application to microtubules and the ribosome

15 September 2018

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Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain

15 September 2018

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Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding

15 September 2018

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Calculation of hydrodynamic properties of globular proteins from their atomic-level structure

15 September 2018

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Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design

15 September 2018

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Refined solution structure of the C-terminal DNA-binding domain of human immunovirus-1 integrase

15 September 2018

1 reference

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Structural principles governing domain motions in proteins

15 September 2018

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Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin

15 September 2018

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Molecular dynamics studies on the HIV-1 integrase catalytic domain

15 September 2018

1 reference

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Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium

15 September 2018

1 reference

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Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar.

15 September 2018

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Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex

15 September 2018

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Brownian dynamics simulation of protein-protein diffusional encounter

15 September 2018

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Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme

15 September 2018

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Solution structure of the N-terminal zinc binding domain of HIV-1 integrase

15 September 2018

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The kinetics of protein-protein recognition.

15 September 2018

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Simulation of the diffusional association of barnase and barstar.

15 September 2018

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Identification of discrete functional domains of HIV-1 integrase and their organization within an active multimeric complex

15 September 2018

1 reference

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Rous sarcoma virus integrase protein: mapping functions for catalysis and substrate binding

15 September 2018

1 reference

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Solution structure of the DNA binding domain of HIV-1 integrase

15 September 2018

1 reference

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The DNA-binding domain of HIV-1 integrase has an SH3-like fold

15 September 2018

1 reference

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The biophysics of ligand-receptor interactions

15 September 2018

1 reference

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Integration of mini-retroviral DNA: a cell-free reaction for biochemical analysis of retroviral integration

15 September 2018

1 reference

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Sequence requirements for integration of Moloney murine leukemia virus DNA in vitro

15 September 2018

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Retroviral DNA integration directed by HIV integration protein in vitro

15 September 2018

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The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro.

15 September 2018

1 reference

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Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity

15 September 2018

1 reference

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Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA

15 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5570655

Genetics of retroviral integration

15 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5570655

Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro

15 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5570655

Retroviral integrase functions as a multimer and can turn over catalytically

15 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5570655

Comparison of simple potential functions for simulating liquid water

15 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1080%2F07391102.2016.1257955

An essential interaction between distinct domains of HIV-1 integrase mediates assembly of the active multimer

21 January 2018

1 reference

12 December 2020

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective

1 reference

12 December 2020

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

1 reference

12 December 2020

Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding

1 reference

12 December 2020

Anti-infectives: clinical progress of HIV-1 integrase inhibitors

1 reference

12 December 2020

HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer

1 reference

12 December 2020

Molecular dynamic simulation of mGluR5 amino terminal domain: essential dynamics analysis captures the agonist or antagonist behaviour of ligands

1 reference

12 December 2020

10.1080/07391102.2016.1257955

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27835934%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27835934%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

PubMed publication ID

27835934

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27835934%20AND%20SRC:MED&resulttype=core&format=json