(Q40578605)

English

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

scientific article published on 4 February 2014

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scholarly article

1 reference

Europe PubMed Central

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7 March 2020

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge (English)

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24493410%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

based on heuristic

inferred from title

virtual screening

1 reference

based on heuristic

inferred from title

Daniel N Santiago

2

1 reference

Europe PubMed Central

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7 March 2020

Diogo Santos Martins

4

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7 March 2020

author name string

Alexander L Perryman

1

1 reference

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7 March 2020

Stefano Forli

3

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7 March 2020

Arthur J Olson

5

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7 March 2020

publication date

4 February 2014

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7 March 2020

Journal of Computer - Aided Molecular Design

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7 March 2020

28

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7 March 2020

4

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7 March 2020

429-441

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7 March 2020

https://scigraph.springernature.com/pub.10.1007/s10822-014-9709-3

0 references

Blind prediction of HIV integrase binding from the SAMPL4 challenge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Allosteric integrase inhibitor potency is determined through the inhibition of HIV-1 particle maturation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Small-molecule inhibitors of the LEDGF/p75 binding site of integrase block HIV replication and modulate integrase multimerization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

New Class of HIV-1 Integrase (IN) Inhibitors with a Dual Mode of Action

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Multimode, Cooperative Mechanism of Action of Allosteric HIV-1 Integrase Inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Predictive power of molecular dynamics receptor structures in virtual screening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Fragment-Based Screen against HIV Protease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

A dynamic model of HIV integrase inhibition and drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

MolProbity: all-atom structure validation for macromolecular crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Python: a programming language for software integration and development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

22 September 2017

Reduced HIV-1 integrase flexibility as a mechanism for raltegravir resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

15 June 2018

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

20 August 2018

Active site binding modes of curcumin in HIV-1 protease and integrase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

20 August 2018

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

20 August 2018

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4053500

20 August 2018

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9709-3

21 January 2018

Identifiers

10.1007/S10822-014-9709-3

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24493410%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

DBLP publication ID

journals/jcamd/PerrymanSFSO14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24493410%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24493410%20AND%20SRC:MED&resulttype=core&format=json

7 March 2020

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