(Q34065423)

30 July 2017

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

1 reference

30 July 2017

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Daniel N Santiago

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

author name string

Nanjie Deng

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Peng He

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Lauren Wickstrom

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Alexander L Perryman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Stefano Forli

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Arthur J Olson

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Ronald M Levy

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

language of work or name

1 reference

7 February 2014

1 reference

Journal of Computer - Aided Molecular Design

30 July 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

volume

28

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

page(s)

475-490

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1007/s10822-014-9711-9

4 June 2020

exact match

0 references

cites work

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Blind prediction of HIV integrase binding from the SAMPL4 challenge

28 July 2018

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Interrogating HIV integrase for compounds that bind- a SAMPL challenge

28 July 2018

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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

28 July 2018

1 reference

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Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4.

28 July 2018

1 reference

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Allosteric inhibition of HIV-1 integrase activity

28 July 2018

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

28 July 2018

1 reference

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

28 July 2018

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Perspective: Alchemical free energy calculations for drug discovery

28 July 2018

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

28 July 2018

1 reference

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Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase

28 July 2018

1 reference

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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

28 July 2018

1 reference

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Theory of binless multi-state free energy estimation with applications to protein-ligand binding

28 July 2018

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Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

28 July 2018

1 reference

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Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

28 July 2018

1 reference

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Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

28 July 2018

1 reference

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On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

28 July 2018

1 reference

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Recent theoretical and computational advances for modeling protein-ligand binding affinities

28 July 2018

1 reference

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Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy

28 July 2018

1 reference

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Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies

28 July 2018

1 reference

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Virtual Screening with AutoDock: Theory and Practice

28 July 2018

1 reference

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Alchemical free energy methods for drug discovery: progress and challenges

28 July 2018

1 reference

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Advances in all atom sampling methods for modeling protein-ligand binding affinities

28 July 2018

1 reference

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

28 July 2018

1 reference

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Improved side-chain torsion potentials for the Amber ff99SB protein force field

28 July 2018

1 reference

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A dynamic model of HIV integrase inhibition and drug resistance

28 July 2018

1 reference

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Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting

28 July 2018

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Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the d

28 July 2018

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Theory of free energy and entropy in noncovalent binding

28 July 2018

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

28 July 2018

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Computations of standard binding free energies with molecular dynamics simulations

28 July 2018

1 reference

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Statistically optimal analysis of samples from multiple equilibrium states

28 July 2018

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

28 July 2018

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

28 July 2018

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Integrated Modeling Program, Applied Chemical Theory (IMPACT)

28 July 2018

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The many roles of computation in drug discovery

28 July 2018

1 reference

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Lead discovery using molecular docking

28 July 2018

1 reference

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The statistical-thermodynamic basis for computation of binding affinities: a critical review

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4137862

Automated docking of flexible ligands: applications of AutoDock

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4137862

Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets

28 July 2018

1 reference

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Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

Let's get honest about sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase.

21 January 2018

1 reference

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In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes

21 January 2018

1 reference

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Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

Ligand configurational entropy and protein binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

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

21 January 2018

1 reference

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The AGBNP2 Implicit Solvation Model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

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Temperature weighted histogram analysis method, replica exchange, and transition paths.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS10822-014-9711-9

High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing.

21 January 2018

1 reference

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

21 January 2018

1 reference

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10.1007/S10822-014-9711-9

28 October 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

journals/jcamd/GallicchioDHWPSFOL14

4 June 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24504704%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

1 reference