(Q35073109)

6 August 2017

title

Predictive power of molecular dynamics receptor structures in virtual screening (English)

1 reference

6 August 2017

4

J Andrew McCammon

1 reference

6 August 2017

Sara E Nichols

1

1 reference

6 August 2017

Riccardo Baron

series ordinal

2

1 reference

6 August 2017

Anthony Ivetac

series ordinal

3

1 reference

6 August 2017

publication date

12 May 2011

1 reference

Journal of Chemical Information and Modeling

6 August 2017

published in

1 reference

6 August 2017

volume

51

1 reference

6 August 2017

issue

6

1 reference

6 August 2017

page(s)

1439-1446

1 reference

Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach

6 August 2017

cites work

1 reference

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Virtual screening: an endless staircase?

8 July 2018

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A flexible docking scheme to explore the binding selectivity of PDZ domains

8 July 2018

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An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

8 July 2018

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Recipes for the selection of experimental protein conformations for virtual screening

8 July 2018

1 reference

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Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures

8 July 2018

1 reference

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

8 July 2018

1 reference

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Computational evaluation of protein-small molecule binding.

8 July 2018

1 reference

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In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

8 July 2018

1 reference

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

8 July 2018

1 reference

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Flexible ligand-flexible protein docking in protein kinase systems

8 July 2018

1 reference

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Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system.

8 July 2018

1 reference

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

8 July 2018

1 reference

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Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

8 July 2018

1 reference

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Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?

8 July 2018

1 reference

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Probing molecular docking in a charged model binding site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Screening drug-like compounds by docking to homology models: a systematic study.

8 July 2018

1 reference

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The GROMOS software for biomolecular simulation: GROMOS05.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Docking and scoring in virtual screening for drug discovery: methods and applications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

The many roles of computation in drug discovery

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Protein flexibility and drug design: how to hit a moving target.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124922

Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4

27 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21534609

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Improving database enrichment through ensemble docking

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21534609

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI200117N

1 reference

journals/jcisd/NicholsBIM11

6 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

6 August 2017

1 reference