(Q34680415)

3 August 2017

title

Docking validation resources: protein family and ligand flexibility experiments (English)

1 reference

3 August 2017

1 reference

Sudipto Mukherjee

1

1 reference

3 August 2017

Trent E Balius

series ordinal

2

1 reference

3 August 2017

Robert C Rizzo

series ordinal

3

1 reference

3 August 2017

publication date

29 October 2010

1 reference

Journal of Chemical Information and Modeling

3 August 2017

published in

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3 August 2017

volume

50

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3 August 2017

issue

11

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3 August 2017

page(s)

1986-2000

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Automated docking screens: a feasibility study

3 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

DOCK 6: combining techniques to model RNA-small molecule complexes

7 July 2018

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Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

7 July 2018

1 reference

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Recommendations for evaluation of computational methods

7 July 2018

1 reference

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Community benchmarks for virtual screening

7 July 2018

1 reference

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

7 July 2018

1 reference

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Bias, reporting, and sharing: computational evaluations of docking methods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Development and validation of a modular, extensible docking program: DOCK 5.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.

7 July 2018

1 reference

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Virtual ligand screening: strategies, perspectives and limitations

7 July 2018

1 reference

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Novel procedure for modeling ligand/receptor induced fit effects.

7 July 2018

1 reference

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The Amber biomolecular simulation programs

7 July 2018

1 reference

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The PDBbind database: methodologies and updates

7 July 2018

1 reference

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Virtual screening of chemical libraries

7 July 2018

1 reference

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Soft docking and multiple receptor conformations in virtual screening

7 July 2018

1 reference

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

7 July 2018

1 reference

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The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Development and testing of a general amber force field

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

The many roles of computation in drug discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Improved protein-ligand docking using GOLD

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Gaussian docking functions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Ligand-protein database: linking protein-ligand complex structures to binding data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

7 July 2018

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=3058392

Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Molecular docking to ensembles of protein structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Automated docking of flexible ligands: applications of AutoDock

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Rational design of potent sialidase-based inhibitors of influenza virus replication

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Flexibases: a way to enhance the use of molecular docking methods

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

A geometric approach to macromolecule-ligand interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Structure-based strategies for drug design and discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Diverse, high-quality test set for the validation of protein-ligand docking performance.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Protein flexibility in ligand docking and virtual screening to protein kinases.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058392

Binding MOAD (Mother Of All Databases)

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21033739

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI1001982

1 reference

journals/jcisd/MukherjeeBR10

3 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 August 2017

1 reference