(Q33743244)

29 July 2017

title

Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library (English)

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29 July 2017

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2

Haruki Nakamura

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29 July 2017

Yoshifumi Fukunishi

1

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29 July 2017

publication date

1 January 2011

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29 July 2017

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29 July 2017

volume

20

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29 July 2017

issue

1

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29 July 2017

page(s)

95-106

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Protein pockets: inventory, shape, and comparison

29 July 2017

cites work

1 reference

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A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

21 June 2018

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Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

21 June 2018

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The flexible pocketome engine for structural chemogenomics

21 June 2018

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Comprehensive structural classification of ligand-binding motifs in proteins

21 June 2018

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Beyond picomolar affinities: quantitative aspects of noncovalent and covalent binding of drugs to proteins

21 June 2018

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Two 'Golden Ratio' indices in fragment-based drug discovery

21 June 2018

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Fast dynamics perturbation analysis for prediction of protein functional sites

21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites.

21 June 2018

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Shape variation in protein binding pockets and their ligands

21 June 2018

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A critical assessment of docking programs and scoring functions

21 June 2018

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LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

21 June 2018

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A computational method for the analysis and prediction of protein:phosphopeptide-binding sites.

21 June 2018

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Evolutionary predictions of binding surfaces and interactions.

21 June 2018

1 reference

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Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047065

Development and validation of a genetic algorithm for flexible docking

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047065

Protein clefts in molecular recognition and function

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047065

The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.

21 June 2018

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SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047065

A geometric approach to macromolecule-ligand interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3047065

MetaPocket: a meta approach to improve protein ligand binding site prediction.

21 June 2018

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Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

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Automated prediction of ligand-binding sites in proteins

21 January 2018

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

21 January 2018

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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

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Pocket extraction on proteins via the Voronoi diagram of spheres.

21 January 2018

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A method for localizing ligand binding pockets in protein structures

21 January 2018

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Detection of multiscale pockets on protein surfaces using mathematical morphology.

21 January 2018

1 reference

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

21 January 2018

1 reference

Ligand efficiency indices as guideposts for drug discovery.

21 January 2018

1 reference

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

Flexible docking using Tabu search and an empirical estimate of binding affinity.

21 January 2018

1 reference

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

21 January 2018

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Structure-based identification of small molecule binding sites using a free energy model

21 January 2018

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12 December 2020

Use of amino acid composition to predict ligand-binding sites

1 reference

12 December 2020

Multiple target screening method for robust and accurate in silico ligand screening

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12 December 2020

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12 December 2020

Identifiers

DOI

10.1002/PRO.540

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29 July 2017

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29 July 2017

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