NDLI: Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.

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Prediction of ligand-binding sites of proteins by molecular docking calculation for a random ligand library.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Fukunishi, Yoshifumi Nakamura, Haruki
Description	Country affiliation: Japan Author Affiliation: Fukunishi Y ( Protein Structural Information Analysis Team, Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan. y-fukunishi@aist.go.jp)
Abstract	A new approach to predicting the ligand-binding sites of proteins was developed, using protein-ligand docking computation. In this method, many compounds in a random library are docked onto the whole protein surface. We assumed that the true ligand-binding site would exhibit stronger affinity to the compounds in the random library than the other sites, even if the random library did not include the ligand corresponding to the true binding site. We also assumed that the affinity of the true ligand-binding site would be correlated to the docking scores of the compounds in the random library, if the ligand-binding site was correctly predicted. We call this method the molecular-docking binding-site finding (MolSite) method. The MolSite method was applied to 89 known protein-ligand complex structures extracted from the Protein Data Bank, and it predicted the correct binding sites with about 80-99% accuracy, when only the single top-ranked site was adopted. In addition, the average docking score was weakly correlated to the experimental protein-ligand binding free energy, with a correlation coefficient of 0.44.
ISSN	09618368
e-ISSN	1469896X
DOI	10.1002/pro.540
Journal	Protein Science
Issue Number	1
Volume Number	20
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2011-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Models, Molecular Proteins Chemistry Small Molecule Libraries Binding Sites Computer Simulation Databases, Protein Ligands Protein Binding Thermodynamics Research Support, Non-u.s. Gov't Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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