Please use this identifier to cite or link to this item: https://doi.org/10.1002/1097-0134(20010501)43:23.0.CO;2-G
Title: Ligand - Protein inverse docking and its potential use in the computer search of protein targets of a small molecule
Authors: Chen, Y.Z. 
Zhi, D.G. 
Keywords: Drug target
Flexible docking
Ligand - protein binding
Ligand - protein interaction
Molecular recognition
Protein cavity
Rational drug design
Tamoxifen
Target of drug
Vitamin E
Issue Date: 1-May-2001
Citation: Chen, Y.Z., Zhi, D.G. (2001-05-01). Ligand - Protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins: Structure, Function and Genetics 43 (2) : 217-226. ScholarBank@NUS Repository. https://doi.org/10.1002/1097-0134(20010501)43:23.0.CO;2-G
Abstract: Ligand - protein docking has been developed and used in facilitating new drug discoveries. In this approach, docking single or multiple small molecules to a receptor site is attempted to find putative ligands. A number of studies have shown that docking algorithms are capable of finding ligands and binding conformations at a receptor site close to experimentally determined structures. These algorithms are expected to be equally applicable to the identification of multiple proteins to which a small molecule can bind or weakly bind. We introduce a ligand - protein inverse-docking approach for finding potential protein targets of a small molecule by the computer-automated docking search of a protein cavity database. This database is developed from protein structures in the Protein Data Bank (PDB). Docking is conducted with a procedure involving multiple-conformer shape-matching alignment of a molecule to a cavity followed by molecular-mechanics torsion optimization and energy minimization on both the molecule and the protein residues at the binding region. Scoring is conducted by the evaluation of molecular-mechanics energy and, when applicable, by the further analysis of binding competitiveness against other ligands that bind to the same receptor site in at least one PDB entry. Testing results on two therapeutic agents, 4H-tamoxifen and vitamin E, showed that 50% of the computer-identified potential protein targets were implicated or confirmed by experiments. The application of this approach may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity of a drug or drug candidate. © 2001 Wiley-Liss, Inc.
Source Title: Proteins: Structure, Function and Genetics
URI: http://scholarbank.nus.edu.sg/handle/10635/131437
ISSN: 08873585
DOI: 10.1002/1097-0134(20010501)43:23.0.CO;2-G
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