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An automated ligand evolution system using Bayesian optimization algorithm

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Title: An automated ligand evolution system using Bayesian optimization algorithm
Authors: Munetomo, Masaharu Browse this author →KAKEN DB
Akama, Kiyoshi Browse this author
Maeda, Haruki Browse this author
Keywords: automated drug design
ligand docking
de novo ligand design approach
probabilistic model-building genetic algorithms
estimation of distribution of algorithms
Bayesian optimization algorithms
Issue Date: May-2009
Publisher: World Scientific and Engineering Academy and Society
Journal Title: WSEAS Transactions on Information Science and Applications
Volume: 6
Issue: 5
Start Page: 788
End Page: 797
Abstract: Ligand docking checks whether a drug chemical called ligand matches the target receptor protein of human organ or not. Docking by computer simulation is becoming popular in drug design process to reduce cost and time of the chemical experiments. This paper presents a novel approach generating optimal ligand structures from scratch based on de novo ligand design approach employing Bayesian optimization algorithm to realize an automated design of drug and other chemical structures. The proposed approach searches an optimal structure of ligand that minimizes bond energy to the receptor protein, and the structure of ligand is generated by adding small fragments of molecules to the base structure. The decision of adding fragments are controlled by Bayesian optimization algorithm which is considered as a promising approach in probabilistic model-building genetic algorithms. We have built a system that automatically generates an optimal structure of ligand, and through numerical experiments performed on a PC cluster, we show the effectiveness of our approach compared to the conventional approach using classical genetic algorithms.
Rights: ©World Scientific and Engineering Academy and Society
Type: article (author version)
Appears in Collections:情報基盤センター (Information Initiative Center) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 棟朝 雅晴

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