標題: SODOCK: Swarm optimization for highly flexible protein-ligand docking
作者: Chen, Hung-Ming
Liu, Bo-Fu
Huang, Hui-Ling
Hwang, Shiow-Fen
Ho, Shinn-Ying
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
關鍵字: flexible docking;scoring function;genetic algorithm;particle swarm optimization;local search
公開日期: 30-一月-2007
摘要: Protein-ligand docking can be formulated as a parameter optimization problem associated with an accurate scoring function, which aims to identify the translation, orientation, and conformation of a docked ligand with the lowest energy. The parameter optimization problem for highly flexible ligands with many rotatable bonds is more difficult than that for less flexible ligands using genetic algorithm (GA)-based approaches, due to the large numbers of parameters and high correlations among these parameters. This investigation presents a novel optimization algorithm SODOCK based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. To improve efficiency and robustness of PSO, an efficient local search strategy is incorporated into SODOCK. The implementation of SODOCK adopts the environment and energy function of AutoDock 3.05. Computer simulation results reveal that SODOCK is superior to the Lamarckian genetic algorithm (LGA) of AutoDock. in terms of convergence performance, robustness, and obtained energy, especially for highly flexible ligands. The results also reveal that PSO is more suitable than the conventional GA in dealing with flexible docking problems with high correlations among parameters. This investigation also compared SODOCK with four state-of-the-art docking methods, namely GOLD 1.2, DOCK 4.0, FlexX 1.8, and LGA of AutoDock 3.05. SODOCK obtained the smallest RMSD in 19 of 37 cases. The average 2.29 angstrom of the 37 RMSD values of SODOCK was better than those of other docking programs, which were all above 3.0 angstrom. (C) 2006 Wiley Periodicals, Inc.
URI: http://dx.doi.org/10.1002/jcc.20542
http://hdl.handle.net/11536/11214
ISSN: 0192-8651
DOI: 10.1002/jcc.20542
期刊: JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume: 28
Issue: 2
起始頁: 612
結束頁: 623
顯示於類別:期刊論文


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