PARTICLE SWARM OPTIMIZATION ON FLEXIBLE DOCKING  

作　　者：YU LIU WENTAO LI RUIXIN MA 

机构地区：[1]School of Software, Dalian University of Technology Dalian 116024, P. R. China

出　　处：《International Journal of Biomathematics》2012年第5期187-201,共15页生物数学学报（英文版）

基　　金：This work was under Grand by the Natural Science Foundation of China （No. 60803074）, and the Fundamental Research Funds for the Central Universi- ties （No. DUT10JR06）.

摘　　要：Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molec- ular docking problem is how to locate a good conformation to dock a ligand to the large molecule. It can be formulated as a parameter optimization problem consisting of a scoring function and a global optimization method. Many docking methods have been developed with primarily these two parts varying. In this paper, a variety of particle swarm optimization （PSO） variants were introduced to cooperate with the semiempir- ical free energy force field in AutoDock 4.05. The search ability and the docking accu- racy of these methods were evaluated by multiple redocking experiments. The results demonstrate that PSOs were more suitable than Lamarckian genetic algorithm （LGA）. Among all of the PSO variants, FIPS takes precedence over others. Compared with the four state-of-art docking methods-GOLD, DOCK, FlexX and AutoDock with LGA, AutoDock cooperated with FIPS is more accurate. Thus, FIPS is an efficient PSO vari- ant which has promising prospects that can be expected in the application to virtual screening.

关 键 词：AUTODOCK particle swarm optimization molecular docking. 

分 类 号：Q510.1[生物学—生物化学] TP301.6[自动化与计算机技术—计算机系统结构]