SODOCK: Swarm optimization for highly flexible protein-ligand docking
SODOCK: Swarm optimization for highly flexible protein-ligand docking
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DOI：
10.1002/jcc.20542
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发表时间：
2007-01-30
影响因子：
3
通讯作者：
Ho, Shinn-Ying
中科院分区：
文献类型：
--
作者：
Chen, Hung-Ming;Liu, Bo-Fu;Ho, Shinn-Ying
蛋白质-配体对接可以被表述为一个参数优化问题，该问题与一个精确的评分函数相关联，其目的是识别与之对接的配体的翻译、取向和构象的能量最低。具有多个可旋转键的高柔性配体的参数优化问题比基于遗传算法（GA）的低柔性配体的参数优化问题更加困难，因为这些配体的参数数量很多，并且这些参数之间具有很高的相关性。提出了一种基于粒子群算法的柔性蛋白质与配体对接优化算法SODOCK。为了提高粒子群算法的效率和鲁棒性，在SODOCK中引入了一种高效的局部搜索策略。SODOCK的实现采用了AutoDock 3.05的环境和能源功能。计算机仿真结果表明，SODOCK算法优于AutoDock的拉马克遗传算法（LGA）。在收敛性能、鲁棒性和获得能量方面，特别适用于高柔性配体。结果还表明，粒子群算法比传统遗传算法更适合于处理参数间高度相关的柔性对接问题。本研究还将SODOCK与GOLD 1.2、DOCK 4.0、FlexX 1.8和AutoDock 3.05的LGA四种最先进的对接方法进行了比较。SODOCK在37例中有19例RMSD最小。SODOCK的37个RMSD值平均为2.29埃，优于其他对接方案，均在3.0埃以上。(C) 2006 Wiley期刊有限公司
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.