FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm
FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm
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DOI：
10.1002/jcc.23108
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发表时间：
2013-01-05
影响因子：
3
通讯作者：
Yang, Yongliang
中科院分区：
文献类型：
--
作者：
Liu, Yu;Zhao, Lei;Yang, Yongliang
蛋白质配体结合的准确预测对于合理的药物设计具有重要意义。我们在此提出了一种称为 FIPSDock 的新颖对接算法，该算法实现了完全知情粒子群 (FIPS) 优化方法的变体，并采用 AutoDock 4.20 套件新开发的能量函数来解决灵活的蛋白质配体对接问题。首先通过多次同源对接实验评估了FIPSDock的搜索能力和对接精度。在对 GOLD 基准集衍生的 77 个蛋白质/配体复合物结构的基准测试中，FIPSDock 获得了 93.5% 的成功预测率，并且优于粒子群优化 (PSO)@AutoDock、SODOCK、AutoDock、DOCK、Glide、GOLD、FlexX、Surflex 和 MolDock 等对接程序。更重要的是，通过对源自 Sutherland-crossdock-set 的 8 个蛋白质靶标（CDK2、ESR1、F2、MAPK14、MMP8、MMP13、PDE4B 和 PDE5A）中的 74 个蛋白质配体复合物进行交叉对接实验，对 FIPSDock 与 PSO@AutoDock、SODOCK 和 AutoDock 4.20 套件进行了评估。值得注意的是，在八个交叉对接实验中的七个中，FIPSDock 优于 PSO@AutoDock、SODOCK 和 AutoDock。结果表明，FIPS 算法可能比传统的基于遗传算法的算法更适合处理高度灵活的对接问题。 (C) 2012 年 Wiley 期刊公司。
The accurate prediction of proteinligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible proteinligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross-docking experiments of 74 proteinligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland-crossdock-set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross-docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm-based algorithms in dealing with highly flexible docking problems. (C) 2012 Wiley Periodicals, Inc.