MolDock: A new technique for high-accuracy molecular docking
MolDock: A new technique for high-accuracy molecular docking
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DOI：
10.1021/jm051197e
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发表时间：
2006-06-01
影响因子：
7.3
通讯作者：
Christensen, Mikael H.
中科院分区：
文献类型：
--
作者：
Thomsen, Rene;Christensen, Mikael H.
在本文中，我们介绍了一种称为MolDock的分子对接算法。MolDock是基于一种新的启发式搜索算法，该算法结合了差分进化和空腔预测算法。MolDock的对接计分函数是对分段线性电位（PLP）的扩展，包含了新的氢键和静电项。为了进一步提高对接精度，引入了重新排序评分函数，从对接算法得到的解中识别出最有希望的对接解。通过将柔性配体与77个蛋白靶点对接，对MolDock的对接精度进行了评价。MolDock能够识别87%的复合物的正确结合模式。相比之下，Glide和Surflex的准确率分别为82%和75%。FlexX在包含76例和55例的子集中分别获得58%和78%的GOLD。
In this article we introduce a molecular docking algorithm called MolDock. MolDock is based on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithm. The docking scoring function of MolDock is an extension of the piecewise linear potential (PLP) including new hydrogen bonding and electrostatic terms. To further improve docking accuracy, a re-ranking scoring function is introduced, which identifies the most promising docking solution from the solutions obtained by the docking algorithm. The docking accuracy of MolDock has been evaluated by docking flexible ligands to 77 protein targets. MolDock was able to identify the correct binding mode of 87% of the complexes. In comparison, the accuracy of Glide and Surflex is 82% and 75%, respectively. FlexX obtained 58% and GOLD 78% on subsets containing 76 and 55 cases, respectively.