Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex
Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex
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DOI：
10.1021/jm050262h
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发表时间：
2005-09-22
影响因子：
7.3
通讯作者：
Villoutreix, BO
中科院分区：
文献类型：
--
作者：
Miteva, MA;Lee, WH;Villoutreix, BO
设计了一种方案，其中FRED、DOCK和Surflex在多步虚拟配体筛选（VLS）程序中组合以筛选四种不同蛋白质的口袋。一个目标是评估链接“免费提供的软件包，以学术用户”对接/评分的准确性和CPU时间消耗的影响。产生了包括49种已知活性物质的65660种化合物的库。我们的程序是成功的，因为对接/评分参数根据结合口袋的性质进行调整，因为基于形状的过滤工具应用之前，灵活的对接。所获得的富集因子与最近研究中报道的富集因子一致。我们认为，共识对接/评分可能是有价值的一些药物发现项目。目前的方案可以在一个处理器上在不到一周的时间内处理整个受体库，这表明即使没有大型计算机资源也可以进行VLS实验。
A protocol was devised in which FRED, DOCK, and Surflex were combined in a multistep virtual ligand screening (VLS) procedure to screen the pocket of four different proteins. One goal was to evaluate the impact of chaining "freely available packages to academic users" on docking/scoring accuracy and CPU time consumption. A bank of 65 660 compounds including 49 known actives was generated. Our procedure is successful because docking/scoring parameters are tuned according to the nature of the binding pocket and because a shape-based filtering tool is applied prior to flexible docking. The obtained enrichment factors are in line with those reported in recent studies. We suggest that consensus docking/scoring could be valuable to some drug discovery projects. The present protocol could process the entire bank for one receptor in less than a week on one processor, suggesting that VLS experiments could be performed even without large computer resources.