TarFisDock: a web server for identifying drug targets with docking approach.
TarFisDock: a web server for identifying drug targets with docking approach.
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TarFisDock：通过对接方法识别药物靶标的网络服务器
DOI：
10.1093/nar/gkl114
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发表时间：
2006-07-01
影响因子：
14.9
通讯作者：
Jiang H
中科院分区：
文献类型：
--
作者：
Li H;Gao Z;Kang L;Zhang H;Yang K;Yu K;Luo X;Zhu W;Chen K;Shen J;Wang X;Jiang H
TarFisDock是一个基于网络的工具，用于在大量蛋白质结构中自动搜索小分子-蛋白质相互作用的过程。它提供PDTD（潜在药物靶标数据库），一个包含698个蛋白质结构的靶标数据库，涵盖15个治疗领域和一个反向配体-蛋白质对接程序。与传统的配体-蛋白质对接相比，反向配体-蛋白质对接旨在通过筛选合适的蛋白质数据库来寻找潜在的蛋白质靶点。这个web服务器的输入文件是要测试的小分子，是标准的mol2格式；然后，TarFisDock通过对接方法为给定的小分子寻找可能的结合蛋白。采用DOCK程序中的配体-蛋白质相互作用能项对蛋白质进行排序。为了检验TarFisDock服务器的可靠性，我们在PDTD中搜索维生素E和4h -他莫昔芬的推定结合蛋白。TarFisDock鉴定出的维生素E结合蛋白的前2位和前10%候选蛋白分别覆盖了实验证实或涉及的已报道靶点的30%和50%；实验证实的4h -他莫昔芬靶点中，30%和50%分别出现在TarFisDock预测候选药物的前2%和5%之中。因此，TarFisDock可能是一个有用的工具，用于靶标鉴定、旧药物的机制研究和从天然产物中发现的探针。TarFisDock及PDTD可于
TarFisDock is a web-based tool for automating the procedure of searching for small molecule–protein interactions over a large repertoire of protein structures. It offers PDTD (potential drug target database), a target database containing 698 protein structures covering 15 therapeutic areas and a reverse ligand–protein docking program. In contrast to conventional ligand–protein docking, reverse ligand–protein docking aims to seek potential protein targets by screening an appropriate protein database. The input file of this web server is the small molecule to be tested, in standard mol2 format; TarFisDock then searches for possible binding proteins for the given small molecule by use of a docking approach. The ligand–protein interaction energy terms of the program DOCK are adopted for ranking the proteins. To test the reliability of the TarFisDock server, we searched the PDTD for putative binding proteins for vitamin E and 4H-tamoxifen. The top 2 and 10% candidates of vitamin E binding proteins identified by TarFisDock respectively cover 30 and 50% of reported targets verified or implicated by experiments; and 30 and 50% of experimentally confirmed targets for 4H-tamoxifen appear amongst the top 2 and 5% of the TarFisDock predicted candidates, respectively. Therefore, TarFisDock may be a useful tool for target identification, mechanism study of old drugs and probes discovered from natural products. TarFisDock and PDTD are available at .