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TarFisDock: a web server for identifying drug targets with docking approach
1 Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203, China 2 Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology Dalian 116023, China 3 School of Pharmacy, East China University of Science and Technology Shanghai 200237, China
*To whom correspondence should be addressed. Tel: +86 21 50807188; Fax: +86 21 50807088; Email: hljiang{at}mail.shcnc.ac.cn
Received January 20, 2006. Revised February 13, 2006. Accepted March 10, 2006.
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 http://www.dddc.ac.cn/tarfisdock/.
Correspondence may also be addressed to Xicheng Wang. Tel: +86 411 84706223; Fax: +86 411 84709390; Email: guixum{at}dlut.edu.cn
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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