title: TarFisDock: a web server for identifying drug targets with docking approach.
abstract: 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/.
authors.affiliation: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Li
authors.forename: Zhenting
authors.initials: Z
authors.lastname: Gao
authors.forename: Ling
authors.initials: L
authors.lastname: Kang
authors.forename: Hailei
authors.initials: H
authors.lastname: Zhang
authors.forename: Kun
authors.initials: K
authors.lastname: Yang
authors.forename: Kunqian
authors.initials: K
authors.lastname: Yu
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Luo
authors.forename: Weiliang
authors.initials: W
authors.lastname: Zhu
authors.forename: Kaixian
authors.initials: K
authors.lastname: Chen
authors.forename: Jianhua
authors.initials: J
authors.lastname: Shen
authors.forename: Xicheng
authors.initials: X
authors.lastname: Wang
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
mesh_terms: D030562:Databases, Protein; D015195:Drug Design; D020407:Internet; D008024:Ligands; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013629:Tamoxifen / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D014584:User-Computer Interface; D014810:Vitamin E / Q000737:chemistry / Q000378:metabolism
chemical_list: D008024:Ligands; D011506:Proteins; D013629:Tamoxifen; D014810:Vitamin E; C016601:afimoxifene