TarFisDock: a web server for identifying drug targets with docking approach

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 rev...

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Main Authors:	Li, Honglin, Gao, Zhenting, Kang, Ling, Zhang, Hailei, Yang, Kun, Yu, Kunqian, Luo, Xiaomin, Zhu, Weiliang, Chen, Kaixian, Shen, Jianhua, Wang, Xicheng, Jiang, Hualiang
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538869/

id	pubmed-1538869
recordtype	oai_dc
spelling	pubmed-15388692006-08-18 TarFisDock: a web server for identifying drug targets with docking approach Li, Honglin Gao, Zhenting Kang, Ling Zhang, Hailei Yang, Kun Yu, Kunqian Luo, Xiaomin Zhu, Weiliang Chen, Kaixian Shen, Jianhua Wang, Xicheng Jiang, Hualiang Article 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 . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538869/ /pubmed/16844997 http://dx.doi.org/10.1093/nar/gkl114 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Li, Honglin Gao, Zhenting Kang, Ling Zhang, Hailei Yang, Kun Yu, Kunqian Luo, Xiaomin Zhu, Weiliang Chen, Kaixian Shen, Jianhua Wang, Xicheng Jiang, Hualiang
spellingShingle	Li, Honglin Gao, Zhenting Kang, Ling Zhang, Hailei Yang, Kun Yu, Kunqian Luo, Xiaomin Zhu, Weiliang Chen, Kaixian Shen, Jianhua Wang, Xicheng Jiang, Hualiang TarFisDock: a web server for identifying drug targets with docking approach
author_facet	Li, Honglin Gao, Zhenting Kang, Ling Zhang, Hailei Yang, Kun Yu, Kunqian Luo, Xiaomin Zhu, Weiliang Chen, Kaixian Shen, Jianhua Wang, Xicheng Jiang, Hualiang
author_sort	Li, Honglin
title	TarFisDock: a web server for identifying drug targets with docking approach
title_short	TarFisDock: a web server for identifying drug targets with docking approach
title_full	TarFisDock: a web server for identifying drug targets with docking approach
title_fullStr	TarFisDock: a web server for identifying drug targets with docking approach
title_full_unstemmed	TarFisDock: a web server for identifying drug targets with docking approach
title_sort	tarfisdock: a web server for identifying drug targets with docking approach
description	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 .
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538869/
_version_	1611386440390803456

TarFisDock: a web server for identifying drug targets with docking approach

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