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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| Veröffentlicht in: | Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W219-W224 |
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| container_title | Nucleic acids research |
| container_volume | 34 |
| creator | Li, Honglin Gao, Zhenting Kang, Ling Zhang, Hailei Yang, Kun Yu, Kunqian Luo, Xiaomin Zhu, Weiliang Chen, Kaixian Shen, Jianhua Wang, Xicheng Jiang, Hualiang |
| 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 http://www.dddc.ac.cn/tarfisdock/. |
| doi_str_mv | 10.1093/nar/gkl114 |
| format | Article |
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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/.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkl114</identifier><identifier>PMID: 16844997</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Databases, Protein ; Drug Design ; Internet ; Ligands ; Proteins - chemistry ; Proteins - metabolism ; Software ; Tamoxifen - analogs & derivatives ; Tamoxifen - chemistry ; Tamoxifen - metabolism ; User-Computer Interface ; Vitamin E - chemistry ; Vitamin E - metabolism</subject><ispartof>Nucleic acids research, 2006-07, Vol.34 (suppl-2), p.W219-W224</ispartof><rights>Copyright Oxford University Press(England) 2006</rights><rights>The Author 2006. Published by Oxford University Press. All rights reserved The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org</rights><rights>The Author 2006. Published by Oxford University Press. All rights reserved 2006</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c530t-476cdc6afd590eb037c16a8664eddd776d565c21c6a26b8b4bbdc439f4f8be173</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538869/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538869/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16844997$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Honglin</creatorcontrib><creatorcontrib>Gao, Zhenting</creatorcontrib><creatorcontrib>Kang, Ling</creatorcontrib><creatorcontrib>Zhang, Hailei</creatorcontrib><creatorcontrib>Yang, Kun</creatorcontrib><creatorcontrib>Yu, Kunqian</creatorcontrib><creatorcontrib>Luo, Xiaomin</creatorcontrib><creatorcontrib>Zhu, Weiliang</creatorcontrib><creatorcontrib>Chen, Kaixian</creatorcontrib><creatorcontrib>Shen, Jianhua</creatorcontrib><creatorcontrib>Wang, Xicheng</creatorcontrib><creatorcontrib>Jiang, Hualiang</creatorcontrib><title>TarFisDock: a web server for identifying drug targets with docking approach</title><title>Nucleic acids research</title><addtitle>Nucl. Acids Res</addtitle><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 http://www.dddc.ac.cn/tarfisdock/.</description><subject>Databases, Protein</subject><subject>Drug Design</subject><subject>Internet</subject><subject>Ligands</subject><subject>Proteins - chemistry</subject><subject>Proteins - metabolism</subject><subject>Software</subject><subject>Tamoxifen - analogs & derivatives</subject><subject>Tamoxifen - chemistry</subject><subject>Tamoxifen - metabolism</subject><subject>User-Computer Interface</subject><subject>Vitamin E - chemistry</subject><subject>Vitamin E - metabolism</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtrFEEUhQtRzBjd-AOkcZGF0KbeDxdCiGYSjIRABMmmqK6q7qlMT9dY1Z2Yf28NM8ToJqu7ON893HsOAG8R_IigIoeDSYfdskeIPgMzRDiuqeL4OZhBAlmNIJV74FXONxAiihh9CfYQl5QqJWbg25VJJyF_iXb5qTLVnW-q7NOtT1UbUxWcH8bQ3oehq1yaumo0qfNjru7CuKhcWdooZr1O0djFa_CiNX32b3ZzH_w4-Xp1fFqfX8zPjo_Oa8sIHGsquHWWm9YxBX0DibCIG8k59c45IbhjnFmMCoJ5IxvaNM5SolraysYjQfbB563vempW3tlyYzK9XqewMuleRxP0v8oQFrqLtxoxIiVXxeBgZ5Dir8nnUa9Ctr7vzeDjlDVGmDAKyZMgUoQriXEB3_8H3sQpDSUFjSHkiDHJnoSwkJvnPmwhm2LOybcPfyGoN3XrUrfe1l3gd4-T-Ivu-i1AvQVCHv3vB92kpeaCCKZPf17r6_n8O1P0UnPyB0aEtiE</recordid><startdate>20060701</startdate><enddate>20060701</enddate><creator>Li, Honglin</creator><creator>Gao, Zhenting</creator><creator>Kang, Ling</creator><creator>Zhang, Hailei</creator><creator>Yang, Kun</creator><creator>Yu, Kunqian</creator><creator>Luo, Xiaomin</creator><creator>Zhu, Weiliang</creator><creator>Chen, Kaixian</creator><creator>Shen, Jianhua</creator><creator>Wang, Xicheng</creator><creator>Jiang, Hualiang</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20060701</creationdate><title>TarFisDock: a web server for identifying drug targets with docking approach</title><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</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c530t-476cdc6afd590eb037c16a8664eddd776d565c21c6a26b8b4bbdc439f4f8be173</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Databases, Protein</topic><topic>Drug Design</topic><topic>Internet</topic><topic>Ligands</topic><topic>Proteins - chemistry</topic><topic>Proteins - metabolism</topic><topic>Software</topic><topic>Tamoxifen - analogs & derivatives</topic><topic>Tamoxifen - chemistry</topic><topic>Tamoxifen - metabolism</topic><topic>User-Computer Interface</topic><topic>Vitamin E - chemistry</topic><topic>Vitamin E - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Honglin</creatorcontrib><creatorcontrib>Gao, Zhenting</creatorcontrib><creatorcontrib>Kang, Ling</creatorcontrib><creatorcontrib>Zhang, Hailei</creatorcontrib><creatorcontrib>Yang, Kun</creatorcontrib><creatorcontrib>Yu, Kunqian</creatorcontrib><creatorcontrib>Luo, Xiaomin</creatorcontrib><creatorcontrib>Zhu, Weiliang</creatorcontrib><creatorcontrib>Chen, Kaixian</creatorcontrib><creatorcontrib>Shen, Jianhua</creatorcontrib><creatorcontrib>Wang, Xicheng</creatorcontrib><creatorcontrib>Jiang, Hualiang</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Honglin</au><au>Gao, Zhenting</au><au>Kang, Ling</au><au>Zhang, Hailei</au><au>Yang, Kun</au><au>Yu, Kunqian</au><au>Luo, Xiaomin</au><au>Zhu, Weiliang</au><au>Chen, Kaixian</au><au>Shen, Jianhua</au><au>Wang, Xicheng</au><au>Jiang, Hualiang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>TarFisDock: a web server for identifying drug targets with docking approach</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucl. Acids Res</addtitle><date>2006-07-01</date><risdate>2006</risdate><volume>34</volume><issue>suppl-2</issue><spage>W219</spage><epage>W224</epage><pages>W219-W224</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><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/.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>16844997</pmid><doi>10.1093/nar/gkl114</doi><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Databases, Protein Drug Design Internet Ligands Proteins - chemistry Proteins - metabolism Software Tamoxifen - analogs & derivatives Tamoxifen - chemistry Tamoxifen - metabolism User-Computer Interface Vitamin E - chemistry Vitamin E - metabolism |
| title | TarFisDock: a web server for identifying drug targets with docking approach |
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