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PDTD: a web-accessible protein database for drug target identification

文献类型：期刊论文

作者Gao, Zhenting1; Li, Honglin1,2; Zhang, Hailei2; Liu, Xiaofeng1; Kang, Ling2; Luo, Xiaomin1; Zhu, Weiliang1; Chen, Kaixian1; Wang, Xicheng2; Jiang, Hualiang1
刊名BMC BIOINFORMATICS
出版日期2008-02-19
卷号9
ISSN号1471-2105
DOI10.1186/1471-2105-9-104
文献子类Article
英文摘要Background: Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository of proteins with three-dimensional (3D) structures. To complete this task, a reverse docking program and a drug target database with 3D structures are necessary. To this end, we have developed a web server tool, TarFisDock (Target Fishing Docking) http://www.dddc.ac.cn/tarfisdock, which has been used widely by others. Recently, we have constructed a protein target database, Potential Drug Target Database (PDTD), and have integrated PDTD with TarFisDock. This combination aims to assist target identification and validation. Description: PDTD is a web-accessible protein database for in silico target identification. It currently contains > 1100 protein entries with 3D structures presented in the Protein Data Bank. The data are extracted from the literatures and several online databases such as TTD, DrugBank and Thomson Pharma. The database covers diverse information of > 830 known or potential drug targets, including protein and active sites structures in both PDB and mol2 formats, related diseases, biological functions as well as associated regulating (signaling) pathways. Each target is categorized by both nosology and biochemical function. PDTD supports keyword search function, such as PDB ID, target name, and disease name. Data set generated by PDTD can be viewed with the plug-in of molecular visualization tools and also can be downloaded freely. Remarkably, PDTD is specially designed for target identification. In conjunction with TarFisDock, PDTD can be used to identify binding proteins for small molecules. The results can be downloaded in the form of mol2 file with the binding pose of the probe compound and a list of potential binding targets according to their ranking scores. Conclusion: PDTD serves as a comprehensive and unique repository of drug targets. Integrated with TarFisDock, PDTD is a useful resource to identify binding proteins for active compounds or existing drugs. Its potential applications include in silico drug target identification, virtual screening, and the discovery of the secondary effects of an old drug (i.e. new pharmacological usage) or an existing target (i.e. new pharmacological or toxic relevance), thus it may be a valuable platform for the pharmaceutical researchers. PDTD is available online at http://www.dddc.ac.cn/pdtd/.
WOS关键词DRUGGABLE GENOME ; OLD DRUGS ; DISCOVERY ; DOCKING ; LIGAND ; RESOURCE ; SITES ; PDB
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
语种英语
WOS记录号WOS:000254011900001
出版者BMC
源URL[http://119.78.100.183/handle/2S10ELR8/272976]  
专题药物发现与设计中心
中科院受体结构与功能重点实验室
新药研究国家重点实验室
通讯作者Li, Honglin
作者单位1.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Drug Discovery & Design Res Ctr, Shanghai 201203, Peoples R China;
2.Dalian Univ Technol, State Key Lab Struct Anal Ind Equipment, Dalian 116023, Peoples R China
推荐引用方式
GB/T 7714		 Gao, Zhenting,Li, Honglin,Zhang, Hailei,et al. PDTD: a web-accessible protein database for drug target identification[J]. BMC BIOINFORMATICS,2008,9.
APA Gao, Zhenting.,Li, Honglin.,Zhang, Hailei.,Liu, Xiaofeng.,Kang, Ling.,...&Jiang, Hualiang.(2008).PDTD: a web-accessible protein database for drug target identification.BMC BIOINFORMATICS,9.
MLA Gao, Zhenting,et al."PDTD: a web-accessible protein database for drug target identification".BMC BIOINFORMATICS 9(2008).

入库方式： OAI收割

来源：上海药物研究所

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