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PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach

文献类型：期刊论文

作者Liu, Xiaofeng3,4,5; Ouyang, Sisheng3; Yu, Biao2; Liu, Yabo2; Huang, Kai2; Gong, Jiayu2; Zheng, Siyuan1; Li, Zhihua2; Li, Honglin2,4,5; Jiang, Hualiang3,4,5
刊名NUCLEIC ACIDS RESEARCH
出版日期2010-07
卷号38页码:W609-W614
ISSN号0305-1048
DOI10.1093/nar/gkq300
文献子类Article
英文摘要In silico drug target identification, which includes many distinct algorithms for finding disease genes and proteins, is the first step in the drug discovery pipeline. When the 3D structures of the targets are available, the problem of target identification is usually converted to finding the best interaction mode between the potential target candidates and small molecule probes. Pharmacophore, which is the spatial arrangement of features essential for a molecule to interact with a specific target receptor, is an alternative method for achieving this goal apart from molecular docking method. PharmMapper server is a freely accessed web server designed to identify potential target candidates for the given small molecules (drugs, natural products or other newly discovered compounds with unidentified binding targets) using pharmacophore mapping approach. PharmMapper hosts a large, in-house repertoire of pharmacophore database (namely PharmTargetDB) annotated from all the targets information in TargetBank, BindingDB, DrugBank and potential drug target database, including over 7000 receptor-based pharmacophore models (covering over 1500 drug targets information). PharmMapper automatically finds the best mapping poses of the query molecule against all the pharmacophore models in PharmTargetDB and lists the top N best-fitted hits with appropriate target annotations, as well as respective molecule's aligned poses are presented. Benefited from the highly efficient and robust triangle hashing mapping method, PharmMapper bears high throughput ability and only costs 1 h averagely to screen the whole PharmTargetDB. The protocol was successful in finding the proper targets among the top 300 pharmacophore candidates in the retrospective benchmarking test of tamoxifen. PharmMapper is available at http://59.78.96.61/pharmmapper.
WOS关键词BREAST-CANCER ; BINDING AFFINITIES ; TAMOXIFEN ; DATABASE ; CHEMOGENOMICS ; INHIBITION ; EXPRESSION ; PREDICTION ; DISCOVERY ; FAMILIES
资助项目Major State Basic Research[2009CB918501] ; Major State Basic Research[2009CB918502] ; National Natural Science Foundation of China[20803022] ; National Natural Science Foundation of China[20721003] ; Shanghai Committee of Science and Technology[09dZ1975700] ; Shanghai Committee of Science and Technology[08JC1407800] ; 863 Hi-Tech Program of China[2007AA02Z304] ; 863 Hi-Tech Program of China[2007AA02Z330] ; Major National Scientific and Technological Project of China[2009ZX09501-001] ; Major National Scientific and Technological Project of China[2009ZX09301-001] ; Shanghai Rising-Star Program[10QA1401800] ; 111 Project[B07023]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:000284148900098
出版者OXFORD UNIV PRESS
源URL[http://119.78.100.183/handle/2S10ELR8/278864]  
专题药物发现与设计中心
通讯作者Li, Honglin
作者单位1.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Bioinformat Ctr, Shanghai 200031, Peoples R China
2.E China Univ Sci & Technol, Sch Informat Sci & Engn, Shanghai 200237, Peoples R China;
3.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, Shanghai 201203, Peoples R China;
4.E China Univ Sci & Technol, Sch Pharm, Shanghai Key Lab Chem Biol, Shanghai 200237, Peoples R China;
5.E China Univ Sci & Technol, Sch Pharm, State Key Lab Bioreactor Engn, Shanghai 200237, Peoples R China;
推荐引用方式
GB/T 7714		 Liu, Xiaofeng,Ouyang, Sisheng,Yu, Biao,et al. PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach[J]. NUCLEIC ACIDS RESEARCH,2010,38:W609-W614.
APA Liu, Xiaofeng.,Ouyang, Sisheng.,Yu, Biao.,Liu, Yabo.,Huang, Kai.,...&Jiang, Hualiang.(2010).PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.NUCLEIC ACIDS RESEARCH,38,W609-W614.
MLA Liu, Xiaofeng,et al."PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach".NUCLEIC ACIDS RESEARCH 38(2010):W609-W614.

入库方式： OAI收割

来源：上海药物研究所

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