Cargando…

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

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 i...

Descripción completa

Detalles Bibliográficos
Autores principales: Liu, Xiaofeng, Ouyang, Sisheng, Yu, Biao, Liu, Yabo, Huang, Kai, Gong, Jiayu, Zheng, Siyuan, Li, Zhihua, Li, Honglin, Jiang, Hualiang
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896160/
https://www.ncbi.nlm.nih.gov/pubmed/20430828
http://dx.doi.org/10.1093/nar/gkq300
_version_ 1782183324344647680
author Liu, Xiaofeng
Ouyang, Sisheng
Yu, Biao
Liu, Yabo
Huang, Kai
Gong, Jiayu
Zheng, Siyuan
Li, Zhihua
Li, Honglin
Jiang, Hualiang
author_facet Liu, Xiaofeng
Ouyang, Sisheng
Yu, Biao
Liu, Yabo
Huang, Kai
Gong, Jiayu
Zheng, Siyuan
Li, Zhihua
Li, Honglin
Jiang, Hualiang
author_sort Liu, Xiaofeng
collection PubMed
description 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.
format Text
id pubmed-2896160
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-28961602010-07-02 PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach Liu, Xiaofeng Ouyang, Sisheng Yu, Biao Liu, Yabo Huang, Kai Gong, Jiayu Zheng, Siyuan Li, Zhihua Li, Honglin Jiang, Hualiang Nucleic Acids Res Articles 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. Oxford University Press 2010-07-01 2010-04-29 /pmc/articles/PMC2896160/ /pubmed/20430828 http://dx.doi.org/10.1093/nar/gkq300 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Liu, Xiaofeng
Ouyang, Sisheng
Yu, Biao
Liu, Yabo
Huang, Kai
Gong, Jiayu
Zheng, Siyuan
Li, Zhihua
Li, Honglin
Jiang, Hualiang
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title_full PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title_fullStr PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title_full_unstemmed PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title_short PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
title_sort pharmmapper server: a web server for potential drug target identification using pharmacophore mapping approach
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896160/
https://www.ncbi.nlm.nih.gov/pubmed/20430828
http://dx.doi.org/10.1093/nar/gkq300
work_keys_str_mv AT liuxiaofeng pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT ouyangsisheng pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT yubiao pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT liuyabo pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT huangkai pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT gongjiayu pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT zhengsiyuan pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT lizhihua pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT lihonglin pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach
AT jianghualiang pharmmapperserverawebserverforpotentialdrugtargetidentificationusingpharmacophoremappingapproach