PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach.
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PharmMapper 服务器：使用药效团映射方法识别潜在药物靶标的网络服务器
DOI：
10.1093/nar/gkq300
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发表时间：
2010-07
影响因子：
14.9
通讯作者：
Jiang H
中科院分区：
文献类型：
--
作者：
Liu X;Ouyang S;Yu B;Liu Y;Huang K;Gong J;Zheng S;Li Z;Li H;Jiang H
计算机药物靶标识别，包括许多用于发现疾病基因和蛋白质的不同算法，是药物发现管道的第一步。当目标的三维结构可用时，目标识别的问题通常转化为寻找潜在目标候选者与小分子探针之间的最佳相互作用模式。药效团是分子与特定靶受体相互作用所必需的特征的空间排列，是除了分子对接方法之外实现这一目标的另一种方法。PharmMapper服务器是一个免费访问的Web服务器，旨在使用药效团映射方法识别给定小分子（药物，天然产物或其他新发现的具有未识别结合靶标的化合物）的潜在靶标候选者。PharmMapper拥有一个大型的内部药效团数据库（即PharmTargetDB），该数据库注释了TargetBank，BindingDB，DrugBank和潜在药物靶标数据库中的所有靶标信息，包括7000多个基于受体的药效团模型（涵盖1500多个药物靶标信息）。PharmMapper根据PharmTargetDB中的所有药效团模型自动找到查询分子的最佳映射姿势，并列出前N个最佳拟合命中与适当的靶标注释，以及呈现相应分子的对齐姿势。得益于高效、健壮的三角形哈希映射方法，PharmMapper具有高吞吐能力，平均仅需1 h即可完成对整个PharmTargetDB的筛选。该协议是成功地找到合适的目标中的前300名候选药效团在他莫昔芬的回顾性基准测试。PharmMapper可在http://59.78.96.61/pharmmapper上获得。
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.
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