The SuMo server:: 3D search for protein functional sites
The SuMo server:: 3D search for protein functional sites
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DOI：
10.1093/bioinformatics/bti645
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发表时间：
2005-10-15
期刊：
影响因子：
5.8
通讯作者：
Geourjon, C
中科院分区：
文献类型：
--
作者：
Jambon, M;Andrieu, O;Geourjon, C
我们为科学界提供了一个Web服务器，可以访问SuMo，这是一个生物信息学系统，用于查找蛋白质任意3D结构或子结构的相似性。SuMo是基于一个独特的大分子表示使用选定的三重化学基团具有自己的几何形状和对称性，无论氨基酸的主链和侧链的限制性概念。启发式提取相似的网站被用来驱动两个主要的大规模的方法。首先，通过将结构与蛋白质数据库（PDB）中发现的每个配体结合位点进行比较，可以在查询结构上搜索配体结合位点。其次，相互作用过程，即在PDB的结构中搜索给定的3D感兴趣位点也是可能的，并且有助于检测药物设计项目中的交叉反应靶标。
We provide the scientific community with a web server which gives access to SuMo, a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on a unique representation of macromolecules using selected triplets of chemical groups having their own geometry and symmetry, regardless of the restrictive notions of main chain and lateral chains of amino acids. The heuristic for extracting similar sites was used to drive two major large-scale approaches. First, searching for ligand binding sites onto a query structure has been made possible by comparing the structure against each of the ligand binding sites found in the Protein Data Bank (PDB). Second, the reciprocal process, i.e. searching for a given 3D site of interest among the structures of the PDB is also possible and helps detect cross-reacting targets in drug design projects.