PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
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DOI：
10.1093/nar/gkh439
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Kolchanov, NA
中科院分区：
文献类型：
--
作者：
Ivanisenko, VA;Pintus, SS;Kolchanov, NA
PDBSiteScan是一个可访问的网络程序，用于搜索三维（3D）蛋白质片段，其结构与已知的活性，结合和翻译后修饰位点相似。通过使用site字段中的站点本地化数据对PDB数据库进行自动化处理，我们将已知站点集合命名为PDBSite。此外，通过分析异质配合物中的原子座标，生成了蛋白质-蛋白质相互作用位点。收集到的网站总数超过8100个；他们被分配到80多个功能组。PDBSiteScan可以自动搜索片段中N、Calpha和C原子与功能位点之间的最大距离不匹配（MDM）不大于用户定义的MDM阈值的3D蛋白质片段。PDBSiteScan要求氨基酸完美匹配。PDBSiteScan能够识别蛋白质三级结构中的功能位点，并允许对具有功能信息的蛋白质进行注释。PDBSiteScan程序可在http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html上获得。
PDBSiteScan is a web-accessible program designed for searching three-dimensional (3D) protein fragments similar in structure to known active, binding and posttranslational modification sites. A collection of known sites we designated as PDBSite was set up by automated processing of the PDB database using the data on site localization in the SITE field. Additionally, protein-protein interaction sites were generated by analysis of atom coordinates in heterocomplexes. The total number of collected sites was more than 8100; they were assigned to more than 80 functional groups. PDBSiteScan provides automated search of the 3D protein fragments whose maximum distance mismatch (MDM) between N, Calpha and C atoms in a fragment and a functional site is not larger than the MDM threshold defined by the user. PDBSiteScan requires perfect matching of amino acids. PDBSiteScan enables recognition of functional sites in tertiary structures of proteins and allows proteins with functional information to be annotated. The program PDBSiteScan is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html.