PDBSiteScan：一个用于在蛋白质三维结构中搜索活性、结合和翻译后修饰位点的程序。

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.

作者信息

Ivanisenko Vladimir A, Pintus Sergey S, Grigorovich Dmitry A, Kolchanov Nickolay A

机构信息

Institute of Cytology and Genetics SBRAS, Lavrentyev Avenue 10, Novosibirsk 630090, Russia.

出版信息

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W549-54. doi: 10.1093/nar/gkh439.

DOI:10.1093/nar/gkh439

PMID:15215447

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC441577/

Abstract

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.

摘要

PDBSiteScan是一个可通过网络访问的程序，用于搜索在结构上与已知活性、结合和翻译后修饰位点相似的三维（3D）蛋白质片段。通过使用SITE字段中位点定位的数据对PDB数据库进行自动处理，建立了一个我们称为PDBSite的已知位点集合。此外，通过分析异源复合物中的原子坐标生成蛋白质-蛋白质相互作用位点。收集到的位点总数超过8100个；它们被分配到80多个功能组。PDBSiteScan可自动搜索三维蛋白质片段，这些片段与功能位点之间N、α-碳原子和C原子的最大距离错配（MDM）不大于用户定义的MDM阈值。PDBSiteScan要求氨基酸完全匹配。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。程序PDBSiteScan可在http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html获取。

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