National Institute of Chemistry, Ljubljana, Slovenia.
Bioinformatics. 2010 May 1;26(9):1160-8. doi: 10.1093/bioinformatics/btq100. Epub 2010 Mar 19.
Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation.
An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein-protein, protein-small ligand and protein-DNA binding sites.
The software is available, as a web tool, free of charge for academic users at http://probis.cmm.ki.si.
利用蛋白质表面局部相似的理化性质三维模式来探测可能缺乏序列和全局结构保守性的结合位点。
本文描述了一种算法 ProBiS，该算法通过局部表面结构比对来检测蛋白质表面上结构相似的位点。它将查询蛋白与蛋白 3D 结构数据库中的成员进行比较，并以亚残基精度检测到蛋白表面上的理化性质相似的结构模式。该程序使用高效的最大团算法识别与查询蛋白具有局部结构相似性的蛋白，并生成这些蛋白与查询蛋白的基于结构的比对。对查询蛋白表面残基进行结构相似性评分，并在查询蛋白表面上以不同颜色表示。该算法已成功用于探测蛋白-蛋白、蛋白-小分子配体和蛋白-DNA 结合位点。
该软件作为一个网络工具，可免费供学术用户在 http://probis.cmm.ki.si 使用。
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