Informatics Institute and Department of Computer Science, University of Missouri, Columbia, MO, USA.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W428-34. doi: 10.1093/nar/gks527. Epub 2012 Jun 11.
PBSword is a web server designed for efficient and accurate comparisons and searches of geometrically similar protein-protein binding sites from a large-scale database. The basic idea of PBSword is that each protein binding site is first represented by a high-dimensional vector of 'visual words', which characterizes both the global and local shape features of the binding site. It then uses a scalable indexing technique to search for those binding sites whose visual words representations are similar to that of the query binding site. Our system is able to return ranked results of binding sites in short time from a database of 194 322 domain-domain binding sites. PBSword supports query by protein ID and by new structures uploaded by users. PBSword is a useful tool to investigate functional connections among proteins based on the local structures of binding site and has potential applications to protein-protein docking and drug discovery. The system is hosted at http://pbs.rnet.missouri.edu.
PBSword 是一个 Web 服务器，旨在高效、准确地比较和搜索来自大型数据库的几何相似的蛋白质-蛋白质结合位点。PBSword 的基本思想是，首先将每个蛋白质结合位点表示为“视觉单词”的高维向量，该向量既描述了结合位点的全局形状特征，也描述了其局部形状特征。然后，它使用可扩展的索引技术来搜索那些其视觉单词表示与查询结合位点相似的结合位点。我们的系统能够在 194322 个域-域结合位点的数据库中，从短时间内返回结合位点的排名结果。PBSword 支持通过蛋白质 ID 和用户上传的新结构进行查询。PBSword 是一种根据结合位点的局部结构来研究蛋白质之间功能联系的有用工具，并且在蛋白质-蛋白质对接和药物发现方面具有潜在的应用。该系统托管在 http://pbs.rnet.missouri.edu。
