Bioinformatics and Genomics Programme, Centre For Genomic Regulation, Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W358-62. doi: 10.1093/nar/gkt383. Epub 2013 May 28.
This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.
本文介绍了 T-RMSD 网络服务器（基于根均方偏差的树），这是一项在线计算基于结构的蛋白质分类的服务。它是为了解决蛋白质结构和功能相似性之间的关系而开发的，它允许使用距离均方根偏差 (dRMSD) 变化对给定的蛋白质家族或一组结构相关的蛋白质进行细粒度的结构聚类。这些距离是在给定的多重序列比对的无间隙列中定义的所有等效残基对之间计算的。使用这些生成的距离矩阵（每个等效位置一个），T-RMSD 生成具有每个聚类节点支持值的结构树，类似于自举值。这些值与树拓扑结构相关联，允许对由树拓扑结构定义的蛋白质或蛋白质组之间的结构距离进行定量估计。由此定义的聚类已被证明具有结构和功能信息。T-RMSD 网络服务器是一个免费的网站，对所有用户开放，可在 http://tcoffee.crg.cat/apps/tcoffee/do:trmsd 上访问。
