National centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560 065, Karnataka, India.
Nucleic Acids Res. 2012 Jan;40(Database issue):D531-4. doi: 10.1093/nar/gkr1096. Epub 2011 Nov 28.
Accurate structure-based sequence alignments of distantly related proteins are crucial in gaining insight about protein domains that belong to a superfamily. The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity. We thus report an automated, updated version of the superfamily alignment database known as PASS2.4, consisting of 1961 superfamilies and 10,569 protein domains, which is in direct correspondence with SCOP (1.75) database. Database organization, improved methods for efficient structure-based sequence alignments and the analysis of extreme distantly related proteins within superfamilies formed the focus of this update. Alignment of family-specific functional residues can be realized using such alignments and is shown using one superfamily as an example. The database of alignments and other related features can be accessed at http://caps.ncbs.res.in/pass2/.
准确的基于结构的远缘蛋白质序列比对对于了解属于超家族的蛋白质结构域至关重要。PASS2 数据库提供了在超家族水平上相关的蛋白质比对，其特点是序列同一性较低。因此，我们报告了一个自动更新的超家族比对数据库版本，称为 PASS2.4，它由 1961 个超家族和 10569 个蛋白质结构域组成，与 SCOP（1.75）数据库直接对应。数据库组织、用于有效基于结构的序列比对的改进方法以及超家族中极端远缘蛋白质的分析是本次更新的重点。可以使用这些比对来实现针对家族特异性功能残基的比对，并以一个超家族为例进行展示。比对数据库和其他相关功能可在 http://caps.ncbs.res.in/pass2/ 上访问。
