National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz028.
The number of protein structures is increasing due to the individual initiatives and rapid development of structure determination techniques. Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common evolutionary origin. Protein Alignments organized as Structural Superfamilies (PASS2) is a database that provides such alignments of members of protein domain superfamilies of known structure and with less than 40% sequence identity. PASS2 has been continuously updated in accordance to Structural Classification of Proteins (SCOP), and now Structural Classification of Proteins - extended (SCOPe). The current update directly corresponds to SCOPe 2.06, dealing with 2006 domain superfamilies of known structure and about 14 000 domains. Alignments have been augmented by features such as hidden Markov models, highly conserved residues, structural motifs and gene ontology terms, which are available for download. In this update, we introduce the concepts of 'extreme structural outliers' and 'split superfamilies' as well.
由于个体倡议和结构测定技术的快速发展，蛋白质结构的数量正在增加。远缘蛋白质的基于结构的序列比对能够研究蛋白质及其结构域之间的结构、进化和功能关系，从而揭示它们的共同进化起源。蛋白质比对组织为结构超家族（PASS2）是一个数据库，提供了具有已知结构的蛋白质域超家族成员的这种比对，并且序列同一性小于 40%。PASS2 根据蛋白质结构分类（SCOP）不断更新，现在是蛋白质结构分类 - 扩展（SCOPe）。当前的更新直接对应于 SCOPe 2.06，涉及到 2006 个具有已知结构的域超家族和约 14000 个结构域。通过隐藏 Markov 模型、高度保守残基、结构基序和基因本体论术语等功能增强了比对，这些功能可用于下载。在本次更新中，我们还引入了“极端结构异常值”和“分裂超家族”的概念。
