Abstract

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.

中文翻译：

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2021年的RepeatsDB：改进的数据和蛋白质串联重复序列结构的扩展分类

摘要

RepeatsDB数据库（URL：https://repeatsdb.org/）提供了来自蛋白质数据库（PDB）的蛋白质串联重复序列结构的注释和分类。蛋白质串联重复序列在生命树的所有分支中无处不在。解决的重复结构的积累为分类和检测提供了新的可能性，但同时也增加了注释的需求。在这里，我们介绍RepeatsDB 3.0，它解决了这些挑战并提出了扩展的分类方案。与以前的版本相比，主要的概念更改是分层分类，将仅基于结构相似性的顶级（类别>拓扑>折叠）与两个需要序列相似性并与Pfam合作描述重复基序的新级别（氏族>家族）相结合。数据增长已通过浏览分类层次结构的改进机制得到解决。以UniProt为中心的新视图统一了来自相同或相似序列的结构的日益频繁的注释。RepeatsDB的此更新符合我们致力于开发可提取，组织和分发有关串联重复蛋白结构的专门信息的资源的承诺。