Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm

Many proteins fold into highly regular and repetitive three dimensional structures. The analysis of structural patterns and repeated elements is fundamental to understand protein function and evolution. We present recent improvements to the CE-Symm tool for systematically detecting and analyzing the internal symmetry and structural repeats in proteins. In addition to the accurate detection of internal symmetry, the tool is now capable of i) reporting the type of symmetry, ii) identifying the smallest repeating unit, iii) describing the arrangement of repeats with transformation operations and symmetry axes, and iv) comparing the similarity of all the internal repeats at the residue level. CE-Symm 2.0 helps the user investigate proteins with a robust and intuitive sequence-to-structure analysis, with many applications in protein classification, functional annotation and evolutionary studies. We describe the algorithmic extensions of the method and demonstrate its applications to the study of interesting cases of protein evolution.

众多蛋白质可折叠为高度规整且具有重复特征的三维结构。对其结构模式与重复单元的分析，是解析蛋白质功能与演化机制的核心基础。我们介绍了CE-Symm工具的最新改进版本，该工具可系统性检测并分析蛋白质内部对称性与结构重复序列。除可精准检测蛋白质内部对称性外，该工具如今新增以下功能：i）输出对称性类型；ii）识别最小重复单元；iii）借助变换操作与对称轴描述重复单元的排布方式；iv）在残基水平上比对所有内部重复序列的相似性。CE-Symm 2.0凭借稳健且直观的序列-结构分析流程，助力研究者开展蛋白质相关研究，其在蛋白质分类、功能注释及演化研究领域具备广泛应用场景。本文阐述了该方法的算法扩展内容，并通过若干典型蛋白质演化案例展示了其应用价值。