Internal structure similarity in proteins can be observed at the domain and subdomain levels. From an evolutionary perspective, structurally similar elements may arise divergently by gene duplication and fusion events but may also be the product of convergent evolution under physicochemical constraints. The characterization of proteins that contain repeated structural elements has implications for many fields of protein science including protein domain evolution, structure classification, structure prediction, and protein engineering. FiRES (Find Repeated Elements in Structure) is an algorithm that relies on a topology‐independent structure alignment method to identify repeating elements in protein structure. FiRES was tested against two hand curated databases of protein repeats: MALIDUP, for very divergent duplicated domains; and RepeatsDB for short tandem repeats. The performance of FiRES was compared to that of lalign, RADAR, HHrepID, CE‐symm, ReUPred, and Swelfe. FiRES was the method that most accurately detected proteins either with duplicated domains (accuracy = 0.86) or with multiple repeated units (accuracy = 0.92). FiRES is a new methodology for the discovery of proteins containing structurally similar elements. The FiRES web server is publicly available at http://fires.ifc.unam.mx. The scripts, results, and benchmarks from this study can be downloaded from https://github.com/Claualvarez/fires.

中文翻译：

---

FiRES：一种从头确定蛋白质内部结构相似性的计算方法。

蛋白质的内部结构相似性可以在结构域和亚结构域水平观察到。从进化的角度来看，结构相似的元素可能因基因复制和融合事件而异质地出现，但也可能是在物理化学约束下趋同进化的产物。包含重复结构元素的蛋白质的表征对蛋白质科学的许多领域都有影响，包括蛋白质结构域进化，结构分类，结构预测和蛋白质工程。FiRES（查找结构中的重复元素）是一种算法，该算法依赖于拓扑独立的结构比对方法来识别蛋白质结构中的重复元素。针对两个手工整理的蛋白质重复数据库对FiRES进行了测试：MALIDUP，用于非常不同的重复域；和RepeatsDB进行短串联重复。将FiRES的性能与lalign，RADAR，HHrepID，CE-symm，ReUPred和Swelfe的性能进行了比较。FiRES是最准确地检测具有重复结构域（准确性= 0.86）或具有多个重复单位（准确性= 0.92）的蛋白质的方法。FiRES是发现包含结构相似元素的蛋白质的新方法。FiRES Web服务器可从http://fires.ifc.unam.mx上公开获得。可以从https://github.com/Claualvarez/fires下载此研究的脚本，结果和基准。86）或多个重复单位（精度= 0.92）。FiRES是发现包含结构相似元素的蛋白质的新方法。FiRES Web服务器可从http://fires.ifc.unam.mx上公开获得。可以从https://github.com/Claualvarez/fires下载此研究的脚本，结果和基准。86）或多个重复单位（精度= 0.92）。FiRES是发现包含结构相似元素的蛋白质的新方法。FiRES Web服务器可从http://fires.ifc.unam.mx上公开获得。可以从https://github.com/Claualvarez/fires下载此研究的脚本，结果和基准。