MOTIVATION Protein structure comparison plays a fundamental role in understanding the evolutionary relationships between proteins. Here, we release a new version of the DaliLite standalone software. The novelties are hierarchical search of the structure database organized into sequence based clusters, and remote access to our knowledge base of structural neighbors. The detection of fold, superfamily and family level similarities by DaliLite and state-of-the-art competitors was benchmarked against a manually curated structural classification. RESULTS Database search strategies were evaluated using Fmax with query-specific thresholds. DaliLite and DeepAlign outperformed TM-score based methods at all levels of the benchmark, and DaliLite outperformed DeepAlign at fold level. Hierarchical and knowledge-based searches got close to the performance of systematic pairwise comparison. The knowledge-based search was four times as efficient as the hierarchical search. The knowledge-based search dynamically adjusts the depth of the search, enabling a trade-off between speed and recall. AVAILABILITY AND IMPLEMENTATION http://ekhidna2.biocenter.helsinki.fi/dali/README.v5.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

中文翻译：

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DaliLite v.5对标倍数检测。

动机蛋白质结构比较在理解蛋白质之间的进化关系中起着基本作用。在这里，我们发布了DaliLite独立软件的新版本。新奇之处是对结构数据库的分层搜索，这些结构数据库被组织成基于序列的簇，并且可以远程访问我们的结构邻居的知识库。DaliLite和最先进的竞争对手检测到的倍数，超家族和家族水平的相似性均以手动分类的结构分类为基准。结果使用具有查询特定阈值的Fmax评估了数据库搜索策略。在所有基准水平上，DaliLite和DeepAlign的性能均优于基于TM得分的方法，而DaliLite在折叠水平上的性能均优于DeepAlign。分层和基于知识的搜索已接近系统成对比较的性能。基于知识的搜索的效率是分层搜索的四倍。基于知识的搜索可动态调整搜索的深度，从而在速度和召回率之间进行权衡。可用性和实现http://ekhidna2.biocenter.helsinki.fi/dali/README.v5.html。补充信息补充数据可从Bioinformatics在线获得。