Background: The rapidly growing protein and annotation databases necessitate the development of efficient tools to process this valuable information. Biologists frequently need to find proteins similar to a given protein, for which BLAST tools are commonly used. With the development of biomedical ontologies, e.g. Gene Ontology, methods were designed to measure function (semantic) similarity between two proteins. These methods work well on protein pairs, but are not suitable for protein query processing.

Objective: Our aim is to facilitate searching of similar proteins in an acceptable time.

Methods: A novel method SimExact for high speed searching of functionally similar proteins has been proposed.

Results: The experiments of this study show that SimExact gives correct results required for protein searching. A fully functional prototype of an online tool (www.datafurnish.com/protsem.php) has been provided that generates a ranked list of the proteins similar to a query protein, with a response time of less than 20 seconds in our setup. SimExact was used to search for protein pairs having high disparity between function similarity and sequence similarity.

Conclusion: SimExact makes such searches practical, which would not be possible in a reasonable time otherwise.

背景：迅速增长的蛋白质和注释数据库需要开发有效的工具来处理这些有价值的信息。生物学家经常需要寻找与给定蛋白质相似的蛋白质，为此通常使用BLAST工具。随着诸如基因本体论之类的生物医学本体论的发展，设计了用于测量两种蛋白质之间的功能（语义）相似性的方法。这些方法适用于蛋白质对，但不适用于蛋白质查询处理。

目的：我们的目的是促进在可接受的时间内搜索相似的蛋白质。

方法：提出了一种新的SimExact方法，用于高速搜索功能相似的蛋白质。

结果：这项研究的实验表明SimExact可以提供蛋白质搜索所需的正确结果。提供了一个在线工具的完整功能原型（www.datafurnish.com/protsem.php），该工具可以生成类似于查询蛋白质的蛋白质排名列表，在我们的设置中，响应时间不到20秒。SimExact用于搜索在功能相似性和序列相似性之间具有高度差异的蛋白质对。

结论：SimExact使此类搜索变得切实可行，否则将无法在合理的时间内实现。