Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá - UNIFEI, Itabira, 35903-087, Brazil.
Department of Computer Science, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, 31270-901, Brazil.
Nucleic Acids Res. 2017 Jul 3;45(W1):W315-W319. doi: 10.1093/nar/gkx337.
Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/.
酶活性位点是蛋白质的重要且保守的功能区域，其鉴定可以成为蛋白质功能预测的宝贵步骤。大多数现有的此类任务的方法都基于活性位点相似性，并存在一些局限性，包括仅对模板残基进行精确匹配、模板大小限制，尽管它们无法找到域间活性位点。为了填补这一空白，我们提出了 GASS-WEB，这是一个用户友好的网络服务器，它使用 GASS（遗传活性位点搜索），这是一种基于进化算法的方法，用于在蛋白质中搜索类似的活性位点。GASS-WEB 可以在两种不同的情况下使用：（i）给定一个感兴趣的蛋白质，以匹配一组特定的活性位点模板；或（ii）给定一个活性位点模板，在蛋白质结构数据库中查找它。该方法在一系列实验中表现非常有效，并且能够正确识别 Catalytic Site Atlas 中 90%以上的已编目的活性位点。它还使用 Critical Assessment of protein Structure Prediction（CASP 10）数据集实现了 0.63 的马修相关系数。在我们的分析中，GASS 在 18 种方法中排名第四。GASS-WEB 可在 http://gass.unifei.edu.br/ 免费获取。
