ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
复制标题
DOI：
10.1093/bioinformatics/bts700
复制
发表时间：
2013-02-01
期刊：
影响因子：
5.8
通讯作者：
Tohsato, Yukako
中科院分区：
文献类型：
--
作者：
Matsuta, Yoshihiko;Ito, Masahiro;Tohsato, Yukako
动机：酶命名系统，通常被称为酶佣金(EC)号，在分类和预测酶反应方面发挥着关键作用。然而，在各种途径中描述了许多反应，但没有官方的EC编号，由于缺乏发表在酶分析上的文章，预计这些反应不会被分配EC编号。结果：提出了一种基于最大公共子结构算法、互信息和支持向量机的非分类酶反应EC数赋值方法，称为酶委托数处理器(ECOH)。刀尖检验表明，该方法预测EC正式编号前三位数(即EC子类)的灵敏度、精度和准确率分别为86.1%、87.4%和99.8%。我们进一步证明，通过检验算法生成的EC子类候选列表中的排名，该方法可以成功地预测落入多个EC子类的85个酶反应的分类。与现有方法相比，ECOH的性能更好，并且在预测EC数方面具有灵活性，因此它对于预测酶功能是有用的。
Motivation: The enzyme nomenclature system, commonly known as the enzyme commission (EC) number, plays a key role in classifying and predicting enzymatic reactions. However, numerous reactions have been described in various pathways that do not have an official EC number, and the reactions are not expected to have an EC number assigned because of a lack of articles published on enzyme assays. To predict the EC number of a non-classified enzymatic reaction, we focus on the structural similarity of its substrate and product to the substrate and product of reactions that have been classified.Results: We propose a new method to assign EC numbers using a maximum common substructure algorithm, mutual information and a support vector machine, termed the Enzyme COmmission numbers Handler (ECOH). A jack-knife test shows that the sensitivity, precision and accuracy of the method in predicting the first three digits of the official EC number (i.e. the EC sub-subclass) are 86.1%, 87.4% and 99.8%, respectively. We furthermore demonstrate that, by examining the ranking in the candidate lists of EC sub-subclasses generated by the algorithm, the method can successfully predict the classification of 85 enzymatic reactions that fall into multiple EC sub-subclasses. The better performance of the ECOH as compared with existing methods and its flexibility in predicting EC numbers make it useful for predicting enzyme function.