E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.
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DOI：
10.1093/bioinformatics/btp223
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发表时间：
2009-06-15
期刊：
影响因子：
--
通讯作者：
Kanehisa M
中科院分区：
文献类型：
--
作者：
Yamanishi Y;Hattori M;Kotera M;Goto S;Kanehisa M
动机：IUBMB的酶命名系统，通常称为酶委员会（EC）编号，在酶反应分类和将酶基因或蛋白质与代谢途径中的反应联系起来方面发挥着关键作用。已知有许多反应存在于各种途径中，但没有任何官方EC编号，其中大多数没有希望获得EC编号，因为缺乏关于酶测定的已发表文章。结果如下：在这篇文章中，我们提出了一种新的方法来预测潜在的EC数给定的反应物对（底物和产物）或未表征的反应，和一个Web服务器命名为E-zyme作为一个应用程序。这项技术基于我们最初的生化转化模式，我们称之为“RDM模式”，包括三个步骤：（i）查询反应物对的图对齐（衬底和产品）用于计算查询RDM模式，（ii）通过将查询RDM模式与和已知EC号相关的模板模式进行比较来进行多层部分模板匹配，以及（iii）选择适当的EC编号的加权主要投票方案。交叉验证实验结果表明，该方法在实际应用中具有较高的覆盖率和预测精度，且性能始终优于传统方法。可用性：E-zyme系统可在http://www.genome.jp/tools/e-zyme/上获得。联系方式：kanehisa@kuicr.kyoto-u.ac.jp
Motivation: The IUBMB's Enzyme Nomenclature system, commonly known as the Enzyme Commission (EC) numbers, plays key roles in classifying enzymatic reactions and in linking the enzyme genes or proteins to reactions in metabolic pathways. There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which have no hope to be given ones because of the lack of the published articles on enzyme assays. Results: In this article we propose a new method to predict the potential EC numbers to given reactant pairs (substrates and products) or uncharacterized reactions, and a web-server named E-zyme as an application. This technology is based on our original biochemical transformation pattern which we call an ‘RDM pattern’, and consists of three steps: (i) graph alignment of a query reactant pair (substrates and products) for computing the query RDM pattern, (ii) multi-layered partial template matching by comparing the query RDM pattern with template patterns related with known EC numbers and (iii) weighted major voting scheme for selecting appropriate EC numbers. As the result, cross-validation experiments show that the proposed method achieves both high coverage and high prediction accuracy at a practical level, and consistently outperforms the previous method. Availability: The E-zyme system is available at http://www.genome.jp/tools/e-zyme/ Contact: kanehisa@kuicr.kyoto-u.ac.jp
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