Classification of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Computational Methods
作者单位：State Key Laboratory of Chemical Resource EngineeringDepartment of Pharmaceutical EngineeringP.O.Box 53Beijing University of Chemical Technology
会议名称：《第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学》
会议日期：2012年
学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术]
关 键 词：Hydrolases Oxidoreductase Reaction classification Kohonen’s Self-Organizing Map(SOM) support vector machine(SVM)
摘 要：The Enzyme Commission(EC) classification system is widely used in chemistry and biology and is maintained by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology(NC-IUBMB).Enzymes are classified into six main classes;each main class is reclassified into several subclasses;a subclass is classified into *** this EC system,each enzyme has its unique EC number:EC a.b.c.d,where a refers to the six main classes of enzymes;b indicates the subclasses;c represents the subsubclasses;d is the serial number of the enzyme in its *** method of enzyme classification is based on several criteria,such as reaction types,substrates,transferred groups,and acceptor groups. In this work,several computational models for classification of reactions catalyzed by hydrolases and oxidoreductases were developed using three different computational methods. The overall breaking and making of bonds of reactions were *** physicochemical properties for the reacting bond in the substrate of each enzymatic reaction were calculated to describe the characteristics of each *** 311 reactions catalyzed by hydrolases (EC 3.b.c.d) and the 651 reactions catalyzed by oxidoreductases(EC l.b.c.d) were classified by Kohonen’s Self-Organizing Map(SOM),by a support vector machine(SVM),and by hierarchical clustering analysis(HCA).For the 311 reactions catalyzed by hydrolases,the classification accuracy of 95.8%by a SOM and 97.7%by an SVM was *** the 651 reactions catalyzed by oxidoreductases,the classification accuracy was 93.4%and 96.3%by a SOM and a SVM,*** similarities of reactions reflected by the physicochemical effects of reacting bonds were compared with the traditional Enzyme Commission(EC) classification system.