Institute for Biochemistry, University of Cologne, Zülpicher Strasse 47, Germany.
Bioinformatics. 2009 Dec 1;25(23):3135-42. doi: 10.1093/bioinformatics/btp549. Epub 2009 Sep 25.
Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis. Frequently rearrangements and deletions of enzymes and sub-subclasses are necessary.
We use the Dugundji-Ugi model for coding of biochemical reactions which is based on electron shift patterns occurring during reactions. Changes of the bonds or of non-bonded valence electrons are expressed by reaction matrices. Our program calculates reaction matrices automatically on the sole basis of substrate and product chemical structures based on a new strategy for maximal common substructure determination, which allows an accurate atom mapping of the substrate and product atoms. The system has been tested for a large set of enzymatic reactions including all sub-subclasses of the EC classification system. Altogether 147 different representative reaction operators were found in the classified enzymes, 121 of which are unique with respect to an EC sub-subclass. The other 26 comprise groups of enzymes with very similar reactions, being identical with respect to the bonds formed and broken.
The analysis and comparison of enzymatic reactions according to their electron shift patterns is defining enzyme groups characterised by unique reaction cores. Our results demonstrate the applicability of the Dugundji-Ugi model as a reasonable pre-classification system allowing an objective and rational view on biochemical reactions.
The program to generate reaction matrix descriptors is available upon request.
根据国际生物化学联合会命名委员会（IUBMB）提出的编号分类方案，酶根据总体反应化学性质进行分类。由于酶反应的多样性，该系统变得非常复杂。将酶分配到酶类需要详细了解该系统并进行手动分析。经常需要对酶和亚类进行重新排列和删除。
我们使用 Dugundji-Ugi 模型对生化反应进行编码，该模型基于反应过程中发生的电子转移模式。键或非键价电子的变化通过反应矩阵表示。我们的程序仅基于底物和产物的化学结构，根据新的最大公共子结构确定策略，自动计算反应矩阵，允许对底物和产物原子进行准确的原子映射。该系统已针对包括 EC 分类系统所有亚类的一系列大型酶反应进行了测试。在分类酶中总共发现了 147 种不同的代表性反应算子，其中 121 种对于 EC 亚类是唯一的。其他 26 种包含具有非常相似反应的酶组，它们在形成和断裂的键方面是相同的。
根据电子转移模式分析和比较酶反应可定义具有独特反应核心的酶组。我们的结果表明，Dugundji-Ugi 模型作为一种合理的预分类系统，可用于对生化反应进行客观和理性的分析。
可根据要求提供生成反应矩阵描述符的程序。
