Körner Robert, Apostolakis Joannis
Institute for Informatics, Ludwig-Maximilians-Universität München, Munich, Germany.
J Chem Inf Model. 2008 Jun;48(6):1181-9. doi: 10.1021/ci7004324. Epub 2008 Jun 6.
Chemical reactions transform the reactant molecules by deleting existing and forming new bonds. The identification of these so-called reacting bonds is important for studying the reaction mechanism and for applications in metabolomics, e.g. for interpreting substrate labeling experiments. Here, we introduce an approach which suggests the simplest possible reaction center at the heavy atom level, with high accuracy. In contrast to current methods the approach is motivated by a simple theoretical model based on a crude approximation of the reaction energetics, and takes the complete reacting system into account. Finally, it recovers all optimal solutions to the problem while removing all symmetry-related, redundant solutions. We apply the method on the complete KEGG database of biochemical reactions, and compare our approach with previous methods. The resulting reaction centers are represented as imaginary transition states, which are molecule-like representations of reaction mechanisms. We provide the statistics of the calculations on the KEGG database and discuss some examples for the different types of alternative solutions found.
化学反应通过消除现有键并形成新键来转化反应物分子。识别这些所谓的反应键对于研究反应机理以及在代谢组学中的应用（例如解释底物标记实验）非常重要。在此，我们介绍一种方法，该方法在重原子水平上以高精度提出尽可能简单的反应中心。与当前方法不同，该方法基于反应能量学的粗略近似的简单理论模型，并且考虑了整个反应系统。最后，它在去除所有与对称性相关的冗余解的同时，恢复了该问题的所有最优解。我们将该方法应用于完整的KEGG生化反应数据库，并将我们的方法与以前的方法进行比较。所得的反应中心表示为假想的过渡态，这是反应机理的类似分子的表示形式。我们提供了KEGG数据库上的计算统计信息，并讨论了所发现的不同类型替代解的一些示例。
