Automatic mapping of atoms across both simple and complex chemical reactions
Automatic mapping of atoms across both simple and complex chemical reactions
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DOI：
10.1038/s41467-019-09440-2
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发表时间：
2019-03-29
影响因子：
16.6
通讯作者：
Grzybowski, Bartosz A.
中科院分区：
文献类型：
--
作者：
Jaworski, Wojciech;Szymkuc, Sara;Grzybowski, Bartosz A.
在化学反应中映射原子对于子结构搜索、自动提取反应规则、识别代谢途径等非常重要。不幸的是，现有的映射算法只能处理相对简单的反应，而不是那些专家化学家将受益于计算机的帮助。在这里，我们报告了算法和专家化学知识的结合如何显着提高原子映射的性能，使机器能够处理即使是最机械复杂的化学和生化转化。我们的方法的主要特点是使用几个，但明智地选择的反应模板，用于生成似是而非的“中间”原子分配，然后引导一个图形理论算法对化学正确的同构映射。该算法的性能明显优于现有的最先进的反应映射器，这表明其在数据库管理，机制分配，以及最重要的是机器提取现代合成规划程序的反应规则中的用途。
Mapping atoms across chemical reactions is important for substructure searches, automatic extraction of reaction rules, identification of metabolic pathways, and more. Unfortunately, the existing mapping algorithms can deal adequately only with relatively simple reactions but not those in which expert chemists would benefit from computer's help. Here we report how a combination of algorithmics and expert chemical knowledge significantly improves the performance of atom mapping, allowing the machine to deal with even the most mechanistically complex chemical and biochemical transformations. The key feature of our approach is the use of few but judiciously chosen reaction templates that are used to generate plausible "intermediate" atom assignments which then guide a graph-theoretical algorithm towards the chemically correct isomorphic mappings. The algorithm performs significantly better than the available state-of-the-art reaction mappers, suggesting its uses in database curation, mechanism assignments, and - above all - machine extraction of reaction rules underlying modern synthesis-planning programs.