An “imaginary transition structure” overlays the molecular graphs of the educt and product sides of an elementary chemical reaction in a single graph to highlight the changes in bond structure. We generalize this idea to reactions with complex mechanisms in a formally rigorous approach based on composing arrow-pushing steps represented as graph-transformation rules to construct an overall composite rule and a derived transition structure. This transition structure retains information about transient bond changes that are invisible at the overall level and can be constructed automatically from an existing database of detailed enzymatic mechanisms. We use the construction to (i) illuminate the distribution of catalytic action across enzymes and substrates and (ii) to search in a large database for reactions of known or unknown mechanisms that are compatible with the mechanism captured by the constructed composite rule.

中文翻译：

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用规则组合表示催化机制

“假想过渡结构”将基本化学反应的离析物和产物侧的分子图叠加在单个图中，以突出键结构的变化。我们以一种形式上严格的方法将这一想法推广到具有复杂机制的反应，该方法基于组合表示为图形转换规则的箭头推动步骤，以构建一个整体复合规则和一个派生的转换结构。这种过渡结构保留了有关瞬态键变化的信息，这些信息在整体水平上是不可见的，并且可以从现有的详细酶促机制数据库中自动构建。