Representing catalytic mechanisms with rule composition

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juri Kolčák*, Christophe V.F.P. Laurent, Daniel Merkle, Nikolai Nøjgaard

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


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.

Original languageEnglish
JournalJournal of Chemical Information and Modeling
Issue number22
Pages (from-to)5513-5524
Publication statusPublished - 28. Nov 2022


  • Catalysis
  • Databases, Factual


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