MechFind: a computational framework for de novo prediction of enzyme mechanisms

Abstract Fewer than one thousand cataloged mechanistic annotations can be found in the open literature and databases. Here, we introduce MechFind, a computational tool that generates element and charge-balanced putative enzyme mechanisms using only the reaction stoichiometry. Unlike methods requiring structural data, MechFind abstracts reaction steps as changes in chemical moieties. It identifies the most parsimonious mechanistic descriptions and re-ranks them based on similarity to known mechanisms. MechFind recovers the validated mechanism for 72% of a curated training dataset within the top ten predictions and is indirectly validated on enzymes absent from the training set. When applied on 14,931 reactions from the Rhea database, MechFind identifies plausible mechanisms for 57% of all entries, generating over 18,000 hypotheses. This resource significantly expands mechanistic annotation and provides detailed reaction steps to support de novo enzyme design and engineering. All codes, curated datasets, and results are available at https://github.com/maranasgroup/MechFind.git (Commit Hash: fcc0896).