MechFind: A computational framework for de novo prediction of enzyme mechanisms.

ABSTRACT: Despite the importance of understanding the step-by-step mechanism of enzymatically catalyzed reactions, fewer than one thousand cataloged mechanistic annotations can be found in the open literature and databases. Herein, we introduce MechFind, a computational tool that generates elementally and charge-balanced putative enzyme mechanisms. Unlike previous methods that require structural data or user-supplied active site residues, MechFind uses only the overall reaction stoichiometry as input, abstracting individual reaction steps as the gain or loss of chemical moieties. An optimization framework then identifies the top ten most parsimonious (i.e., fewest steps) mechanistic descriptions for the overall transformation, which are then re-ranked based on their mechanistic similarity to a datab

SUBMITTER: Hartley AD 

PROVIDER: S-EPMC12485929 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature