EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.

ABSTRACT: Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as 'Easy' Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literatur

SUBMITTER: Ribeiro AJM 

PROVIDER: S-EPMC10555830 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature