Fig. 3: Illustration of the mechanism search algorithm used by EzMechanism.
From: EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions
a, Example of a configuration that matches three rules (identified by the three different colors). Each rule match leads to the creation of a new configuration. b, Example of a configuration graph that represents the catalytic space explored by EzMechanism. Green arrow edges represent steps in the search that are prioritized according to the prioritization algorithm. Numbers in the configurations exemplify the order followed by the software to match the rules to each configuration. Orange, reactant configuration; red, products configuration; yellow, configuration matched with rules and gray, other configurations. c, A cleaner representation of the two possible mechanisms that are present in b. Every path that links the reactants with the products configuration represents a potential mechanism.
