kMech is an Enzyme mechanism language that translates enzymatic reactions and inhibition models into elementary xCellerator reactions.
It includes a comprehensive collection of single and multiple substrate enzyme reactions and regulatory mechanisms that extends xCellerator function with enzymatic reactions. Each mechanism uses a function expansion to translate the Enzyme reaction into a set of elementary xCellerator reactions.
kMech is installed by default as an xCellerator plugin. To utilize kMech functions you should include the line
in your Mathematica notebook.
All enzymatic reactions implemented in kMech are invoked using the wrapper Enz around a reaction with canonical form
where the number of allowed substrates, products, and enzymes depend on the type of reaction and inhibition; a typical kMech call will look like
Enz[arrow, reaction[rates], inhibition]where:
arrow is a reaction in the canonical form given above;
reaction is one of the kMech enzymatic reactions: BiBi, BiTer, BiUni, MulS, OrderedBiBi, OrderedBiUni, PingPong, PingPongTerTerF, PingPongTerTerR, RandomBiBi, TerBi, TerTer, UniBi, UniUni
rates is a sequence of rate constants appropriate to the particular reaction mechanism.
inhibition is a sequence of functions describing the type of competition and/or inhibition.