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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
<<kMech.m
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.