Kinematic modeling of biochemical pathways

A computer-implemented method comprising:

• obtaining an initial energy profile for a reaction, wherein the reaction is part of a pathway or process in a system to be modeled;
• deriving forward and reverse rate constants for each component step of a plurality of component steps representing the reaction based on the initial energy profile, wherein each component step is represented by a standard mathematical construct comprising a set of forward and reverse rate equations that apply the forward and reverse rate constants to one or more concentrations of molecules, respectively;
• deriving a in silico behavior of the reaction based on the contribution of each component step of the plurality of component steps to a rate of change of the molecules within the reaction, wherein the contribution of each component is determined from the standard mathematical construct applying the forward and reverse rate constants to the one or more concentrations of molecules, respectively;
• predicting, using a prediction model, a new energy profile for the reaction based on the derived in silico behavior of the reaction, wherein the predicting comprises learning a set of parameters including waypoints or free energy states, which are changeable to define a path of the reaction from substrate to product to fit the in silico behavior of the reaction to an expected behavior of the reaction;
• deriving updated forward and reverse rate constants for each component step of the plurality of component steps representing the reaction based on the new energy profile;
• and
• deriving an updated in silico behavior of the reaction based on the contribution of each component step of the plurality of component steps to the rate of change of the molecules within the reaction, wherein the contribution of each component is determined from the standard mathematical construct applying the updated forward and reverse rate constants to the one or more concentrations of molecules, respectively.

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:

• obtaining an initial energy profile for a reaction, wherein the reaction is part of a pathway or process in a system to be modeled;
• deriving forward and reverse rate constants for each component step of a plurality of component steps representing the reaction based on the initial energy profile, wherein each component step is represented by a standard mathematical construct comprising a set of forward and reverse rate equations that apply the forward and reverse rate constants to one or more concentrations of molecules, respectively;
• deriving a in silico behavior of the reaction based on the contribution of each component step of the plurality of component steps to a rate of change of the molecules within the reaction, wherein the contribution of each component is determined from the standard mathematical construct applying the forward and reverse rate constants to the one or more concentrations of molecules, respectively;
• predicting, using a prediction model, a new energy profile for the reaction based on the derived in silico behavior of the reaction, wherein the predicting comprises learning a set of parameters including waypoints or free energy states, which are changeable to define a path of the reaction from substrate to product to fit the in silico behavior of the reaction to an expected behavior of the reaction;
• deriving updated forward and reverse rate constants for each component step of the plurality of component steps representing the reaction based on the new energy profile;
• and
• deriving an updated in silico behavior of the reaction based on the contribution of each component step of the plurality of component steps to the rate of change of the molecules within the reaction, wherein the contribution of each component is determined from the standard mathematical construct applying the updated forward and reverse rate constants to the one or more concentrations of molecules, respectively.