This resource provides a set of of mechanistic models of functional components to use as building blocks to construct computational models of biological systems.
Description
Models of biochemical systems—including signaling pathways, electrophysiological systems, and cellular metabolism—are built from models of individual components such as enzymes, transporters, and ion channels. This databank of open source of component models uses a consistent notation, obeying a common set of criteria, with clear documentation and links to the primary literature. Code modules for enzymes and transporters can be downloaded in CellML or MATLAB, for use with the BISEN package.
Enzyme Mechanisms for Biochemical Reactions
Aconitase
Alpha-ketogluterate dehydrogenase
Fumarate reductase (Fumarase)
Malate dehydrogenase
NAD-linked isocitrate dehydrogenase
Pyruvate dehydrogenase
Succinyl-CoA synthase
Transporters and Pumps involving Biochemical Reactants
NADH-ubiquinone oxidoreductase (Complex I)
Ubiquinol-cytochrome c reductase (Complex III)
ATP/magnesium phosphate carrier
Inorganic Cation Transport
Calcium rapid uptake pathway
Na+/Ca2+ exchanger
Na+/H+ exchanger