A Computerized Metabolic Map. 2. Relational Structure, Extended Modeling, and a Graphical Interface

We have developed a computer representation of biochemical metabolism which allows stepwise selection of possible metabolic routes, retrieval of relevant associated information, and data entry to expand the underlying system. The system is based upon a data model that forges links between chemical substances, reactions, enzymes, and associated information. At the most fundamental level, sequential links can be viewed between metabolic reactions that occur in cells. In addition, variation in species as well as subcellular locale for reactions are represented. Our system allows a particularly relaxed definition of both reaction and enzyme. Thus, reactions include binding proteins (such as hormone receptors) that are neither catalytic nor involve transport steps. Enzymes include transport steps (which are formally translocation catalysts), and the model extends to representing enzymes as substrates of other enzymes. Thus, steps in hormone signaling such as hormone-receptor binding and noncatalytic binding of intracellular signal molecules can be incorporated into the same structure and output to the same sequence as steps involving enzymatic transformation or transport steps.