Pathway Databases

In a second example we show elements of databases containing data about pathways, which are, as mentioned in the introduction, at least one ofthe main targets ofdrug action. Pathway databases are freely available for academic purposes and, in comparing them with other types of molecular databases, we can see that they offer data of relatively high quality. Typical pathway databases include BRENDA [13], KEGG [14], and EcoCyc [15]. In this section we discuss the structure and application of pathway databases.

The first element of our simplified example (Figure 11.5) is the class metabolism, which contains at least all pathways of an organism. Currently, more than 80 pathways are annotated and published in databases. Pathways consist of elementary reactions that are specifically catalyzed by enzymes (>4000). For example, the glycolysis pathway, a central pathway, includes 10 reactions and occurs in many eukaryotic and prokaryotic organisms. The pathway shows complex dynamics (periodic, chaotic), which are caused by several nonlinear reactions. To give an example, one of these reactions is catalyzed irreversibly by the enzyme phosphofructokinase (PFK). PFK consumes the metabolite d-fructose 6-phosphate and produces d-fructose 1,6-bispho-sphate. At the same time ATP is converted to ADP, the substrate (ATP) inhibits the reaction, and ADP acts as activator. Pathway data is highly specific for different organisms and tissues and needs to be stored adequately.

Fig. 11.5 Conceptual scheme of a pathway database.
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