Fig. 2: A typical representation of a mathematical model as a reaction diagram in the Virtual Cell software.
From: Leveraging public AI tools to explore systems biology resources in mathematical modeling
Yellow nodes: reaction processes. Green nodes: chemical species participating in these processes. In Model 1, the EGF ligand’s binding to an EGFR receptor leads to the formation of a complex of EGF and EGFR in the membrane called Ra, and then the dimerization of two Ra complexes leading to the formation of a dimer D—a complex on a membrane consisting of two ligands EGF and two receptors EGFR. In Model 2, Model 1 is extended by adding a reaction of phosphorylation transforming D dimer into its phosphorylated form Dp, which binds with the Grb2 protein to form a DpG complex. In Model 3, Model 2 is extended by adding interactions with Shc and Sos proteins.
