Automated visualization of rule-based models
Fig 4
(A) The full model AR graph from Fig 3C. (B) Removing atoms and rules with low priority, such as free binding sites, unphosphorylated states and the unbinding rule. (C) Grouping structurally similar atoms, e.g., Sub_pY = phosphorylated states of p1 and p2, Enz|Sub = bond linking Enz and Sub. (D) Grouping rules with similar edge signatures, e.g., rules R2 and R3 both have a context edge from Enz|Sub and a product edge into Sub_pY. (E) Each group is merged into a single node that combines all incident edges. Panels B-C are semi-automated, whereas panels D-E are fully automated.