Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications
Fig 5
Binding (A) and unbinding (B) of the SH2 domain of Grb2 to the Y1068 site of EGFR in the phosphorylated (“p”) state. The first arrow specifies the direction of the forward reaction: a downward arrow indicates that the forward rule creates a bond, while an upward arrow indicates that the forward rule breaks a bond. The color of the box reflects the nature of the forward direction: a green box denotes that the forward rule creates a bond, while a red box denotes that the forward rule destroys a bond. C. Intramolecular binding. Grb2 is already part of a complex with EGFR (indicated by a dashed line), and it binds/unbinds via its SH3 domain (shown by a solid bond). The rule shown is reversible and establishes a new bond between the SH2 domain of Grb2 and the phosphorylated Y1068 site of EGFR.