Graphical representations of Lck. a) Lck is represented by a molecular entity graph [27, 67]. Each component in a protein is represented by a circle. The box that contains all these circles represents the Lck molecule. b) Domains and sites of post-translational modification in Lck are represented in a hierarchical molecular entity graph. Arrows indicate the containing relationships. Each component is represented as a node in the graph. The tyrosine residues Y192, Y394, and Y505 have phosphorylated (P) and unphosphorylated (U) internal states. This graph follows the conventions used in GetBonNie . c) Lck is represented by a hierarchical chemical species graph. In a chemical species graph, the state of each domain or site that has more than one internal state is clearly defined. Here, "U" and "P" under Y192 and Y505 specify that Y192 and Y505 can be in unphosphorylated and phosphorylated states, respectively. The undirected line (with no arrow) between SH2 and Y505 indicates that the SH2 domain of Lck is bound intramolecularly to the phosphorylated Y505 residue.