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. Author manuscript; available in PMC: 2009 Apr 30.
Published in final edited form as: IET Syst Biol. 2008 Sep;2(5):363–368. doi: 10.1049/iet-syb:20080092

Figure 2.

Figure 2

(a) Rules are based on the knowledge of modular structure of proteins, such as interaction of ligand with extracellular domain of the receptor is independent from the state of intracellular tyrosines. Here, a receptor consists of 4 elements (domains): extracellular ecd and 3 tyrosines that can be in two states: either unphosphorylated (U) or phosphorylated (P). Thus, the total number of potential phosphoforms of this receptor is 23=8. However, the rule does not specify a state of any of phosphosites, which implies that the rule is applied to all potential phosphoforms, thus corresponding to at least 8 bidirectional reactions parameterized by the same on and off rates. Lines in italic demonstrate encoding of this description in BioNetGen Language (BNGL). (b) The screenshot of rules representation in the BNG@VCell application. The model illustrates BNGL file that includes specification of parameters, molecules, initial species, and rules.