Site-specific details of the proteins and interactions considered in the model.

<p>Proteins, interactions, and the functional components that mediate interactions are represented according to the conventions of Chylek et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#pcbi.1003217-Chylek2" target="_blank">[42]</a>. The numbering of arrows is the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#pcbi-1003217-g001" target="_blank">Fig. 1</a>. The double-arrowed lines represent reversible binding interactions. The lines ending with an open circle represent enzyme-substrate relationships and point to sites of phosphorylation. In the model, sites Ser-33, Ser-37, and Thr-41, which are substrates, are lumped together as a single site labeled S33/37. site Ser-45, which is a substrate, is labeled S45. In the model, the seven 20-aa repeats of APC are lumped into two distinct sites labeled 1 and 3. For further information about the model, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#s4" target="_blank">Materials and Methods</a>. A complete and executable specification of the model is provided in the Supporting Information as a plain-text BioNetGen input file (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#pcbi.1003217.s005" target="_blank">Text S2</a>). Note that there is a correspondence between the arrows shown here and the rules of the model (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#pcbi.1003217.s004" target="_blank">Text S1</a>). Model parameter values are summarized in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003217#pcbi-1003217-t001" target="_blank">Table 1</a>.