The chosen model systems will be described in more detail in their corresponding Results and Discussion sections, but Figure demonstrates we have included both subtle and largescale conformational changes. For example, Figure showcases a relatively large (~10 Å) conformational change between two protein loop conformations, in which (due to the size of the change), novel interactions would be expected to be found in one conformation and not the other. On the other hand, Figure showcases a model system where the difference is subtle changes in the side chain conformations of an active site, meaning the differences between states are likely to be substantially more subtle and potentially harder to capture. Finally, all three systems selected have some degree of experimentally characterized allostery that we can compare our results to. This will enable us to evaluate our package's ability to find both local and distal interactions that are associated with a conformational change of interest.