We applied our package to three model systems (Figure ) to showcase and test the capabilities of our package towards several different objectives (assessing the impact of ligand binding, describing protein conformational changes, characterizing allosteric signaling pathways, and understanding the origin of enhanced catalytic rates). The model systems were also chosen in part due to the available experimental data with which we could compare our results to. over the course of directed evolution (DE). Mutations both local and distal across this series of variants altered the active site side chain conformations of several residues which lead to enhanced catalytic activity. We will study how the protein interaction network was altered as a result of these mutations, which led to a population shift and ultimately enhanced activity, using regression analysis.