KIF performed well at identifying both local and distal interactions/residues associated with each conformational change studied. By tuning the question being asked (i.e., what is the target variable) and the feature/interaction selection (whether to include/exclude certain residues) a user can to some extent control whether the output of KIF will focus on more local interactions or more distal interactions. The per interaction and per residue scores that can be calculated with KIF enable analysis at different levels of detail. As we showcased with the PDZ3 domain, we believe the per residue scores are best suited to providing an overview of the system and for making comparisons with experimental data (if available). On the other hand, the per interactions scores can be used to focus on understanding a region of interest in greater detail.