This file format standardization generates consistent residue and atom labelling schemes that facilitate comparison across related proteins. KIN analysis can be performed on the PDB structures directly, or biomolecular simulations can be run using AmberMD and the resulting trajectories analyzed with KIN. As alluded to in Figure , RINs can then be constructed with non-covalent interactions classified into any of the following types: salt bridge, hydrogen bond, cation-π, π-π, hydrophobic and van der Waals (vdWs) interactions. If MD simulations are performed to generate a structural ensemble for each protein, then KIN uses an adjustable cutoff to determine how frequently an interaction must be present for inclusion in that protein's RIN. For example, if the cutoff is set to 10%, contacts will be included if present for at least 10% of the simulation time. where lines indicate a contact between two residues. The color of the line reflects the interaction type whilst the thickness is proportional to the level of conservation. (bottom) Summary of the interaction type, type of interacting residues (main-chain, Mc, or side-chain, Sc) and conservation scores for a subset of the interactions preserved in the protein family of interest.