MD simulations of the PDZ3 domain with the CRIPT peptide bound were performed using the PDB ID: 1BE9, with simulations of the unbound form performed by removing the CRIPT peptide from the structure. For the peptide bound simulations, the N-and C-termini of the peptide side chain was capped with an acetyl group and a N-methyl amide group respectively and the partially missing side chains for PDZ3 residue F301 and peptide residue K5 (using the numbering from PDB ID: 1BE9 57 ) were completed using PyMOL. The protonation states of all residues were kept at their standard states and the histidine tautomerization states (Table ) and any necessary Asn or Gln "flips" were determined using MolProbity. MD simulations were performed using AMBER18 and run for 200 ns with the last 100 ns of each simulation used in the PyContact calculations (to enable the unliganded simulations to first relax after removing the peptide). PyContact was performed on 20,000 equally spaced frames obtained from both the bound and unbound MD simulations (0.1 ns timestep), with all PDZ3 domain residues used in the calculation (i.e., the peptide was not included in the bound simulation PyContact calculation).