2.3 Interfacial properties
We used our in-house server, PIC, to obtain interactions arising from two domains by taking care of multiple occupancies of atoms.
A Python script obtained from Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC) was used for the recognition of interfacial residues, which is based on the change in solvent accessibility upon complex formation.
Interaction energies of DDIs were calculated using PPCheck, which measures energies as sum of van der Waals, hydrogen bond, and electrostatic interactions. The energy of the proteins was minimized using GROMACS for those proteins which showed unfavourable calculated energies.