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.