2.1 Dataset
The Propairs database of legitimate protein-protein docking complexes
enlists crystal structures of bound complexes, defined as biological
complexes in the Protein Data Bank (PDB), and their corresponding
unbound protein structure(s). A total of 2378 bound complexes that have
corresponding unbound structures of the interacting partners were
collected. It was ensured that the crystal structures of the bound
complex are of better than 3Å resolution. Structures in the bound form
were required to have the same oligomeric state as in the unbound form
to ensure that the perturbation is not influenced by the docking of any
other protein molecule. The dataset was further curated to remove
structures with missing residues. Any multiple occupancies were
corrected to obtain a conformer with single occupancy, based on highest
occupancy value, for all its atoms. 895 chains from a bound complex with
interfacial sites were paired with the corresponding chain in the
unbound form to make the working dataset for this analysis. The list of
all the protein chains along with the analysis of their network
information can be found in Supplementary Table 1.