2.5 Anchor residues
Anchor residues and their ΔSASA (solvent accessible surface area) were
calculated for the both PPI and PepPI benchmark datasets from ANCHOR
webserver [13]. ΔSASA is the change in the solvent accessible
surface area for the side-chain upon binding. The program also estimates
the contribution of side-chain to the binding free energy. ΔSASA and
binding free energy were calculated for all interface residues. Anchor
residues were identified that burry the solvent accessible surface area,
ΔSASA ≥ 100 Å2 upon binding.
Results and Discussion
Protein-protein and protein-peptide benchmark dataset having 134 and 50
dimer complexes, respectively, were used for calculations and analysis.
To identify the hotspots, all interface residues of both partner chains
in the complex were mutated to alanine and relative binding affinity
(∆∆G) values were calculated upon mutation of all these 184 complexes.
Ala scan was carried out using Bioluminate residue scanning module
[37-38]. The positive value of ∆∆G indicates loss in binding
affinity upon mutation and suggest quantitatively the importance of the
particular residue. A negative value refers to the gain in binding
affinity indicating that the mutant binds better.