The binding free energy of the wild-type and mutant complexes were further estimated using the MM/GBSA approach which calculates ΔΔG_bind based on molecular dynamics simulation of the protein-protein complex. The prediction which was achieved using HawkDock is intermediate both in accuracy and computational effort between strict alchemical perturbation and empirical scoring methods. The output revealed the total binding energy scores on per-residue bases for both wild-type and mutant complexes (Tables 5 and 6). Detailed contribution of each residue in the complex can be accessed from the Supplementary Tables 1-6.

Table 5. HawkDock-MM/GBSA per-residue binding energy table for the wild-type protein-protein complexes. The output displays the mutated chains, residue positions, van der Waals potential, electrostatic potential, generalized born scores, solvent accessibility and the total binding energy score.