The binding free energy of the wild-type and mutant complexes were
further estimated using the MM/GBSA approach which calculates
ΔΔGbind 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.