3.6 Binding free energy
The binding free energy (MM-PBSA) calculated from MD trajectories showed
that the total binding energies of all complexes were observed in an
acceptable range. The results of MM-PBSA are given in table 5. In
particular, complex Scaf1-EGFR DIII presented the lowest binding free
energy and higher binding affinity with the receptor, suggesting a more
stable protein conformation. These free energy calculations validated
the molecular docking results, showing that this scaffold was favorably
binding to EGFR DIII and can be determined as a suitable CDR acceptor to
mimic the panitumumab-EGFR interaction.