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.