3.2 Molecular docking analysis
To screen newly designed scaffolds targeting the EGFR on the surface of cancer cells, a molecular docking study was performed using the HADDOCK webserver. The results showed the binding of the ligands in the same position and orientation with acceptable binding scores as compared to the reference complexes. It verified that the selected docking parameters were optimal. Docked scaffolds are ranked based on their docking scores. Docking results revealed that three selected scaffolds out of 36 had docking scores between the range of -99 to -145.8, in which Scaf1 showed the best docking score in comparison to scFv and 5SX4 complex. The complex of all three selected scaffolds and the reference of scFv with EGFR DIII were analyzed in molecular dynamic analysis.