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.