2.3 Docking
To find potential candidates against the EGFR DIII, molecular docking
was carried out to screen conformations of designed ligands with high
stability at the binding site of EGFR DIII by the HADDOCK 2.2 web server
[12]. Initially, molecular docking analysis was performed with the
reference molecules in the active site of EGFR to re-produce the same
conformation similar to the co-crystallized ligand (5SX4). The result of
scFv docking with EGFR DIII was also used as the second reference
molecule. Among all generated receptor-ligand complexes, models with
lower binding energy were selected for MD simulation.