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.