Surflex-Dock [31] is used to dock ligands into a protein-binding site and it is particularly successful at eliminating false positive results [32] while offering unparalleled enrichment in virtual highthroughput screening combined with state-of-the-art speed, accuracy, and usability [33, 34] . To test the feasibility of using Surflex-Dock for docking MHC molecules and peptides, 50 peptide-MHC complexes retrieved from the PDB database were separated and re-docked using the Surflex-Dock program. The RMSD was calculated for each modelled pair and crystal structure pair to evaluate the docking program.