As described in the Materials and Methods, 50 peptide-MHC complexes were selected from the PDB database to validate the docking process. All the peptides were extracted from the complexes, before they were re-docked to the corresponding MHC molecules using Surflex-Dock. When compared with the corresponding initial complexes, the average RMSD was 1.8 and the docking scores were all greater than 8.0 (Table 2) . Docking was also successfully performed with v-src C-tail peptide 517-524 (LPACVLEV) and an identified T cell epitope [23] to the modelled B12 MHC class I molecule, where the docking score was 10.91 and the docking complex conformation was rational. Thus, it was appropriate to use Surflex-Dock for screening T cell epitopes based on their homology-modelled structures.