The four haplotypes selected in this study belonged to 11 commonly encountered unique haplotypes (B2, B4, B5, B6, B7, B12, B13, B14, B15, B19, and B21) and the motifs of their binding peptides were previously reported [22, 23] . The peptide-binding groove of the chicken MHC class I molecule contains a1 and a2 domains [18] , so only those two domains were used for modelling and analysis in this study. BLASTP search results showed that the chicken MHC class I molecule 3BEV (PDB accession number) belonging to the B21 haplotype had the highest sequences identity and similarity with the four target sequences. The sequence identity and similarity between 3BEV and B4, B12, B15, and B19 were 84.3%, 84.3%, 87.1%, and 89.9%, and 89.3%, 89.9%, 91%, and 93.3%, respectively. The sequence alignments of the four target sequences and 3BEV are shown in Fig. 1. 3BEV has been crystallized to a high resolution of 2.1 Å , so it was selected as the template for modelling the four protein structures.