The analysis of amino acid sequences of the Infectious Bursal Disease virus (IBDV) and chicken MHC II proteins was done to identify their features. Antigenicity plot of the 1011 residue long IBDV sequence revealed 38 potential antigenic sites of the virus. Eleven MHC II binding peptides of IBDV VP2 were also predicted. Protein interface recognition sites for IBDV VP2 and chicken MHC II were predicted using a software PIR. In case of IBDV VP2, 21 residues and in case of chicken MHC II, 26 residues were identified as very likely to be involved in protein interface formation. Protein docking of amino acid sequences of IBD Virus and chicken MHC II molecules indicated a possible receptor – ligand type relationship.
Keywords: IBD virus, Infectious Bursal Disease, MHC II, bioinformatic analysis, chicken, host -pathogen interaction.