Abstract

Although discontinuous epitopes make up 90% of total number of B-cell epitopes, however, because of difficulties in the development of method for their prediction, most of the B-cell epitope prediction methods today focus on continuous epitopes. To serve for the development of vaccine against H5N1 virus, we have been studying on in silico prediction of T- and B-cell continuous as well as B-cell discontinuous epitopes on H5N1 viral antigens. In this study, using the homology modeling method, we have generated structures of matrix protein of the H5N1 virus and predicted B-cell discontinuous epitopes. 60 out of 72 predicted residues were similar with those reported by the CEP method (Conformational Epitope Prediction). All predicted aminoacid residues were hydrophilic, polar, electrically charged and located on the surface of the antigen structures.