Antigenic epitopes of viral polyprotein: an approach for fragment based peptide vaccines from Papaya Ringspot virus

Papaya ringspot is a destructive disease characterized by a yellowing and stunting of the crown of papaya trees and assay was designed to help assign putative genome polyprotein analysis of Papaya ringspot virus strain W. We used different methods for the prediction of linear epitopes using a combination of a hidden Markov model and a propensity scale method. Data set was collected from the literature, and data sets of epitopes in the genome polyprotein having twenty four antigenic determinants in 675 residues long sequence. The structural homology modeling method is allows potential drug targets to identify active sites i.e. linear epitopes, which form antibodies in host cells. The method integrates prediction of peptide MHC class I binding; proteasomal C terminal cleavage and TAP transport efficiency. The challenges for the future are to establish the function of all of protein structures. In this assay we use of multiple methods towards the accurate identification of antigenic epitopes. The proposed approach is useful not only for plant and viral biology but it covers the wide area of vaccines and antibodies for therapeutic purposes in humans.