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A virus disease caused of crop losses to groundnut in Andhra Pradesh during kharif in the year 2000. It was presumed to be caused by Groundnut bud necrosis virus (GBNV), a virus known to be widely distributed in India. It is one among the important infestations affecting groundnut cultivation especially during summer. Nucleocapsid peptides of groundnut bud necrosis virus are most suitable for subunit vaccine development because with single epitope, the immune response can be generated in large population. Analysis shows MHC class II binding peptides of coat protein from SMV are important determinant for protection of many plants form viral infection. In this assay we predicted the binding affinity of SMV genome polyprotein having 276 amino acids, which shows 268 nonamers. In this analysis, we found the SVM based MHCII-IAb peptide regions, 171-PLAYYQNVK, 95-RTEAFIRTK, 90-DWTFKRTEA, 37-KAFYDANKT, (optimal score is 1.059); MHCII-IAd peptide regions, 159-LSSMTGLAP, 68-KSGKYVFCG, 11-KIKELLAGG, 49-TFTNCLNIL, (optimal score is 0.702); MHCII-IAg7 peptide regions, 128-PLVAAYGLN, 127-LPLVAAYGL, 18-GGSADVEIE, 39-FYDANKTLE, (optimal score is 1.551); and MHCII-RT1.B peptide regions, 49-TFTNCLNIL, 247-DKAFSASLS, 110-KSKNDAAKQ, 92-TFKRTEAFI , (optimal score is 1.092) which represented predicted binders from nucleocapsid protein. The method integrates prediction of peptide MHC class I binding; proteasomal C terminal cleavage and TAP transport efficiency of the nucleocapsid protein of GBNV. Thus a small fragment of antigen can induce immune response against whole antigen. This theme is implemented in designing subunit and synthetic peptide vaccines.

The bee venom is used for treating a wide variety of conditions from acute tendonitis to chronic back pain to rheumatoid arthritis (RA). The major treatment is gene therapy or recombinant DNA vaccines involved in targeting multiple antigenic components to direct and empower the immune system to protect the host from infection. Limitations of therapy for the treatment of patients suffering from various adverse reaction and contraindications are always experienced. Antigenic epitopes on melittin protein of Apis dorsata are important determinants of protection against rheumatoid arthritis. As our knowledge of the immune responses to a protein antigen progressed, it became clear that the whole protein is not necessary for raising the immune response, but small segments as 4-AILKVLSTGLPALIS-18 of protein called the antigenic determinants or the epitopes, are sufficient for eliciting the desired immune response. Immunization cassettes should be capable of immunizing broad immunity against both humoral and cellular epitopes, thus giving vaccines the maximum ability to deal with A. dorsata immune escape against rheumatoid arthritis.

Peptide fragments from alfalfa mosaic virus involved multiple antigenic components directing and empowering the immune system to protect the host from infection. MHC molecules are cell surface proteins, which take active part in host immune reactions and involvement of MHC class-I & II in response to almost all antigens. Coat protein of alfalfa mosaic virus contains 221 aa residues. Analysis found five MHC ligands in coat protein as 64-LSSFNGLGV-72; 86- RILEEDLIY-94; 96-MVFSITPSY-104; 100- ITPSYAGTF-108; 110- LTDDVTTED-118; having rescaled binding affinity and c-terminal cleavage affinity more than 0.5. The predicted binding affinity is normalized by the 1% fractil. The MHC peptide binding is predicted using neural networks trained on c-terminals of known epitopes. In analysis predicted MHC/peptide binding is a log transformed value related to the IC50 values in nM units. Total numbers of peptides found are 213. Predicted MHC binding regions act like red flags for antigen specific and generate immune response against the parent antigen. So a small fragment of antigen can induce immune response against whole antigen. This theme is implemented in designing subunit and synthetic peptide vaccines. The sequence analysis method allows potential drug targets to identify active sites against plant diseases. The method integrates prediction of peptide MHC class I binding; proteosomal c-terminal cleavage and TAP transport efficiency.

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