Coxsackieviruses are non-enveloped viruses with linear single-stranded RNA. Group B coxsackieviruses were noted to cause a spastic paralysis due to focal muscle injury and degeneration of neuronal tissue. Peptide fragments of Coxsackievirus-B coat protein can be used to select nonamers for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Analysis shows MHC class II binding peptides of coat protein from Coxsackievirus-B are important determinant for protection of host form viral infection. In this assay we predicted the binding affinity of coat protein having 281 amino acids, which shows 273 nonamers. These peptides are from a set of aligned peptides known to bind to a given MHC molecule as the predictor of MHC-peptide binding. MHCII molecules bind peptides in similar yet different modes and alignments of MHCII-ligands were obtained to be consistent with the binding mode of the peptides to their MHC class, this means the increase in affinity of MHC binding peptides may result in enhancement of immunogenicity of coat protein nonamers. Binding ability prediction of antigen peptides to major histocompatibility complex (MHC) class I & II molecules is important in vaccine development from Coxsackievirus.

Prediction of the binding ability of antigen peptides to major histocompatibility complex (MHC) class molecules is important in vaccine development from Human papilloma virus-16. The variable length of each binding peptide complicates this prediction. Such predictions can be used to select epitopes for use in rational vaccine design and to increase the understanding of roles of the immune system in infectious diseases. Antigenic epitopes of capsid protein L1 form Human papilloma virus-16 are important determinant for protection of many disorders form viral infection. This study shows active part in host immune reactions and involvement of MHC class-I and MHC II in response to almost all antigens. We also found the SVM based MHCII-IAb, MHCII-IAd, MHCII-IAg7 and MHCII- RT1.B peptide regions, which represented predicted binders from viral capsid protein (Table-1). These peptide nonamers are from a set of aligned peptides known to bind to a given MHC molecule as the predictor of MHC-peptide binding. Analysis shows potential drug targets to identify active sites against diseases.