Computational protocol: Molecular Evolution of the Capsid Gene in Norovirus Genogroup I

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Protocol publication

[…] Using multiple methods such as LEPS, BCPRED, FBCPRED, BepiPred, Antigenic, and LBtope, we predicted the B-cell linear epitopes in the deduced amino acid sequences of the NoV capsid protein in the reference strains. In the present study, we accepted the epitopes as those identified with 4 or more methods and with >10 consecutive amino acids. The detailed data are shown in . Many epitopes were estimated in the capsid protein of each NoV GI genotype. Of them, an epitope of GI.1 (aa377–388) may be associated with the histo-blood group antigen (HBGA) binding sites (Ser377, Pro378, and Ser380) (). In addition, 1–3 epitopes in each genotype were found in the P2 domain. In the present GI strains, a consensus epitope motif, PAPxGFP, was predicted in the P2 domain in 7 of the 9 genotypes (GI.1, 3–7, and 9). These results suggested that a few viral binding sites of host cells are linked to the epitope sites in the capsid protein of the viruses. […]

Pipeline specifications

Software tools BepiPred, LBtope
Application Immune system analysis
Organisms Norovirus GI, Homo sapiens, Great Island virus