B-Cell Epitopes, MHC Class I and MHC Class II Binding Predications

A portion of the immunogenic F or HN that interacts with B-lymphocyte was assess by hydrophilic and accessible propensity scale methods and hidden Markov model programmed software from Immune Epitope Database IEDB analysis resource (http:www.iedb.org/). For linear B-cell epitopes, BepiPred was used with default threshold value of 0.4. Surface accessibility was predicted by Emini surface accessibility tool of IEDB while the antigenicity sites by the Kolaskar and Tongaonker antigenicity method with a default threshold of 1.042 (42). Peptide binding to the MHC class I and MHC class II molecules were assessed by the IEDB tools at http://tools.iedb.org/mhci/ and http://tools.iedb/mhcii/ respectively with comparison with HLA alleles by artificial neural network (ANN), stabilized matrix network (SMN), or NetMHCII pan in addition to consensus method from combination libraries. Epitope length set as 9 mers of conserved epitopes that bind to HLA at a score ≤ 1.0 percentile rank were selected.