PREDIVAC: CD4+T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

Background: CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by MHC class II proteins. The ability to account for MHC class II polymorphism is critical for epitope-based vaccine design tools, as different allelic variants can have different peptide repertoires. In addition, the specificity of CD4+ T-cells is often directed to a very limited set of immunodominant peptides in pathogen proteins. The ability to predict what epitopes are most likely to dominate an immune response remains a challenge. Results: We developed the computational tool Predivac to predict CD4+ T-cell epitopes. Predivac can make predictions for 95% of all MHC class II protein variants (allotypes), a substantial advance over other available methods. Predivac bases its prediction on the concept of specificity-determining residues. The performance of the method was assessed both for high-affinity HLA class II peptide binding and CD4+ T-cell epitope prediction. In terms of epitope prediction, Predivac outperformed three available pan-specific approaches (delivering the highest specificity). A central finding was the high accuracy delivered by the method in the identification of immunodominant and promiscuous CD4+ T-cell epitopes, which play an essential role in epitope-based vaccine design. Conclusions: The comprehensive HLA class II allele coverage along with the high specificity in identifying immunodominant CD4+ T-cell epitopes makes Predivac a valuable tool to aid epitope-based vaccine design in the context of a genetically heterogeneous human population. The tool is available at: http://predivac.biosci.uq.edu.au/.