Finding Functional T-epitopes

Exhibit 1. Predicted and actual CTL epitopes for Blike glycoprotein of HPV8. The only strong epitope predicted by EpiQuest T in the mature sequence corresponds to the only existing functional HLA-A2 epitope in this protein.

Exhibit 2. Other examples of sensitivity  of  EpiQuest-T. The program detects as the main epitope the sequence of the actual strong CTL-epitope in the sequence. To view the full size image, click on it.

EpiQuest™-T

All current programs that predict T-epitopes are based on either of two algorithms: most of them searches for peptide capable of fitting the groove of the respective MHC molecule (and be presented to T-cell receptor). A few programs are looking for cleavage sites in the molecule that may generate peptides that can be presented by MHC.

 

However, the fact that the peptide can be presented by MHC does not mean that it can stimulate an effective immune response. If one looks at the databases of predicted and actually working peptides (what one would call “strong epitope”), a very small fraction actually works in functional assays. EpiQuest-T finds the areas of protein sequence that with a high probability contain “strong T-epitopes”.

 

With examples presented, you can see that it finds the only working epitope, and with high precision. EpiQuest-T currently (v.2.1.7) works for CTL epitopes of HLA-A002 haplotype; other haplotypes are in development.

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