Predictor for the effect of amino acid composition on CD4Â + T cell epitopes preprocessing

Predictive tools for all levels of CD8 + T cell epitopes processing have reached a maturation level. Good prediction algorithms have been developed for proteasomal cleavage, TAP and MHC class I peptide binding. The same cannot be said of CD4 + T cell epitopes. While multiple algorithms of varying accuracy have been proposed for MHC class II peptide binding, the preprocessing of CD4 + T cell epitopes is still lacking a good prediction algorithm. CD4 + T cell epitopes generation includes several stages, not all which are well-defined. We here group these stages to produce a generic preprocessing stage predictor for the cleavage processes preceding the presentation of epitopes to CD4 + T cell. The predictor is learnt using a combination of in vitro cleavage experiments and observed naturally processed MHC class II binding peptides. The properties of the predictor highlight the effect of different factors on CD4 + T cell epitopes preprocessing. The most important factor emerging from the predictor is the secondary structure of the cleaved region in the protein. The effect of the secondary structure is expected since CD4 + T cell epitopes are not denatured before cleavage. A website developed based on this predictor is available at: http://peptibase.cs.biu.ac.il/PepCleave_cd4/.