We were able to achieve similar performances while testing the model on other peptide scanning data, e.g. La Rosa et al. [19] (HLA-A2 restricted CMV epitope, data not shown). Thus, our . The x-axis shows the relative IFNc secretion measured for 171 single mutants of SLFNTVATL (SFL9). Immunogenicity was grouped in four bins with average ELISPOT responses of 0, 0.15, 0.50 and 0.85 of maximal ELISPOT for SFL9. In both figures the y-axis shows the predicted CTL recognition in terms of BLOSUM35 similarity scores (see Eq. 2). Unfavorable (non-conservative) substitutions (low x) are associated with a low similarity score (low y) whereas conservative substitutions (high x) in general are associated with higher similarity scores (high y). (B) Observed and predicted recognition of patient derived SLYNTVATL (SYL9) variants with 0-3 mutations. The axis shows the relative IFNc and peptide similarity scores. Note, that the IFNc response falls to a half when peptide similarity is around 0.85. doi:10.1371/journal.pone.0001831.g002 model was able to predict cross-reactivity of T cell clones measured in at least two different peptide-scanning library studies.