6). In contrast, the nonimmunogenic binders were evenly distributed around the corrected baseline (Fig. 6). The difference between the two groups of peptides was statistically highly significant

(p < 0.001, unpaired, one-tailed t-test). Ribociclib cell line Importantly, if we the reversed the baseline correction strategy and made it stability balancing; in effect asking whether affinity could provide a signal beyond stability suitable for differentiating between immunogenic and nonimmunogenic peptides, we did not find any significant difference between the two groups (p > 0.1, unpaired, one-tailed t-test). Thus, this bioinformatics-driven analysis suggested that predicted stability is a better discriminator of immunogenicity than predicted affinity is. Finally, addressing whether the two predictors identified any systematic differences in affinity motifs as compared with stability motifs, we randomly selected 500,000 natural 9-mer peptides, predicted their affinities and stabilities. Analyzing the upper 2% (10,000) predicted binders, SAHA HDAC we sorted them by predicted-binding affinity and split them in a pair-wise manner into two groups: a high-stability group and a low-stability

group. In this way, the average predicted binding is equal between the two groups (p = 0.4, paired t-test). It was next calculated how large a fraction of the peptides in each group had preferred amino acids in each, or both, primary anchor position P2 and P9 where the preferred amino acids at P2 were L and M, and preferred amino acids at P9 were V, L, and I. The results of the analysis showed

a significant reduction in the concurrent Tacrolimus (FK506) presence of both anchors in the group of low-stability peptides compared to high-stability peptide, and a corresponding increase in peptides missing optimal P2 anchor residues, but not in peptides missing optimal P9 anchor residues (Table 3). Thus, the ANN-driven analysis confirms the experimental findings that unstable binders tend to lack an optimal anchor residue in P2. Many sequential processes are involved in both the generation and recognition of MHC-I-restricted CTL ligands. A picture of the sequence and relative contribution of these different processes in the generation of T-cell epitopes is emerging (as excellently reviewed in [[6, 22, 23]]), however, it is still incomplete and may still lack important undiscovered components [[6, 22, 23]]. Roughly, it has been estimated that one of 7–8 possible peptides are successfully generated by the processing machinery, that one in 50–200 processed peptides are successfully bound to MHC-I, and that one of two pMHC-I complexes are successfully matched by a corresponding specificity in the T-cell repertoire [[6, 22, 23]].