Figure 3.

a-c) Predicted length preference of selected MHC molecules according to different models. Binding to selected HLA molecules was predicted for 80,000 8–15-mer peptides and the frequency of peptide lengths in the top 2% predicted peptides calculated. d) Correlation of predicted and observed ligand length for different models. Binding to all HLA alleles present in both binding affinity and eluted ligand data sets was predicted using the four different prediction methods for 80,000 8–15-mer peptides. Subsequently, the occurrence of different peptide lengths in the top 2% predicted peptides for each molecule was calculated, and the correlation coefficient between these frequencies and the length frequencies in the eluted ligand data set calculated.