Fig. 2

Binding preferences learned by the single NNAlign [29] models trained on binding affinity (BA) or eluted ligand (EL) data. In the top row, motifs for the DRB1*01:01 allele are shown, with overlined logo plots (right) corresponding to models trained on EL data, and the non-overlined logo (left) corresponding to the BA trained model. Similarly, binding motifs for DRB1*15:01 and DRB5*01:01 are displayed in the middle and bottom row respectively, with overlined logos (right) also indicating the EL-trained model preferences, and the non-overlined logo plot (left) indicating the BA preference. Logos were constructed from the predicted binding cores in the top 1% scoring predictions of 900.000 random natural peptides for BA and from the top 0.1% scoring predictions for EL