Fig. 2.

Fine-tuning improves pMHC-peptide binder classification to state-of-the-art levels. (A) Structure prediction for a non-interacting peptide-MHC pair using AlphaFold before (Left) and after (Right) fine-tuning on joint structure prediction and binder classification. The peptide is incorrectly predicted to bind the MHC in the first case but not the second. (B and C) Binder/non-binder peptide classification ROC curves on test sets (Methods): (B) MHC Class I, (C) MHC Class II. AlphaFold (green), combined structure prediction-classification model (purple), and NetMHCpan (pink).