Rosetta FlexPepDock Compared to Rosetta Flex ∆∆G, developed mainly for scoring protein-protein interfaces, the Rosetta FlexPepDock method was developed to predict peptide conformations within a binding pocket but also score the protein-peptide interactions. As crystallographic MHC class I protein-peptide complexes are available, the Rosetta FlexPepDock refinement protocol was used (-pep_refine) . The protocol starts by repacking all the side chains (-ex1 -ex2aro -use_input_sc), removing clashes between the protein and the mutated peptide, followed by peptide backbone optimization and rigid-body orientation using a Monte-Carlo with minimization approach, in addition to the on-the-fly side chain optimization. No low-resolution (centroid) pre-optimization was applied before the initial side chain repacking step. The protocol was repeated 50 times, outputting 50 models. The models were ranked based on the reweighed score, and the model with the lowest reweighed score was selected. The calculations are repeated for each peptide position using all the 20 natural amino acids. The method was already benchmarked on MHC class I protein-peptide complexes, including non-canonical amino acids .