Left: peptide-peptide distance matrices of MHC class I binding peptides, collected from the MHCBN dataset. Peptides that bind to each of the proteins were grouped together and labeled accordingly. Following Observation 1, a "good" distance matrix should therefore be block diagonal. Top left: The Euclidean peptide-peptide distance matrix in (see Methods for details). Bottom left: The peptide-peptide distance matrix computed using the DistBoost algorithm. Right: protein-peptide affinity matrices. The affinity between a peptide and a specific protein is computed by measuring the average distance of the peptide to all peptides known to bind to that protein (see eq. 1). Top right: the Euclidean affinity matrix. Bottom right: the DistBoost affinity matrix. DistBoost was trained on binding peptides from all of the proteins simultaneously.