Comparative results of DistBoost (left plot and bars C-D) and RANKPEP (bars A-B) on 24 MHC class II molecules. Plot legends are identical to Fig 4. As may be seen, on 19 out of the 24 molecules, DistBoost outperforms both PSSM methods. On this dataset the use of negative constraints only slightly improves performance. For numerical comparison, see additional file 1: Pepdist _SupplementaryMaterials.ps, Table 2.