Supplementary Figure 9: Comparison and structural anlaysis of MARIA and NetMHCIIpan for mutated CLIP peptides.

(a) Key amino acid residues on CLIP peptide (PVSKMRMATPLLMQALP) interacting with HLA-DRB1*01:01 complex. Based on published crystal structures (PDB ID 3PDO), seven amino acids in the natural ligand of HLA-DR (CLIP) form hydrogen bonds with either HLA-DRA1 or HLA-DRB1*01:01. (b) MARIA scores change consistently with the influence of CLIP amino acid mutations. Seven mutated CLIP HLA-DR complexes with single amino acid substitution was created in silico according to the key residues defined in a. Mutated peptide atom positions in the HLA-DR environment were optimized with FlexPepDock. M107W, L113R, and M115R have higher MARIA percentile than CLIP WT (91.60% percentile), which is consistent with their gaining of hydrogen bonds or enhanced Van der Waals interactions resulting from mutations. R108 has lower MARIA percentile than CLIP WT, which is consistent with its loss of one hydrogen bound. K106R and K106D have about the same MARIA scores as WT (91.42% and 90.48%) despite opposite charges of these two mutants. Structure analysis showed the amino acid side chain in the position 106 does not contribute to hydrogen bond forming. Six out of seven mutants have about the same NetMHCIIpan percentiles compared to WT (99.85%-99.99%). NetMHCIIpan percentiles were calculated with 100% - NetMHCIIpan rank.