Figure 4

Comparison of binding contributions of 20 amino acids at position 1 of the scoring matrices generated by SMM, SMM^PMBEC, and SMM^BLOSUM. SMM was trained on the 9-mer peptide binding data set (total of 1869 data points) for HLA A*3101, yielding a single scoring matrix with dimensions 20 × 9, where the rows represent 20 residues while the columns represent 9 positions of a peptide. The scoring matrix generated by SMM serves as a reference point when binding data is well covered. SMM^PMBEC and SMM^BLOSUM, on the other hand, were trained on the 20 derived data sets, each one lacking peptides containing a residue at position 1. The figure plots the scoring matrix values for the residue specified on the x-axis in the second column of the scoring matrix of SMM alongside corresponding elements from the 20 scoring matrices of SMM^PMBEC and SMM^BLOSUM.