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Figure 4 | BMC Bioinformatics

Figure 4

From: Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

Figure 4

Comparison of binding contributions of 20 amino acids at position 1 of the scoring matrices generated by SMM, SMMPMBEC, and SMMBLOSUM. 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. SMMPMBEC and SMMBLOSUM, 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 SMMPMBEC and SMMBLOSUM.

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