Figure 8.

Visualization of the contribution of different residues in MHC binding. Variable importance projection (VIP) of the PLS regression prediction of ln(ic50) of peptide binding using the first three principal components of each of the amino acids in the 9-mer as predictors (PC1) Principal component 1, polarity correlate; (PC2) principal compent 2, size correlate, (PC3) principal component 3, electronic correlate. Coloration is column-relative indicated by the scales for each position in the binding (a copy of this figure with details of color scaling can be found in Additional File 8; Figure S8). The colors compare the relative importance of the particular numbered residue of the binding domain among the MHC-I alleles indicated. Cells in the matrix with VIP >1 are the most relevant in explaining the binding affinity. The amino acid in the binding domain of the particular MHC-I allele (A) or MHC-II (B) in each column is indicated on the left. A 9 amino acid binding domain is shown using the standard for the MHC binding groove numbered N-terminus to C-terminus 1 through 9. For MHC-II three additional amino acids are added to each the N-terminus and C-Terminus.