Visualization of peptide binding to MHC-I and MHC-II. Variable importance projection (VIP) of the PLS regression prediction of ln(ic50) of peptide binding by using the first three principal components of the amino acids in each of the amino acids in the 9-mer as predictors for MHC-I (5A)and 15-mer for MHC-II (5B). Coloration is uniform over all cells in the matrix for each principal component (a copy of this figure with details of color scaling can be found in Additional File 8; Figure S5). The colors compare the relative importance of the particular numbered residue of the binding domain among all of the MHC alleles indicated. (PC1) Principal component 1 (polarity correlate), (PC2) Principal component 2 (size correlate), and (PC3) Principal component 3 (elctronic correlate). Cells in the matrix with VIP >1 are the most relevant in explaining the binding affinity. The particular MHC allele in each row 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-I. A 15 amino acid binding domain is shown using the standard for the MHC-II binding groove numbered N-terminus to C-terminus 1 through 9 flanked by 3 amino acids on the N-terminus and C-terminus.
Bremel and Homan Immunome Research 2010 6:7 doi:10.1186/1745-7580-6-7