Figure 7From: An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approachesVisualization of the contribution of the different physical properties of amino acid to the peptide binding to MHC-II. 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 15-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 domain (a copy of this figure with details of color scaling can be found in Additional File 8; Figure S7). The amino acid in the binding domain of the particular MHC-II allele in each column is indicated on the left. A 15-amino acid binding domain is shown using the standard for the MHC binding groove numbered N-terminus to C-terminus 1 through 9 along with the additional 3 N-terminal and 3 C-terminal residues. The colors compare the relative importance of the particular numbered residue of the binding domain among the MHC-II alleles indicated. Cells in the matrix with VIP >1 are the most relevant in explaining the binding affinity.Back to article page