Fig. 2

PigMatrix algorithm. a Residues in contact with the peptide are determined with respect to a crystal structure of either an SLA allele (Ssc) or an HLA supertype allele (Hc). Class I supertype alleles are represented by three HLA molecules. b Contact residues defined by either Ssc or Hc are extracted from HLA sequences and compiled into a library of HLA pockets (HLA pocket library). Pocket A positions and the extracted pocket sequences for Ssc and Hc are marked with *. c For a target SLA allele, contact residues (defined by Ssc or Hc) are identified by aligning the SLA sequence to a reference HLA sequence. d SLA pocket sequences are compared to those in the HLA pocket library to identify the best human match. e Binding coefficients of the best human match for each SLA pocket sequence are compiled to build a PigMatrix. Coefficients are represented in red to blue scale (high to low binding likelihood)