Overview of the iMatrix and homologous peptide antigens. (A) Data sets for constructing PPI matrices and iMatrix. The MHC-peptide and TCR-peptide interfaces are modelling by PPI matrices and iMatrix, respectively. (B) The template-based scoring functions infer the homologous peptide antigens through structural templates, experimental peptides, and complete pathogen genome databases. (C) Homologous peptide antigens of the template (e.g., PDB entry: 2bnq) by searching the experimental peptides and complete pathogen genome databases. (D) Amino acid profiles of the homologous peptide antigens of the template (2bnq).