There are three classes that capture information about the 3D structure of complexes: Epitope-MHC Complex, Epitope-MHC-TCR Complex, and Antigen-Antibody Complex. The Epitope-MHC Complex, Epitope-MHC-TCR Complex, and Antigen-Antibody Complex classes are used as restrictions on properties of the MHC Binding, T Cell Response, and B Cell Response classes respectively ( Figures 5A, 6A, and 6B) . These Complex classes capture the Protein Data Bank (PDB) Identifier, which provides detailed information about 3D structures. The Protein Data Bank [22, 23] contains approximately 1600 3D structures that are of immunological interest. Other information that is not available in PDB, such as the atom pairs that are involved in the interactions between molecules, the specific residues, the contact area of the molecules, and allosteric effect, is also captured here.