Figure 2.

An artificial immune system model of a T cell repertoire. (A) Our artificial immune system (AIS) represents TCRs by a binding motif—the peptide sequence they bind to most strongly (left). Since TCR binding to peptides on MHC-I (HLA-A2:01) focuses on the six residues at positions 3–8 of the peptide, TCRs are represented as 6-AA sequences. Their affinity for any given peptide equals the maximum number of adjacent positions where the TCR binding motif matches the peptide (right). (B) This AIS model can be adapted to distinguish strings from different languages rather than self from foreign peptides. We replace 6-AA peptides with 6-letter strings randomly extracted from books in different languages (which consist of the letters (a–z) and the underscore to represent space and punctuation signs). In the language AIS, we speak of general “motifs” rather than “TCRs” to distinguish them from the TCRs in our immune system model.