Model
Focus on the energetics of binding of TCR to peptide:
Assume a pairwise interaction between the peptide amino-acids and corresponding ones on the TCR, resulting in binding energy
(Miazawa-Jernigan matrix J)
A. Kosmrlj, A. Jha, E.S. Huseby, M. Kardar, & A.K. Chakraborty, PNAS 105, 16671 (2008) (offlline)
Thymic selection of TCRs is modeled using the interaction E as follows:
Candidate TCR sequences are randomly generated. (This ignores potential V(D)J generation bias.)
The binding energy of any TCR is calculated against a repertoire of M self-peptides.
(Experimental justification)
