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)

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Thymic selection of TCRs is modeled using the interaction E as follows:

Candidate TCR sequences are randomly generated,

The binding energy of any TCR is calculated against a repertoire of M self-peptides.

Experimental justification:

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