Table 2 Effect of preferences at TCR contacts and positions outside the peptide core. Table of modified CII261-273 peptides with associated measured IC50 values and the predictions of selected MHC-II prediction algorithms.
Peptide | Positions modified | Measured IC50 (nM) | NetMHCII 2.3 IC50 (nM) | NetMHCIIpan 4.0 EL Rank (%) |
|---|---|---|---|---|
AAGFKGEQGPKGEPG | — | 2910 | 165 | 0.3 |
AAGFKGEQGPKGYPG | P10 | 115 | 138 | 0.4 |
AGGFKGEQGPKGYNG | P(-2), P10, P11 | 134 | 100 | 0.4 |
AAGFKGEQGPKGGPG | P10 | 12,101 | 161 | 0.4 |
AIGFKGEQGPKGGVG | P(-2), P10, P11 | 23,274 | 144 | 0.6 |
AAEFRNEDGPLGEPG | TCR Contacts | 80 | 636 | 0.3 |
AAFFGWEWGPDGEPG | TCR Contacts | 5,668 | 4,540 | 28 |
AAGFPGEQGPKGEPG | P2 |  > 50,000 | 12,348 | 31 |
