ITCell Help Page
Input Fields
- MHC type: it is possible to pick the type from the drop down menu or upload your own peptide-MHC structure (or model) in PDB
format. If uploading a custom pMHC structure it must:
- contain exactly three chains, labeled A, B and C in that order, where
the MHC is chains A and B, and the peptide chain C
- be structurally aligned with ITCell's pre-provided pMHCs, such as
DRB1*1201
- contain at most one MODEL record.
- TCR structure: Please upload TCR structure (or model) in PDB format.
- Antigen sequence: paste the sequence in FASTA format.
- e-mail address: the link with the
results of your request is sent to this address.
- Job name: optional user-provided prefix for the job name.
Output Table
The output table contains the peptides and their pMHCII, pMHCII-TCR and total normalized Z-scores as well as raw scores. The table is sorted by the total Z-score.
| Rank | Number | Peptide | Total Z-Score | pMHC Z-score | TCR Z-score | Total Score | pMHC score | TCR score |
|---|
| 1 | 298 | PKYVKQNTLKLA | -4.29 | -1.49 | -2.80 | -3834.901 | -1469.825 | -2365.076 |
| 2 | 137 | SGFFSRLNWLTK | -3.98 | -1.85 | -2.13 | -3811.219 | -1556.216 | -2255.003 |
| 3 | 210 | GSRPWVRGLSSR | -3.35 | -1.43 | -1.92 | -3677.416 | -1456.036 | -2221.38 |
| 4 | 184 | TSLYVQASGRVT | -3.09 | -2.33 | -0.76 | -3700.545 | -1669.618 | -2030.927 |
| 5 | 95 | PDYASLRSLVAS | -3.05 | -1.92 | -1.13 | -3664.554 | -1572.672 | -2091.882 |
| 6 | 92 | YDVPDYASLRSL | -2.99 | -1.94 | -1.05 | -3654.948 | -1576.865 | -2078.083 |
| 7 | 194 | VTVSTRRSQQTI | -2.81 | -1.86 | -0.95 | -3618.679 | -1557.399 | -2061.28 |
| 8 | 178 | STNQEQTSLYVQ | -2.79 | -2.45 | -0.34 | -3659.844 | -1697.544 | -1962.3 |
| 9 | 150 | GSTYPVLNVTMP | -2.70 | -1.22 | -1.48 | -3554.695 | -1406.122 | -2148.573 |
| 10 | 226 | WTIVKPGDVLVI | -2.58 | -1.31 | -1.27 | -3540.344 | -1426.903 | -2113.441 |
| 11 | 300 | YVKQNTLKLATG | -2.56 | -0.89 | -1.67 | -3508.883 | -1329.259 | -2179.624 |
| 12 | 164 | DNFDKLYIWGIH | -2.47 | -0.21 | -2.26 | -3444.223 | -1167.546 | -2276.677 |
| 13 | 94 | VPDYASLRSLVA | -2.45 | -1.08 | -1.37 | -3504.088 | -1373.17 | -2130.918 |
| 14 | 234 | VLVINSNGNLIA | -2.41 | -1.32 | -1.09 | -3515.827 | -1431.378 | -2084.449 |
| 15 | 148 | KSGSTYPVLNVT | -2.36 | -2.31 | -0.05 | -3577.71 | -1664.529 | -1913.181 |
| 16 | 227 | TIVKPGDVLVIN | -2.35 | -1.38 | -0.97 | -3508.534 | -1443.688 | -2064.846 |
| 17 | 193 | RVTVSTRRSQQT | -2.33 | -1.59 | -0.74 | -3520.188 | -1493.738 | -2026.45 |
| 18 | 169 | LYIWGIHHPSTN | -2.31 | 0.63 | -2.94 | -3358.835 | -970.534 | -2388.301 |
| 19 | 304 | NTLKLATGMRNV | -2.28 | -0.95 | -1.33 | -3467.157 | -1342.404 | -2124.753 |
| 20 | 216 | RGLSSRISIYWT | -2.18 | -1.48 | -0.70 | -3488.951 | -1468.158 | -2020.793 |
