Table 4.
Predictive performance of the superMHC method compared with those of NetMHCII-2.3, NetMHCIIpan-3.2, and their consensus method on the new test set in terms of RMSE.
| MHC Molecules | #Peptides | NetMHCII-2.3 | NetMHCIIpan-3.2 | Consensus (Net) | superMHC |
| DRB1_0101 | 1427 | 0.241 | 0.244 | 0.240 | 0.249 |
| DRB1_0301 | 912 | 0.235 | 0.222 | 0.224 | 0.230 |
| DRB1_0302 | 148 | 0.260 | 0.233 | ||
| DRB1_0401 | 1392 | 0.210 | 0.221 | 0.212 | 0.238 |
| DRB1_0402 | 6 | 0.351 | 0.238 | 0.288 | 0.292 |
| DRB1_0404 | 34 | 0.211 | 0.203 | 0.203 | 0.178 |
| DRB1_0405 | 14 | 0.202 | 0.236 | 0.213 | 0.229 |
| DRB1_0701 | 125 | 0.284 | 0.277 | 0.277 | 0.278 |
| DRB1_0801 | 9 | 0.186 | 0.126 | 0.153 | 0.105 |
| DRB1_0806 | 118 | 0.363 | 0.326 | ||
| DRB1_0813 | 1370 | 0.251 | 0.229 | ||
| DRB1_0819 | 116 | 0.213 | 0.206 | ||
| DRB1_0901 | 28 | 0.200 | 0.256 | 0.223 | 0.260 |
| DRB1_1101 | 163 | 0.338 | 0.350 | ||
| DRB1_1104 | 7 | 0.339 | 0.292 | ||
| DRB1_1201 | 115 | 0.335 | 0.340 | ||
| DRB1_1202 | 124 | 0.370 | 0.353 | ||
| DRB1_1301 | 9 | 0.352 | 0.399 | ||
| DRB1_1302 | 17 | 0.371 | 0.423 | ||
| DRB1_1402 | 125 | 0.255 | 0.237 | ||
| DRB1_1404 | 30 | 0.198 | 0.193 | ||
| DRB1_1412 | 116 | 0.310 | 0.313 | ||
| DRB1_1501 | 132 | 0.298 | 0.300 | ||
| DRB1_1502 | 6 | 0.361 | 0.447 | ||
| DRB1_1601 | 16 | 0.240 | 0.233 | ||
| DRB3_0101 | 41 | 0.281 | 0.242 | ||
| DRB3_0301 | 159 | 0.297 | 0.313 | ||
| DRB4_0101 | 18 | 0.193 | 0.207 | ||
| DRB5_0101 | 1331 | 0.226 | 0.237 | ||
| DRB5_0102 | 8 | 0.231 | 0.219 | ||
| DRB5_0202 | 16 | 0.190 | 0.233 | ||
| HLA-DPA10103-DPB10201 | 751 | 0.126 | 0.118 | ||
| HLA-DQA10302-DQB10301 | 9 | 0.203 | 0.045 | ||
| Average I | 8892 | 0.236 | 0.225 | 0.226 | 0.229 |
| Average II | 0.261 | 0.259 |
“Average I” is calculated over 9 MHC molecules covered by NetMHCII-2.3. “Average II” is calculated over all 33 MHC molecules. The smallest RMSE score in each row is marked in bold.