Table 1.
Performances of the individual prediction tools on the HLA-A*0201 peptides from the community binding resource.
| Tool | AROC | 0.99 Specificity | 0.95 Specificity | ||||
| Rank1 | Sensitivity | Threshold2 | Rank | Sensitivity | Threshold | ||
| ARB Matrix | 0.935 | 4 | 0.188 | 2.190 | 2 | 0.601 | 42.950 |
| NetMHC 2.0 ANN | 0.932 | 1 | 0.286 | 153.000 | 1 | 0.611 | 920.000 |
| SMM | 0.922 | 2 | 0.201 | 38.092 | 4 | 0.543 | 454.865 |
| Bimas | 0.920 | 3 | 0.198 | 324.068 | 3 | 0.552 | 47.991 |
| SYFPEITHI | 0.885 | 8 | 0.170 | 27.000 | 5 | 0.421 | 24.000 |
| Multipred ANN | 0.884 | 9 | 0.140 | 5.820 | 7 | 0.373 | 5.560 |
| NetMHC 2.0 Matrix | 0.872 | 6 | 0.177 | 24.329 | 10 | 0.358 | 20.129 |
| SVMHC MHCPEP | 0.870 | 12 | 0.115 | 1.000 | 11 | 0.334 | 0.520 |
| Logistic Regression | 0.862 | 13 | 0.101 | 0.364 | 9 | 0.364 | 0.108 |
| SVMHC SYFPEITHI | 0.854 | 7 | 0.176 | 0.950 | 8 | 0.367 | 0.490 |
| HLA Ligand | 0.825 | 10 | 0.137 | 141.000 | 14 | 0.274 | 127.000 |
| Rankpep | 0.822 | 15 | 0.077 | 103.000 | 13 | 0.306 | 83.000 |
| MHCPred (Interactions) | 0.818 | 5 | 0.182 | 43.350 | 6 | 0.377 | 99.080 |
| MHCPred (position only) | 0.814 | 11 | 0.116 | 21.330 | 12 | 0.311 | 65.310 |
| Multipred HMM | 0.798 | 14 | 0.090 | 7.530 | 15 | 0.244 | 7.090 |
| Predep | 0.788 | 16 | 0.045 | -6.000 | 16 | 0.217 | -5.130 |
The predictive performance of each tool for the HLA-A*0201 community binding data is shown using two measures: AROC score, and sensitivity when specificity is 0.99 and 0.95. 1Indicates how the sensitivity of each tool compares to that of the other tools at the indicated specificity; the tool with rank 1 has the highest sensitivity. 2The scoring threshold corresponding to the indicated specificity.