Table 8.
Endogenous HLA-DR ligand benchmark
| SYF | # | NetMHCIIpan-1.0 | NetMHCIIpan-2.0 | TEPITOPE |
|---|---|---|---|---|
| Ave per ligand | 1164 | 0.800 | 0.829 | |
| Ave per allele | 28 | 0.788 | 0.797 | |
| In TEPITOPE | 17 | 0.768 | 0.786 | 0.799 |
| !In TEPITOPE | 11 | 0.819 | 0.814 | |
| IEDB | # | NetMHCIIpan-1.0 | NetMHCIIpan-2.0 | TEPITOPE |
| Ave per epitope | 1325 | 0.729 | 0.751 | |
| Ave per allele | 42 | 0.759 | 0.781 | |
| In TEPITOPE | 20 | 0.745 | 0.747 | 0.755 |
| !In TEPITOPE | 22 | 0.772 | 0.812 | |
NetMHCIIpan-1.0 is the method described by Nielsen et al. [29], NetMHCIIpan-2.0 is the pan-specific method described here, and TEPITOPE is the method described by Sturniolo et al. [1]. Ave per ligand/epitope gives the average AUC over the 1164/1325 ligands/epitopes in the benchmark data set. Ave per allele gives the average over the per allele averaged AUC values. In TEPITOPE gives the per allele average of the subset of alleles characterized by the TEPITOPE method, and !In TEPITOPE give the per-allele average performance of the alleles not characterized by the TEPITOPE method. AUC values were calculated as described in the text. For each benchmark subset, the best performing method is highlighted in bold.