New Approaches to in silico Design of Epitope-Based Vaccines

104 APPENDIX B. EPITOPE DISCOVERY
Table B.6: Leave-one-out validation performance of pan-specific MHC-I binding predictors.
The table lists the allele-wise PCCs of the pan-specific predictors NetMHCpan and Uni-
Tope in a leave-one-out validation. Performance is measured in a five-fold cross validation on the
IEDB h9 data and the given folds.
Allele NetMHCpan UniTope
HLA-A*01:01 0.378 0.215
HLA-A*02:01 0.857 0.798
HLA-A*02:02 0.805 0.782
HLA-A*02:03 0.795 0.809
HLA-A*02:06 0.803 0.817
HLA-A*03:01 0.760 0.734
HLA-A*11:01 0.835 0.736
HLA-A*23:01 0.811 0.672
HLA-A*24:02 0.647 0.507
HLA-A*24:03 0.729 0.228
HLA-A*26:01 0.535 0.408
HLA-A*29:02 0.692 0.553
HLA-A*30:01 0.633 0.628
HLA-A*30:02 0.559 0.478
HLA-A*31:01 0.695 0.661
HLA-A*33:01 0.638 0.636
HLA-A*68:01 0.688 0.513
HLA-A*68:02 0.721 0.592
HLA-A*69:01 0.711 0.546
HLA-B*07:02 0.516 0.292
HLA-B*08:01 0.385 0.043
HLA-B*15:01 0.443 0.357
HLA-B*18:01 0.624 0.474
HLA-B*27:05 -0.057 0.010
HLA-B*35:01 0.656 0.618
HLA-B*40:01 0.426 0.278
HLA-B*40:02 0.769 0.815
HLA-B*44:02 0.802 0.753
HLA-B*44:03 0.731 0.797
HLA-B*45:01 0.556 0.570
HLA-B*51:01 0.668 0.635
HLA-B*53:01 0.753 0.801
HLA-B*54:01 0.614 0.513
HLA-B*57:01 0.740 0.575
HLA-B*58:01 0.453 0.224
Average 0.639 0.545