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Table 2 LOO benchmark comparison of MHC2SKpan with four well-known pan-specific methods on NielsenSet2. MRTA, Tepan, Pan1.0, Pan2.0 and MKpan are the abbreviations for MultiRTA, TEPITOPEpan, MetaMHCIIpan-1.0, MetaMHCIIpan-2.0 and MHC2SKpan, respectively. For each allele, we display the largest value in boldface.

From: MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction

   AUC PCC
allele count MRTA Tepan Pan1.0 Pan2.0 MKpan MRTA Tepan Pan1.0 Pan2.0 MKpan
DRB1*01:01 5166 0.801 0.726 0.778 0.794 0.802 0.619 0.447 0.571 0.627 0.628
DRB1*03:01 1020 0.751 0.663 0.746 0.792 0.778 0.438 0.277 0.465 0.560 0.543
DRB1*04:01 1024 0.763 0.724 0.775 0.802 0.801 0.534 0.423 0.591 0.652 0.657
DRB1*04:04 663 0.835 0.783 0.852 0.869 0.862 0.623 0.504 0.693 0.731 0.714
DRB1*04:05 630 0.808 0.760 0.808 0.823 0.828 0.566 0.456 0.594 0.626 0.631
DRB1*07:01 853 0.817 0.759 0.825 0.886 0.889 0.620 0.499 0.655 0.753 0.761
DRB1*08:02 420 0.786 0.773 0.841 0.869 0.851 0.523 0.452 0.637 0.70 0.679
DRB1*09:01 530 0.674 0.615 0.653 0.684 0.674 0.380 0.259 0.406 0.474 0.471
DRB1*11:01 950 0.819 0.726 0.799 0.875 0.894 0.603 0.450 0.580 0.721 0.761
DRB1*13:02 498 0.698 0.661 0.658 0.648 0.639 0.365 0.326 0.323 0.337 0.341
DRB1*15:01 934 0.729 0.694 0.738 0.769 0.763 0.513 0.437 0.533 0.598 0.597
DRB3*01:01 549 0.813 0.675 0.716 0.733 0.70 0.603 0.332 0.449 0.474 0.423
DRB4*01:01 446 0.746 0.694 0.724 0.762 0.764 0.508 0.370 0.448 0.515 0.529
DRB5*01:01 924 0.788 0.680 0.831 0.879 0.883 0.543 0.421 0.627 0.722 0.737
average 14607 0.773 0.710 0.767 0.799 0.795 0.531 0.404 0.541 0.606 0.605