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Table 3 Results of MHC-PPM in MHC class II predictions in Wang2010 dataset [23].

From: Prediction of peptides binding to MHC class I and II alleles by temporal motif mining

Allele # Peptides ARB SMM-align NN-align MHC-PPM
  ALL SR ALL SR ALL SR ALL SR ALL SR
HLA-DPA1*0103-DPB1*0201 1404 603 0.823 0.745 0.921 0.767 0.943 0.793 0.931 0.772
HLA-DPA1*01-DPB1*0401 1337 540 0.847 0.746 0.930 0.767 0.947 0.802 0.935 0.751
HLA-DPA1*0201-DPB1*0101 1399 604 0.824 0.743 0.909 0.786 0.944 0.818 0.938 0.806
HLA-DPA1*0201-DPB1*0501 1410 586 0.859 0.709 0.923 0.728 0.956 0.787 0.948 0.773
HLA-DPA1*0301-DPB1*0402 1407 602 0.821 0.771 0.932 0.818 0.949 0.828 0.935 0.815
HLA-DQA1*0101-DQB1*0501 1739 584 0.871 0.741 0.930 0.783 0.945 0.805 0.949 0.754
HLA-DQA1*0102-DQB1*0602 1629 593 0.777 0.708 0.838 0.734 0.880 0.762 0.842 0.730
HLA-DQA1*0301-DQB1*0302 1719 596 0.748 0.637 0.807 0.663 0.851 0.693 0.845 0.709
HLA-DQA1*0401-DQB1*0402 1701 585 0.845 0.643 0.896 0.761 0.922 0.742 0.920 0.778
HLA-DQA1*0501-DQB1*0201 1658 589 0.855 0.700 0.901 0.736 0.932 0.777 0.919 0.766
HLA-DQA1*0501-DQB1*0301 1689 602 0.844 0.756 0.910 0.801 0.927 0.811 0.915 0.771
HLA-DRB1*0101 6427 3504 0.770 0.710 0.798 0.756 0.843 0.763 0.821 0.758
HLA-DRB1*0301 1715 1136 0.753 0.728 0.852 0.808 0.887 0.829 0.828 0.747
HLA-DRB1*0401 1769 1221 0.731 0.668 0.781 0.721 0.813 0.734 0.763 0.711
HLA-DRB1*0404 577 474 0.707 0.681 0.816 0.789 0.823 0.803 0.885 0.717
HLA-DRB1*0405 1582 1049 0.771 0.716 0.822 0.767 0.870 0.794 0.831 0.734
HLA-DRB1*0701 1745 1175 0.767 0.736 0.834 0.796 0.869 0.811 0.846 0.804
HLA-DRB1*0802 1520 1017 0.702 0.649 0.741 0.689 0.796 0.698 0.752 0.687
HLA-DRB1*0901 1520 1042 0.747 0.654 0.765 0.696 0.810 0.713 0.762 0.671
HLA-DRB1*1101 1794 1204 0.800 0.777 0.864 0.829 0.900 0.847 0.858 0.811
HLA-DRB1*1302 1580 1070 0.727 0.667 0.797 0.754 0.814 0.732 0.768 0.717
HLA-DRB1*1501 1769 1171 0.763 0.696 0.796 0.741 0.852 0.756 0.813 0.745
HLA-DRB3*0101 1501 987 0.709 0.678 0.819 0.780 0.856 0.798 0.782 0.718
HLA-DRB4*0101 1521 1011 0.785 0.747 0.816 0.762 0.870 0.789 0.860 0.772
HLA-DRB5*0101 1769 1198 0.760 0.697 0.832 0.776 0.886 0.795 0.843 0.812
H-2-Iab 660 546 0.800 0.775 0.855 0.830 0.858 0.847 0.824 0.807
Average    0.785 0.711 0.849 0.763 0.882 0.782 0.858 0.755
WeightedAverage    0.784 0.709 0.843 0.762 0.879 0.778 0.853 0.754
  1. Each method contains results from all of the peptides (ALL) and the similarity reduced data (SR). The best-performing method for each allele in ALL dataset is marked by bold and the best performing method in SR dataset is underlined.