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Table 2 Prediction performances as measured by AUC values of ROC curves.

From: Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

MHC Data Size SMM SMMPMBEC NetMHC
H-2_Db 303 0.909 0.901 0.933
H-2_Dd 85 0.813 0.837 0.925
H-2_Kb 223 0.811 0.833 0.850
H-2_Kd 176 0.928 0.931 0.939
H-2_Kk 164 0.772 0.793 0.790
H-2_Ld 102 0.932 0.942 0.977
HLA_A-0101 1157 0.977 0.977 0.982
HLA_A-0201 3089 0.946 0.946 0.957
HLA_A-0202 1447 0.898 0.899 0.900
HLA_A-0203 1443 0.916 0.916 0.921
HLA_A-0206 1437 0.913 0.916 0.927
HLA_A-0301 2094 0.927 0.928 0.937
HLA_A-1101 1985 0.938 0.939 0.951
HLA_A-2301 104 0.793 0.840 0.852
HLA_A-2402 197 0.803 0.801 0.825
HLA_A-2403 254 0.919 0.932 0.918
HLA_A-2601 672 0.916 0.924 0.956
HLA_A-2902 160 0.912 0.916 0.935
HLA_A-3001 669 0.935 0.941 0.947
HLA_A-3002 92 0.878 0.830 0.744
HLA_A-3101 1869 0.925 0.925 0.928
HLA_A-3301 1140 0.923 0.925 0.915
HLA_A-6801 1141 0.885 0.885 0.883
HLA_A-6802 1434 0.899 0.899 0.899
HLA_A-6901 833 0.867 0.880 0.880
HLA_B-0702 1262 0.959 0.960 0.965
HLA_B-0801 708 0.932 0.956 0.955
HLA_B-1501 978 0.937 0.940 0.941
HLA_B-1801 118 0.881 0.880 0.838
HLA_B-2705 969 0.936 0.941 0.938
HLA_B-3501 736 0.883 0.889 0.875
HLA_B-4002 118 0.832 0.843 0.754
HLA_B-4402 119 0.731 0.739 0.778
HLA_B-4403 119 0.757 0.753 0.763
HLA_B-4501 114 0.825 0.866 0.862
HLA_B-5101 244 0.876 0.895 0.886
HLA_B-5301 254 0.889 0.885 0.899
HLA_B-5401 255 0.923 0.935 0.903
HLA_B-5701 59 0.826 0.843 0.826
HLA_B-5801 988 0.942 0.945 0.961
Mamu_A-01 525 0.855 0.854 0.861
Mamu_A-02 283 0.765 0.783 0.809
Mamu_A-11 468 0.883 0.894 0.894
Mamu_B-01 205 0.949 0.956 0.967
Mamu_B-17 300 0.934 0.943 0.954
Patr_B-0101 132 0.964 0.975 0.969
average AUC   0.887 0.894 0.897
t-test|SMM   NA 0.001 0.057
t-test|NetMHC   0.057 0.470 NA
  1. For each MHC-specific binding data set, 5-fold cross validation was carried out using one of the four methods listed. Area-Under-Curve (AUCs) from the 5-fold cross validations are presented here. Also shown are p-values of average AUC values calculated using Student's t-test (2-tail, paired) with respect to the SMM and NetMHC prediction methods.