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Table 4 Effect of flanking peptides on the binding affinity to HLA DRB1*1501 allele.

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

  Experimental ARB NetMHCIIpan SMM_align NN_align MHC-PPM
Sequence IC50(nM) IC50(nM) IC50(nM) IC50(nM) IC50(nM) IC50(nM)
ENPVVHFFKNIVTPR 33 21.9 10 21 8 11
VVHFFKNIVHAAA 33 21.9 9.2 52 10.7 139
VVHFFKNIVTAAA 45 21.9 9.5 20 11.5 224
VVHFFKNIVTK AA 35 21.9 8.1 20 10.5 142
VVHFFKNIVTAK A 4 21.9 8.1 20 9.8 83
VVHFFKNIVTAAK 5 21.9 8.9 20 11.1 263
D AVVHFFKNITVA 326 82.5 23.6 25 23.8 316
AD VVHFFKNITVA 454 82.5 23.8 25 23.9 320
AAD VHFFKNITVA 264 1286.7 45 30 74.4 392
RMSE   371.90 190.78 191.84 187.13 134.35
Pearson's Corr.   0.349 0.728 0.041 0.540 0.721
  1. Experimental affinity measurements are from [11]. Predictions of other values calculated from the IEDB website[21]. MHC-PPM has the lowest root mean squared error (RMSE) and has a correlation score approximately equal to the top performing method.