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Table 1 Summary of the HLA-DR benchmark results.

From: Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

AUC
Allele SMM Gibbs TEPITOPE SVRMHC MHCpred ARB SMM-PRF NetMHCII N
A 0.730 0.697     0.758 0.749 0.756 14
B 0.740 0.705 0.736    0.762 0.748 0.750 11
C 0.710 0.690 0.714 0.688   0.719 0.719 0.722 5
D 0.737 0.710 0.723   0.606 0.717 0.749 0.754 3
Pearson correlation
Allele SMM Gibbs TEPITOPE SVRMHC MHCpred ARB SMM-PRF NetMHCII N
A 0.420 0.368     0.464 0.436 0.448 14
C 0.408 0.369   0.157   0.431 0.428 0.435 5
D 0.458 0.384    0.218 0.425 0.480 0.487 3
Spearman's rank correlation
Allele SMM Gibbs TEPITOPE SVRHMM MHCpred ARB SMM-PRF NetMHCII N
A 0.430 0.372     0.464 0.445 0.453 14
B 0.443 0.378 0.428    0.479 0.458 0.463 11
C 0.398 0.353 0.430 0.377   0.424 0.422 0.427 5
D 0.450 0.365 0.434   0.210 0.407 0.474 0.481 3
  1. The predictive performance is shown in terms of the average area under the ROC curve (upper panel), the average Pearson's correlation (middle panel), and the average Spearman's rank correlation (lower panel) for the SMM (SMM-align), Gibbs sampler [4], TEPITOPE [3], SVRMHC [7], MHCpred [15], and ARB [12] methods, respectively. The SMM-PRF method refers to the extended SMM align method including penalties for longer peptides and short amino terminal peptide flanking residues, and the NetMHCII method refers to the extended SMM align method including direct encoding of peptide flanking residues and penalties for longer peptides and short amino terminal peptide flanking residues. The last column gives the number of alleles included in each average. In A is shown the average performance for all 14 HLA-DR alleles, in B the average performance for the subset of 11 alleles covered by the TEPITOPE method, in C the average performance for the five alleles covered by the SVRMHC method, and in D the average performance for the three alleles covered by the MHCpred method. For each allele, the performance of the SMM-align, Gibbs sampler, and NetMHCII methods was estimated using five-fold cross-validation as described in Methods.