Additional file 1.
Predictive performance for 14 HLA-DR alleles in the quantitative IEDB benchmark data set. The performance is estimated using five-fold cross-validation, and the predictive performance is estimated in terms of the Pearson's correlation. SMM-align is the SMM-align method described by Nielsen et al.  re-trained on the quantitative benchmark data set. NN is the standard NN-based method, NN-W is the NN-based method including data redundancy step-size rescaling, NN-P1 is the NN-based method including PSSM-P1 amino acid encoding, NN-W-P1 is the NN-based method including step-size rescaling and P1 amino acid encoding. NN-xPFR is the NN-W-P1 method excluding peptide-flanking residue encoding. For each allele, the best performing NN method is highlighted in bold and the best performing of all methods is underlined.
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Nielsen and Lund BMC Bioinformatics 2009 10:296 doi:10.1186/1471-2105-10-296