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

BMC Bioinformatics

Table 4 Summary of the mouse H2-IA benchmark.

The predictive performance is shown in terms of the average area under the ROC curve. The methods included in the benchmark are SMM (SMM-align), NetMHCII (the extended SMM-align method including direct encoding of peptide flanking residues and penalties for longer peptides and short amino terminal peptide flanking residues), ARB [12], and PredBalbc [22]. The performance of the SMM and NetMHCII methods was estimated using five-fold cross-validation as described in Methods.

ISSN: 1471-2105