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Open Access Research article

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

Morten Nielsen*, Claus Lundegaard and Ole Lund

Author Affiliations

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark

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BMC Bioinformatics 2007, 8:238  doi:10.1186/1471-2105-8-238

Published: 4 July 2007

Additional files

Additional file 1:

Details of the benchmark calculation covering the 14 HLA-DR alleles. The predictive performance is shown in terms of the Pearson's correlation (upper table) and the Spearsman's rank correlation (lower table) for the SMM-align, Gibbs sampler [1], TEPITOPE [2], SVRMHC [3], MHCpred [4], and ARB methods, respectively. The SMM-PRF method refers to the extended SMM-align method including penalties for long peptides and short amino terminal peptide flanking residues, and the NetMHCII method refers to the final extended SMM align method including direct encoding of peptide flanking residues and penalties for longer peptides and short amino terminal peptide flanking residues. The first column gives the allele names as 1*0101 for DRB1*0101 etc The last column gives the number of peptide data included for each allele. For each allele, the performance of the SMM-align, Gibbs sampler, and NetMHCII methods was estimated using five-fold cross-validation as described in the text.

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Additional file 2:

MHC-II binding affinity as a function of peptide length for three MHC-II alleles, DRB1*0101, DRB1*0401, and DRB1*1501. In the left figure results for the DRB1*0101 allele are displayed, and the right figure shows an average over the 3 alleles. For each data set, the mean binding affinity for peptides of a given length is shown as a function of the peptide length. In black is shown the curves for the data in the AntiJen data set [5]. In red is shown the curves for the data in the IEDB data set [15]. The green curves show histograms of the length distribution of natural MHC ligands as downloaded from the SYFPEITHI database [31]. As suggested by Cheng et al., values for peptide lengths where no affinity data are available are set to the mean binding value over the entire data set. All curves are smoothed using a running mean of length three. It is clear from the figure that the AntiJen and IEDB data sets have very distinct mean binding profiles for short peptides (length < 15 amino acids). In this regime of peptide lengths, the IEDB data set, in contrast to the AntiJen data set, seems to follow an affinity profile in agreement with the observed length profile for natural MHC-II ligands. For longer peptides, both the AntiJen and IEDB data sets follow a similar affinity profile that deviate strongly from the length profile of natural MHC-II ligands.

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