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Supplementary material

Here, you will find the data set used for training and testing, as well as the T cell epitope data used for evalaution of the NetMHCIIpan-3.2 method.

Training data

The training binding data are partitioned in 5 files to be used for cross-validation. For instance does the train1 file contain training data, and test1 file test data for the first cross-validation partitioning. It is critical that this data partitioning is maintained.

The format for each of the files is

AAAGAEAGKATTEEQ 0.190842        DRB1_0101
AAAGAEAGKATTEEQ 0.006301        DRB1_0301
AAAGAEAGKATTEEQ 0.066851        DRB1_0401
AAAGAEAGKATTEEQ 0.006344        DRB1_0405
AAAGAEAGKATTEEQ 0.035130        DRB1_0701
AAAGAEAGKATTEEQ 0.006288        DRB1_0802
AAAGAEAGKATTEEQ 0.176268        DRB1_0901
AAAGAEAGKATTEEQ 0.042555        DRB1_1101
AAAGAEAGKATTEEQ 0.114855        DRB1_1302
AAAGAEAGKATTEEQ 0.006377        DRB1_1501

where the first column gives the peptide, the second column the log50k transformed binding affinity (i.e. 1 - log50k( aff nM)), and the last column the class II allele.

When classifying the peptides into binders and non-binders for calculation of the AUC values for instance, a threshold of 500 nM is used. This means that peptides with log50k transformed binding affinity values greater than 0.426 are classified as binders.

train1 (Train data) test1 (Test data)
train2 (Train data) test2 (Test data)
train3 (Train data) test3 (Test data)
train4 (Train data) test4 (Test data)
train5 (Train data) test5 (Test data)

T cell evaluation data

T cell evalaution data

The format is

>0705172A=AAHAEINEA=H2-IAb 385 gi|223299|prf||0705172A

where the first part of the fasta header contains the proteinID (0705172A), the epitope (AAHAEINEA), and the MHC restriction (H2-IAb)


K. K. Jensen, M. Andreatta, P. Marcatili, J. A. Greenbaum, Z. Yan, A. Sette, B. Peters, and M. Nielsen
Running title: Improved methods for predicting peptide binding affinity to MHC class II molecules Jurnal