Supplementary material for update to the NetCTL method (version 1.2):

Original method

An integrative approach to CTL epitope prediction. A combined algorithm integrating MHC-I binding, TAP transport efficiency, and proteasomal cleavage predictions.

The two data sets used in the benchmark calculation are given below in the FASTA format. For each entry is given the Swiss-Prot name of the protein "hosting" the epitope, the epitope position, the epitope sequence, and the HLA supertype.

SYFPEITHI dataset
HIV dataset
HIV_EpiJen dataset
List of known CTL epitopes from SYFPEITHI and the Los Alamos HIV databases
Difference between the A1, A2, and A3 epitope-protein pairs for the HIV and HIV_EpiJen datasets
Supplementary figure: Comparing specificities on the HIV EpiJen dataset

References

M. V. Larsen, C. Lundegaard, K. Lamberth, S. Buus, S. Brunak, O. Lund, and M. Nielsen An integrative approach to CTL epitope prediction. A combined algorithm integrating MHC binding, TAP transport efficiency, and proteasome cleavage predictions. European Journal of Immunology 2005 Aug;35(8):2295-303.