Theoretical Biology & Bioinformatics

tree of life


  • NetChop : A web server to predict cellular proteolysis (Immuno- and constitutive proteasome, TAP).
  • NetMHC and NetMHCpan : Web servers to predict peptide binding to MHC molecules (several alleles and supertypes are available).
  • CD8 T cell immunogenicity: This tool uses amino acid properties as well as their position within the peptide to predict the immunogenicity of a class I peptide MHC (pMHC) complex.

    Related Publications:

    • Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Kesmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013 Oct;9(10):e1003266. doi: 10.1371/journal.pcbi.1003266.
    • Calis JJ, de Boer RJ, Kesmir C. Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol. 2012;8(3):e1002412. doi: 10.1371/journal.pcbi.1002412.
    • Nielsen M, Lundegaard C, Lund O, Kesmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 2005 Apr;57(1-2):33-41.
    • Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens. 2003 Nov;62(5):378-84. PubMed PMID: 14617044.