Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis

Ivan Dimitrov, Panayot Garnev, Darren R. Flower, Irini Doytchinova

Research output: Contribution to journalArticlepeer-review


A proteochemometrics approach was applied to a set of 2666 peptides binding to 12 HLA-DRB1 proteins. Sequences of both peptide and protein were described using three z-descriptors. Cross terms accounting for adjacent positions and for every second position in the peptides were included in the models, as well as cross terms for peptide/protein interactions. Models were derived based on combinations of different blocks of variables. These models had moderate goodness of fit, as expressed by r2, which ranged from 0.685 to 0.732; and good cross-validated predictive ability, as expressed by q2, which varied from 0.678 to 0.719. The external predictive ability was tested using a set of 356 HLA-DRB1 binders, which showed an r2(pred) in the range 0.364-0.530. Peptide and protein positions involved in the interactions were analyzed in terms of hydrophobicity, steric bulk and polarity.
Original languageEnglish
Pages (from-to)236-243
Number of pages8
JournalEuropean Journal of Medicinal Chemistry
Issue number1
Early online date13 Oct 2009
Publication statusPublished - Jan 2010


  • amino acid sequence
  • computational biology
  • HLA-DR antigens
  • HLA-DRB1 chains
  • least-squares analysis
  • ligands
  • molecular models
  • molecular sequence data
  • peptides
  • protein conformation
  • proteomics
  • quantitative structure-activity relationship
  • substrate specificity


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