Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach

Atanas Patronov, Ivan Dimitrov, Darren R Flower, Irini Doytchinova

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MHC class II proteins bind oligopeptide fragments derived from proteolysis of pathogen antigens, presenting them at the cell surface for recognition by CD4+ T cells. Human MHC class II alleles are grouped into three loci: HLA-DP, HLA-DQ and HLA-DR. In contrast to HLA-DR and HLA-DQ, HLA-DP proteins have not been studied extensively, as they have been viewed as less important in immune responses than DRs and DQs. However, it is now known that HLA-DP alleles are associated with many autoimmune diseases. Quite recently, the X-ray structure of the HLA-DP2 molecule (DPA*0103, DPB1*0201) in complex with a self-peptide derived from the HLA-DR a-chain has been determined. In the present study, we applied a validated molecular docking protocol to a library of 247 modelled peptide-DP2 complexes, seeking to assess the contribution made by each of the 20 naturally occurred amino acids at each of the nine binding core peptide positions and the four flanking residues (two on both sides).
Original languageEnglish
Article number32
JournalBMC Structural Biology
Issue number32
Publication statusPublished - 14 Jul 2011

Bibliographical note

© 2011 Patronov et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


  • alleles
  • binding Sites
  • X-ray crystallography
  • MHC Class II genes
  • HLA-DP antigens
  • HLA-DP beta-chains
  • humans
  • molecular models
  • peptides
  • thermodynamics


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