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

Patronov, Atanas, Dimitrov, Ivan, Flower, Darren R and Doytchinova, Irini (2011). Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach. BMC Structural Biology, 11 (32),


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).

Publication DOI:
Divisions: Life & Health Sciences > Pharmacy
Life & Health Sciences
Additional Information: © 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.
Uncontrolled Keywords: alleles,binding Sites,X-ray crystallography,MHC Class II genes,HLA-DP antigens,HLA-DP beta-chains,humans,molecular models,peptides,thermodynamics,Structural Biology
Full Text Link: http://www.biom ... 1472-6807/11/32
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
Published Date: 2011-07-14
Authors: Patronov, Atanas
Dimitrov, Ivan
Flower, Darren R ( 0000-0002-8542-7067)
Doytchinova, Irini



Version: Published Version

License: Creative Commons Attribution

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