quantitative predictions of peptide binding to any hla-dr molecule of known sequence netmhciipan定量预测肽绑定到任何hla-dr分子netmhciipan已知的序列.pdfVIP

Quantitative Predictions of Peptide Binding to Any HLA- DR Molecule of Known Sequence: NetMHCIIpan 1 1 1 2 2 Morten Nielsen *, Claus Lundegaard , Thomas Blicher , Bjoern Peters , Alessandro Sette , Sune 3 3 1 Justesen , Søren Buus , Ole Lund 1 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark, 2 La Jolla Institute for Allergy and Immunology, San Diego, California, United States of America, 3 Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark Abstract CD4 positive T helper cells control many aspects of specific immunity. These cells are specific for peptides derived from protein antigens and presented by molecules of the extremely polymorphic major histocompatibility complex (MHC) class II system. The identification of peptides that bind to MHC class II molecules is therefore of pivotal importance for rational discovery of immune epitopes. HLA-DR is a prominent example of a human MHC class II. Here, we present a method, NetMHCIIpan, that allows for pan-specific predictions of peptide binding to any HLA-DR molecule of known sequence. The method is derived from a large compilation of quantitative HLA-DR binding events covering 14 of the more than 500 known HLA-DR alleles. Taking both peptide and HLA sequence information into account, the method can generalize and predict peptide binding also for HLA-DR molecules where experimental data is absent. Validation of the method includes identification of endogenously derived HLA class II ligands, cross-validation, leave-one-molecule-out, and binding motif ident