Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence NetMHCIIpan 英文参考文献.docVIP

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Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence NetMHCIIpan 英文参考文献.doc

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Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence NetMHCIIpan 英文参考文献

QuantitativePredictionsofPeptideBindingtoAnyHLA- DRMoleculeofKnownSequence:NetMHCIIpan MortenNielsen1*,ClausLundegaard1,ThomasBlicher1,BjoernPeters2,AlessandroSette2 ,Sune Justesen3,S?renBuus3,OleLund1 1Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark, 2La Jolla Institute for Allergy and Immunology,SanDiego,California,UnitedStatesofAmerica,3LaboratoryofExperimentalImmunology,FacultyofHealthSciences,UniversityofCopenhagen,Denmark Abstract CD4positive Thelper cells controlmany aspects ofspecific immunity.These cells arespecificfor peptides derivedfrom proteinantigensandpresentedbymoleculesoftheextremelypolymorphicmajorhistocompatibilitycomplex(MHC)classII system. The identification of peptides that bindtoMHCclass II moleculesis 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,thatallowsforpan-specificpredictionsofpeptidebindingtoanyHLA-DRmoleculeofknownsequence.The methodisderivedfromalargecompilationofquantitativeHLA-DRbindingeventscovering14ofthemorethan500known HLA-DRalleles.TakingbothpeptideandHLAsequenceinformationintoaccount,themethodcangeneralizeandpredict 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 identificationforhithertouncharacterizedHLA-DRmolecules.Thevalidationshowsthatthemethodcansuccessfullypredict binding for HLA-DR molecules—even in the absence of specific data for the particular molecule in question. Moreover, whencomparedtoTEPITOPE,currentlytheonlyotherpubliclyavailablepredictionmethodaimingatprovidingbroadHLA- DRalleliccoverage,NetMHCIIpanperformsequivalentlyforallelesincludedinthetrainingofTEPITOPEwhileoutperforming TEPITOPE on novel alleles. We propose that the method c