Benchmarking B-Cell Epitope Prediction for the Design of Peptide-Based Vaccines Problems and Prospects英文文献资料.docVIP

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Benchmarking B-Cell Epitope Prediction for the Design of Peptide-Based Vaccines Problems and Prospects英文文献资料.doc

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Benchmarking B-Cell Epitope Prediction for the Design of Peptide-Based Vaccines Problems and Prospects英文文献资料

HindawiPublishingCorporation JournalofBiomedicineandBiotechnology Volume2010,ArticleID910524,14pages doi:10.1155/2010/910524 ReviewArticle BenchmarkingB-CellEpitopePredictionfortheDesignof Peptide-BasedVaccines:ProblemsandProspects SalvadorEugenioC.Caoili DepartmentofBiochemistryandMolecularBiology,CollegeofMedicine,UniversityofthePhilippinesManila, 547PedroGilStreet,Ermita,Manila1000,Philippines CorrespondenceshouldbeaddressedtoSalvadorEugenioC.Caoili,badong@.ph Received18September2009;Revised12December2009;Accepted18February2010 AcademicEditor:YongqunOliverHe Copyright?2010SalvadorEugenioC.Caoili.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttribution License,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperly cited. Tobettersupportthedesignofpeptide-basedvaccines,re?nementofmethodstopredictB-cellepitopesnecessitatesmeaningful benchmarkingagainstempiricaldataonthecross-reactivityofpolyclonalantipeptideantibodieswith proteins,suchthatthe positivedatare?ectfunctionallyrelevantcross-reactivity(whichisconsistentwithantibody-mediatedchangeinproteinfunction) andthenegativedatare?ectgenuineabsenceofcross-reactivity(ratherthanapparentabsenceofcross-reactivityduetoartifactual maskingofB-cellepitopesinimmunoassays).ThesedataareheterogeneousinviewofmultiplefactorsthatcomplicateB-cell epitopeprediction,notablyphysicochemicalfactorsthatde?nekeystructuraldi?erencesbetweenimmunizingpeptidesandtheir cognateproteins(e.g.,unmatchedelectricalchargesalongthepeptide-proteinsequencealignments).Ifthedataarepartitioned withrespecttothesefactors,iterativeparallelbenchmarkingagainsttheresultingsubsetsofdataprovidesabasisforsystematically identifyingandaddressingthelimitationsofmethodsforB-cellepitopepredictionasappliedtovaccinedesign. 1.Introduction For this application, the re?nement of methods to predict B-cellepitopesnecessitatesbenchmarkingagainstempirical data[8]. The timely development of new vaccines is imperat