Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach 英文参考文献.docVIP

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Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach 英文参考文献.doc

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Prediction of Peptide Reactivity with Human IVIg through a Knowledge-Based Approach 英文参考文献

PredictionofPeptideReactivitywithHumanIVIg throughaKnowledge-BasedApproach NicolaBarbarini*,AlessandraTiengo,RiccardoBellazzi LaboratoryofBiomedicalInformatics‘‘MarioStefanelli’’,DepartmentofComputerEngineeringandSystemsScience,UniversityofPavia,Pavia,Italy Abstract Thepredictionofantibody-protein(antigen)interactionsisverydifficultduetothehugevariabilitythatcharacterizesthe structureoftheantibodies.Theregionoftheantigenboundtotheantibodiesiscalledepitope.Experimentaldataindicate that many antibodies react with a panel of distinct epitopes (positive reaction). The Challenge 1 of DREAM5 aims at understanding whether there exists rules for predicting the reactivity of a peptide/epitope, i.e., its capability to bind to humanantibodies.DREAM5providedatrainingsetofpeptideswithexperimentallyidentifiedhighandlowreactivitiesto humanantibodies.Onthebasisofthistrainingset,theparticipantstothechallengewereaskedtodevelopapredictive model of reactivity. A test set was then provided to evaluate the performance of the model implemented so far. We developed a logistic regression model to predict the peptide reactivity, by facing the challenge as a machine learning problem.Theinitialfeatureshavebeengeneratedonthebasisoftheavailableknowledgeandtheinformationreportedin thedataset.Ourpredictivemodelhadthesecondbestperformanceofthechallenge.Wealsodevelopedamethod,based onaclusteringapproach,ableto‘‘in-silico’’generatealistofpositiveandnegativenewpeptidesequences,asrequestedby the DREAM5 ‘‘bonus round’’ additional challenge. The paper describes the developed model and its results in terms of reactivity prediction, and highlights some open issues concerning the propensity of a peptide to react with human antibodies. Citation:BarbariniN,TiengoA,BellazziR(2011)PredictionofPeptideReactivitywithHumanIVIgthroughaKnowledge-BasedApproach.PLoSONE6(8):e23616. doi:10.1371/journal.pone.0023616 Editor:MarkIsalan,CenterforGenomicRegulation,Spain ReceivedMarch1,2011;AcceptedJuly21,2011;PublishedAugus