Prediction of Cell Penetrating Peptides by Support Vector Machines 英文参考文献.docVIP

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Prediction of Cell Penetrating Peptides by Support Vector Machines 英文参考文献.doc

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Prediction of Cell Penetrating Peptides by Support Vector Machines 英文参考文献

PredictionofCellPenetratingPeptidesbySupport VectorMachines WilliamS.Sanders1,2*,C.IanJohnston1,2,SusanM.Bridges2,4,ShaneC.Burgess3,2,KennethO. Willeford1 1Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi, United States of America, 2Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi, United States of America, 3Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University,Mississippi,UnitedStatesofAmerica,4DepartmentofComputerScienceandEngineering,MississippiStateUniversity,Mississippi,UnitedStatesofAmerica Abstract Cellpenetratingpeptides(CPPs)arethosepeptidesthatcantransversecellmembranestoentercells.Onceinsidethecell, different CPPs can localize to different cellular components and perform different roles. Some generate pore-forming complexesresultinginthedestructionofcellswhileotherslocalizetovariousorganelles.Useofmachinelearningmethods topredictpotentialnewCPPswillenablemorerapidscreeningforapplicationssuchasdrugdelivery.Wehaveinvestigated theinfluenceofthecompositionoftrainingdatasetsontheabilitytoclassifypeptidesascellpenetratingusingsupport vectormachines(SVMs).Weidentified111knownCPPsand34knownnon-penetratingpeptidesfromtheliteratureand commercial vendors and used several approaches to build training data sets for the classifiers. Features were calculated fromthedatasetsusingasetofbasicbiochemicalpropertiescombinedwithfeaturesfromtheliteraturedeterminedtobe relevant in the prediction of CPPs. Our results using different training datasets confirm the importance of a balanced trainingsetwithapproximatelyequalnumberofpositiveandnegativeexamples.TheSVMbasedclassifiershavegreater classification accuracy than previously reported methods for the prediction of CPPs, and because they use primary biochemical properties of the peptides as features, these classifiers provide insight into the properties needed for cell- penetration.ToconfirmourSVMcla