Prediction of Protein Phosphorylation Sites by Using the Composition of k-Spaced Amino Acid Pairs 英文参考文献.docVIP

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Prediction of Protein Phosphorylation Sites by Using the Composition of k-Spaced Amino Acid Pairs 英文参考文献.doc

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Prediction of Protein Phosphorylation Sites by Using the Composition of k-Spaced Amino Acid Pairs 英文参考文献

PredictionofProteinPhosphorylationSitesbyUsingthe Compositionofk-SpacedAminoAcidPairs XiaoweiZhao,WenyiZhang,XinXu,ZhiqiangMa*,MinghaoYin* CollegeofComputerScienceandInformationTechnology,NortheastNormalUniversity,Changchun,People’sRepublicofChina Abstract As one of the most widespread protein post-translational modifications, phosphorylation is involved in many biological processes such as cell cycle, apoptosis. Identification of phosphorylated substrates and their corresponding sites will facilitatetheunderstandingofthemolecularmechanismofphosphorylation.Comparingwiththelabor-intensiveandtime- consuming experiment approaches, computational prediction of phosphorylation sites is much desirable due to their convenienceandfastspeed.Inthispaper,anewbioinformaticstoolnamedCKSAAP_PhSitewasdevelopedthatignored the kinase information and only used the primary sequence information to predict protein phosphorylation sites. The highlightofCKSAAP_PhSitewastoutilizethecompositionofk-spacedaminoacidpairsastheencodingscheme,andthen thesupportvectormachinewasusedasthepredictor.TheperformanceofCKSAAP_PhSitewasmeasuredwithasensitivity of84.81%,aspecificityof86.07%andanaccuracyof85.43%forserine,asensitivityof78.59%,aspecificityof82.26%andan accuracyof80.31%forthreonineaswellasasensitivityof74.44%,aspecificityof78.03%andanaccuracyof76.21%for tyrosine.Experimentalresultsobtainedfromcrossvalidationandindependentbenchmarksuggestedthatourmethodwas verypromisingtopredictphosphorylationsitesandcanbeservedasausefulsupplementtooltothecommunity.Forpublic access,CKSAAP_PhSiteisavailableat44/cksaap_phsite/. Citation:ZhaoX,ZhangW,XuX,MaZ,YinM(2012)PredictionofProteinPhosphorylationSitesbyUsingtheCompositionofk-SpacedAminoAcidPairs.PLoS ONE7(10):e46302.doi:10.1371/journal.pone.0046302 Editor:LukaszKurgan,UniversityofAlberta,Canada ReceivedMay23,2012;AcceptedAugust30,2012;PublishedOctober22,2012 Copyright: ? 2012 Zhao et al. This is an open-access article distributed under the terms of the Creat