Functional Representation of Enzymes by Specific Peptides 英文参考文献.docVIP

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Functional Representation of Enzymes by Specific Peptides 英文参考文献.doc

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Functional Representation of Enzymes by Specific Peptides 英文参考文献

FunctionalRepresentationofEnzymes bySpecificPeptides Vered Kunik1,Yasmine Meroz2,Zach Solan2,Ben Sandbank1,Uri Weingart2,Eytan Ruppin1,3,David Horn2* 1SchoolofComputerScience,TelAvivUniversity,TelAviv,Israel,2SchoolofPhysicsandAstronomy,TelAvivUniversity,TelAviv,Israel,3SacklerSchoolofMedicine,Tel AvivUniversity,TelAviv,Israel Predicting the function of a protein from its sequence is a long-standing goal of bioinformatic research. While sequencesimilarityisthemostpopulartoolusedforthispurpose,sequencemotifsmayalsosubservethisgoal.Here we develop a motif-based method consisting of applying an unsupervised motif extraction algorithm (MEX) to all enzymesequences,andfilteringtheresultsbythefour-levelclassificationhierarchyoftheEnzymeCommission(EC). Theresultingmotifsserveasspecificpeptides(SPs),appearingonsinglebranchesoftheEC.Incontrasttoprevious motif-basedmethods,thenewmethoddoesnotrequireanypreprocessingbymultiplesequencealignment,nordoes itrelyonover-representationofmotifswithinECbranches.TheSPsobtainedcompriseonaverage8.464.5amino acids,andspecifythefunctionsof93%ofallenzymes,whichismuchhigherthanthecoverageof63%providedby ProSite motifs. The SP classification thus compares favorably with previous function annotation methods and successfully demonstrates an added value in extreme cases where sequence similarity fails. Interestingly, SPs cover mostoftheannotatedactiveandbindingsiteaminoacids,andoccurinactive-siteneighboring3-Dpocketsinahighly statistically significant manner. The latter are assumed to have strong biological relevance to the activity of the enzyme. Further filtering of SPs by biological functional annotations results in reduced small subsets of SPs that possessverylargeenzymecoverage.Overall,SPsbothformaveryusefultoolforenzymefunctionalclassificationand bearresponsibilityforthecatalyticbiologicalfunctioncarriedoutbyenzymes. Citation:KunikV,MerozY,SolanZ,SandbankB,WeingartU,etal.(2007)Functionalrepresentationofenzymesbyspecificpeptides.PLoSComputBi