Prodepth Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only 英文参考文献.docVIP

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Prodepth Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only 英文参考文献.doc

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Prodepth Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only 英文参考文献

Prodepth:PredictResidueDepthbySupportVector RegressionApproachfromProteinSequencesOnly JiangningSong1,2.*,HaoTan1.,KhalidMahmood1,4,RubyH.P.Law1,AshleyM.Buckle1,GeoffreyI. Webb3,TatsuyaAkutsu2,JamesC.Whisstock1,4* 1DepartmentofBiochemistryandMolecularBiology,MonashUniversity,Clayton,Melbourne,Victoria,Australia,2BioinformaticsCenter,InstituteforChemicalResearch, KyotoUniversity,Gokasho,Uji,Kyoto,Japan,3FacultyofInformationTechnology,MonashUniversity,Clayton,Melbourne,Victoria,Australia,4ARCCentreofExcellence forStructuralandFunctionalMicrobialGenomics,MonashUniversity,Clayton,Melbourne,Victoria,Australia Abstract Residuedepth(RD)isasolventexposuremeasurethatcomplementstheinformationprovidedbyconventionalaccessible surfacearea(ASA)anddescribestowhatextentaresidueisburiedintheproteinstructurespace.Previousstudieshave establishedthatRDiscorrelatedwithseveralproteinproperties,suchasproteinstability,residueconservationandamino acidtypes.AccuratepredictionofRDhasmanypotentiallyimportantapplicationsinthefieldofstructuralbioinformatics, forexample,facilitatingtheidentificationoffunctionallyimportantresidues,orresiduesinthefoldingnucleus,orenzyme activesitesfromsequenceinformation.Inthiswork,weintroduceanefficientapproachthatusessupportvectorregression to quantify the relationship between RD and protein sequence. We systematically investigated eight different sequence encoding schemes including both local and global sequence characteristics and examined their respective prediction performances. For the objective evaluation of our approach, we used 5-fold cross-validation to assess the prediction accuracies and showed that the overall best performance could be achieved with a correlation coefficient (CC) of 0.71 between the observed and predicted RD values and a root mean square error (RMSE) of 1.74, after incorporating the relevantmultiplesequencefeatures.Theresultssuggestthatresiduedepthcouldbereliablypredictedsolelyfromprotein primary sequences: local sequence environmen