Scoring function to predict solubility mutagenesis 英文参考文献.docVIP

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Scoring function to predict solubility mutagenesis 英文参考文献.doc

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Scoring function to predict solubility mutagenesis 英文参考文献

Scoringfunctiontopredictsolubilitymutagenesis Tianetal. Tianetal.AlgorithmsforMolecularBiology2010,5:33 /content/5/1/33(7October2010) Tianetal.AlgorithmsforMolecularBiology2010,5:33 /content/5/1/33 RESEARCH OpenAccess Scoringfunctiontopredictsolubilitymutagenesis YeTian1,ChristopherDeutsch2,BalaKrishnamoorthy1* Abstract Background:Mutagenesisiscommonlyusedtoengineerproteinswithdesirablepropertiesnotpresentinthe wildtype(WT)protein,suchasincreasedordecreasedstability,reactivity,orsolubility.Experimentalistsoftenhave tochooseasmallsubsetofmutationsfromalargenumberofcandidatestoobtainthedesiredchange,and computationaltechniquesareinvaluabletomakethechoices.Whileseveralsuchmethodshavebeenproposedto predictstabilityandreactivitymutagenesis,solubilityhasnotreceivedmuchattention. Results:Weuseconceptsfromcomputationalgeometrytodefineathreebodyscoringfunctionthatpredictsthe changeinproteinsolubilityduetomutations.Thescoringfunctioncapturesbothsequenceandstructure information.Byexploringtheliterature,wehaveassembledasubstantialdatabaseof137single-andmultiple- pointsolubilitymutations.Ourdatabaseisthelargestsuchcollectionwithstructuralinformationknownsofar.We optimizethescoringfunctionusinglinearprogramming(LP)methodstoderiveitsweightsbasedontraining. Startingwithdefaultvaluesof1,wefindweightsintherange[0,2]sothatpredictionsofincreaseordecreasein solubilityareoptimized.WecomparetheLPmethodtothestandardmachinelearningtechniquesofsupport vectormachines(SVM)andtheLasso.Usingstatisticsforleave-one-out(LOO),10-fold,and3-foldcrossvalidations (CV)fortrainingandprediction,wedemonstratethattheLPmethodperformsthebestoverall.FortheLOOCV,the LPmethodhasanoverallaccuracyof81%. Availability:Executablesofprograms,tablesofweights,anddatasetsofmutantsareavailablefromthefollowing webpage:/~kbala/OptSolMut.html. Introduction Mostcomputationally efficientscoringfunctionsana- Correlations between sequence andstructure influence lyze protein structure atthe atomic level oratthe AA to a large ex