Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm 英文参考文献.docVIP

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Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm 英文参考文献.doc

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Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm 英文参考文献

PredictingTransmembraneHelixPackingArrangements usingResidueContactsandaForce-DirectedAlgorithm TimothyNugent,DavidT.Jones* BioinformaticsGroup,DepartmentofComputerScience,UniversityCollegeLondon,London,UnitedKingdom Abstract Alpha-helicaltransmembraneproteinsconstituteroughly30%ofatypicalgenomeandareinvolvedinawidevarietyof important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has beendirectedtowarddevelopingamethodtopackthehelicestogether.Here,wepresentanovelapproachtopredictlipid exposure,residuecontacts,helix-helixinteractionsandfinallytheoptimalhelicalpackingarrangementoftransmembrane proteins.Usingmoleculardynamicsdata,wehavetrainedandcross-validatedasupportvectormachine(SVM)classifierto predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a secondSVMtopredictresiduecontactswhicharethenusedtodeterminehelix-helixinteractionwithupto65%accuracy understringentcross-validationonanon-redundanttestset.Ourmethodisalsoabletodiscriminatenativefromdecoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimalhelicalpackingarrangementwhichdemonstratessuccessforproteinscontainingupto13transmembranehelices. Thissoftwareisfreelyavailableassourcecodefromhttp://bioinf.cs.ucl.ac.uk/memsat/mempack/. Citation: Nugent T, Jones DT (2010) Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm. PLoS ComputBiol6(3):e1000714.doi:10.1371/journal.pcbi.1000714 Editor:ArneElofsson,StockholmUniversity,Sweden ReceivedNovember10,2009;AcceptedFebruary10,2010;PublishedMarch19,2010 Copyright: ? 2010 Nugent, Jones. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestrictedus