Prediction of Co-Receptor Usage of HIV-1 from Genotype 英文参考文献.docVIP

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Prediction of Co-Receptor Usage of HIV-1 from Genotype 英文参考文献.doc

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Prediction of Co-Receptor Usage of HIV-1 from Genotype 英文参考文献

PredictionofCo-ReceptorUsageofHIV-1fromGenotype J.NikolajDybowski.,DominikHeider.,DanielHoffmann* DepartmentofBioinformatics,CenterforMedicalBiotechnology,UniversityofDuisburg-Essen,Essen,Germany Abstract Human Immunodeficiency Virus 1 uses for entry into host cells a receptor (CD4) and one of two co-receptors (CCR5 or CXCR4).Recently,anewclassofantiretroviraldrugshasenteredclinicalpracticethatspecificallybindtotheco-receptor CCR5,andthusinhibitvirusentry.Accuratepredictionoftheco-receptorusedbythevirusinthepatientisimportantasit allowsforpersonalizedselectionofeffectivedrugsandprognosisofdiseaseprogression.Wehaveinvestigatedwhetheritis possible to predict co-receptor usage accurately by analyzing the amino acid sequence of the main determinant of co- receptorusage,i.e.,thethirdvariableloopV3ofthegp120protein.Wedevelopedatwo-levelmachinelearningapproach that in the first level considers two different properties important for protein-protein binding derived from structural modelsofV3andV3sequences.Thesecondlevelcombinesthetwopredictionsofthefirstlevel.Thetwo-levelmethod predicts usage of CXCR4 co-receptor for new V3 sequences within seconds, with an area under the ROC curve of 0.93760.004.Moreover,itisrelativelyrobustagainstinsertionsanddeletions,whichfrequentlyoccurinV3.Theapproach could help clinicians to find optimal personalized treatments, and it offers new insights into the molecular basis of co- receptorusage.Forinstance,itquantifiestheimportanceforco-receptorusageofapocketthatprobablyisresponsiblefor bindingsulfatedtyrosine. Citation:DybowskiJN,HeiderD,HoffmannD(2010)PredictionofCo-ReceptorUsageofHIV-1fromGenotype.PLoSComputBiol6(4):e1000743.doi:10.1371/ journal.pcbi.1000743 Editor:ThomasLengauer,Max-Planck-Institutfu¨rInformatik,Germany ReceivedOctober28,2009;AcceptedMarch16,2010;PublishedApril15,2010 Copyright: ? 2010 Dybowski et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unres