title: Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest.
abstract: HIV-1 coreceptor usage and phenotype mainly determined by V3 loop are associated with the disease progression of AIDS. Predicting HIV-1 coreceptor usage and phenotype facilitates the monitoring of R5-to-X4 switch and treatment decision-making. In this study, we employed random forest to predict HIV-1 biological phenotype, based on 37 random features of V3 loop. In comparison with PSSM method, our RF predictor obtained higher prediction accuracy (95.1% for coreceptor usage and 92.1% for phenotype), especially for non-B non-C HIV-1 subtypes (96.6% for coreceptor usage and 95.3% for phenotype). The net charge, polarity of V3 loop and five V3 sites are seven most important features for predicting HIV-1 coreceptor usage or phenotype. Among these features, V3 polarity and four V3 sites (22, 12, 18 and 13) are first reported to have high contribution to HIV-1 biological phenotype prediction.
authors.affiliation: Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology, Zhenjiang, Jiangsu, PR China.
authors.forename: Shungao
authors.initials: S
authors.lastname: Xu
authors.forename: Xinxiang
authors.initials: X
authors.lastname: Huang
authors.forename: Huaxi
authors.initials: H
authors.lastname: Xu
authors.forename: Chiyu
authors.initials: C
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D010641:Phenotype; D015728:Receptors, HIV / Q000235:genetics / Q000502:physiology*; D012984:Software
chemical_list: D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D015728:Receptors, HIV