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Volumn 5, Issue 12, 2010, Pages

Proteochemometric modeling of the susceptibility of mutated variants of the HIV-1 virus to reverse transcriptase inhibitors

Author keywords

[No Author keywords available]

Indexed keywords

ABACAVIR; ANTIVIRUS AGENT; DIDANOSINE; DNA POLYMERASE; EMTRICITABINE; LAMIVUDINE; RNA DIRECTED DNA POLYMERASE INHIBITOR; STAVUDINE; TENOFOVIR; ZALCITABINE; ZIDOVUDINE; ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT;

EID: 78650736464     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014353     Document Type: Article
Times cited : (26)

References (41)
  • 1
    • 11144233697 scopus 로고    scopus 로고
    • HIV Reverse Transcriptase structures: Designing new inhibitors and understanding mechanisms of drug resistance
    • Jingshan R, Stammers DK (2005) HIV Reverse Transcriptase structures: designing new inhibitors and understanding mechanisms of drug resistance. Trends Pharmacol Sci 26: 4-7.
    • (2005) Trends Pharmacol Sci , vol.26 , pp. 4-7
    • Jingshan, R.1    Stammers, D.K.2
  • 2
    • 77954090011 scopus 로고    scopus 로고
    • Available, Accessed 2010 Apr 26
    • UNAIDS and WHO: AIDS epidemic update 2009. Available: http://data. unaids.org/pub/Report/2009/2009_epidemic_update_en.pdf. Accessed 2010 Apr 26.
    • (2009) UNAIDS and WHO: AIDS epidemic update
  • 4
    • 0034566114 scopus 로고    scopus 로고
    • Inhibitors of HIV-1 Reverse Transcriptase
    • Parniak MA, Sluis-Cremer N (2000) Inhibitors of HIV-1 Reverse Transcriptase. Adv Pharmacol 49: 67-109.
    • (2000) Adv Pharmacol , vol.49 , pp. 67-109
    • Parniak, M.A.1    Sluis-Cremer, N.2
  • 5
    • 0024999452 scopus 로고
    • Retroviral Reverse Transcriptase: Synthesis, structure, and function
    • Goff SP (1990) Retroviral Reverse Transcriptase: synthesis, structure, and function. J Acquir Immune Defic Syndr 3: 817-831.
    • (1990) J Acquir Immune Defic Syndr , vol.3 , pp. 817-831
    • Goff, S.P.1
  • 6
    • 0036050539 scopus 로고    scopus 로고
    • Strategies in the design of anti-viral drugs
    • De Clercq E (2002) Strategies in the design of anti-viral drugs. Nat Rev Drug Disc 1: 13-25.
    • (2002) Nat Rev Drug Disc , vol.1 , pp. 13-25
    • De Clercq, E.1
  • 7
    • 0025912292 scopus 로고
    • Factors contributing to the inhibition of HIV Reverse Transcriptase by chain-terminating nucleotides in vitro and in vivo
    • Goody RS, Muller B, Restle T (1991) Factors contributing to the inhibition of HIV Reverse Transcriptase by chain-terminating nucleotides in vitro and in vivo. FEBS Lett 7: 1-5.
    • (1991) FEBS Lett , vol.7 , pp. 1-5
    • Goody, R.S.1    Muller, B.2    Restle, T.3
  • 8
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy
    • Coffin JM (1995) HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267: 483-489.
    • (1995) Science , vol.267 , pp. 483-489
    • Coffin, J.M.1
  • 9
    • 1242274541 scopus 로고    scopus 로고
    • Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious
    • Gao F, Chen Y, Levy DN, Conway JA, Kepler TB, et al. (2004) Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. J Virol 78: 2426-2433.
    • (2004) J Virol , vol.78 , pp. 2426-2433
    • Gao, F.1    Chen, Y.2    Levy, D.N.3    Conway, J.A.4    Kepler, T.B.5
  • 10
    • 0043092351 scopus 로고    scopus 로고
    • Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
    • Beerenwinkel N, Daumer M, Oette M, Korn K, Hoffmann D, et al. (2003) Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res 31: 3850-3855.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3850-3855
    • Beerenwinkel, N.1    Daumer, M.2    Oette, M.3    Korn, K.4    Hoffmann, D.5
  • 11
    • 27744541149 scopus 로고    scopus 로고
    • Computational methods for the design of effective therapies against drug resistant HIV strains
    • Beerenwinkel N, Sing T, Lengauer T, Rahnenfuhrer J Roomp K, et al. (2005) Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics 21: 3943-3950.
    • (2005) Bioinformatics , vol.21 , pp. 3943-3950
    • Beerenwinkel, N.1    Sing, T.2    Lengauer, T.3    Rahnenfuhrer, J.4    Roomp, K.5
  • 12
  • 13
    • 52649119802 scopus 로고    scopus 로고
    • Prediction of phenotypic susceptibility to antiretroviral drugs using physicochemical properties of primary enzymatic structure combined with artificial neural networks
    • Kjaer J, Hoj L, Fox Z, Lundgren JD (2008) Prediction of phenotypic susceptibility to antiretroviral drugs using physicochemical properties of primary enzymatic structure combined with artificial neural networks. HIV Med 9: 642-652.
    • (2008) HIV Med , vol.9 , pp. 642-652
    • Kjaer, J.1    Hoj, L.2    Fox, Z.3    Lundgren, J.D.4
  • 14
    • 34548720347 scopus 로고    scopus 로고
    • Mining complex genotypic features for predicting HIV-1 drug resistance
    • Saigo H, Uno T, Tsuda K (2007) Mining complex genotypic features for predicting HIV-1 drug resistance. Bioinformatics 23: 2455-2462.
    • (2007) Bioinformatics , vol.23 , pp. 2455-2462
    • Saigo, H.1    Uno, T.2    Tsuda, K.3
  • 15
    • 46249127515 scopus 로고    scopus 로고
    • Selecting anti-HIV therapies based on a variety of genomic and clinical factors
    • Rosen-Zvi M, Altmann A, Prosperi M, Aharoni E, Neuvirth H, et al. (2008) Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Bioinformatics 24: i399-406.
    • (2008) Bioinformatics , vol.24
    • Rosen-Zvi, M.1    Altmann, A.2    Prosperi, M.3    Aharoni, E.4    Neuvirth, H.5
  • 16
    • 65549132916 scopus 로고    scopus 로고
    • Predicting the response to combination antiretroviral therapy: Retrospective validation of geno2pheno-THEO on a large clinical database
    • Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, et al. (2009) Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis 199: 999-1006.
    • (2009) J Infect Dis , vol.199 , pp. 999-1006
    • Altmann, A.1    Däumer, M.2    Beerenwinkel, N.3    Peres, Y.4    Schülter, E.5
  • 18
    • 0035895752 scopus 로고    scopus 로고
    • Development of proteo-chemometrics: A novel technology for the analysis of drug-receptor interactions
    • Lapinsh M, Prusis A, Gutcaits A, Lundstedt T, Wikberg JE (2001) Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions. Biochim Biophys Acta 1525: 180-190.
    • (2001) Biochim Biophys Acta , vol.1525 , pp. 180-190
    • Lapinsh, M.1    Prusis, A.2    Gutcaits, A.3    Lundstedt, T.4    Wikberg, J.E.5
  • 19
    • 0036264678 scopus 로고    scopus 로고
    • Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands
    • Lapinsh M, Prusis P, Wikberg JE (2002) Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands. Mol Pharmacol 61: 1465-1475.
    • (2002) Mol Pharmacol , vol.61 , pp. 1465-1475
    • Lapinsh, M.1    Prusis, P.2    Wikberg, J.E.3
  • 20
    • 0038115355 scopus 로고    scopus 로고
    • QSAR and proteochemometric analysis of the interaction of a series of organic compounds with melanocortin receptor subtypes
    • Lapinsh M, Prusis P, Mutule I, Mutulis I, Wikberg JE (2003) QSAR and proteochemometric analysis of the interaction of a series of organic compounds with melanocortin receptor subtypes. J Med Chem 46: 2572-2579.
    • (2003) J Med Chem , vol.46 , pp. 2572-2579
    • Lapinsh, M.1    Prusis, P.2    Mutule, I.3    Mutulis, I.4    Wikberg, J.E.5
  • 21
    • 28444472402 scopus 로고    scopus 로고
    • Improved approach for proteochemometrics modeling: Application to organic compound - amine G protein-coupled receptor interactions
    • Lapinsh M, Prusis P, Uhlén S, Wikberg JE (2005) Improved approach for proteochemometrics modeling: application to organic compound - amine G protein-coupled receptor interactions. Bioinformatics 21: 4289-4296.
    • (2005) Bioinformatics , vol.21 , pp. 4289-4296
    • Lapinsh, M.1    Prusis, P.2    Uhlén, S.3    Wikberg, J.E.4
  • 22
    • 11244311579 scopus 로고    scopus 로고
    • Proteochemometric mapping of the interaction of organic compounds with melanocortin receptor subtypes
    • Lapinsh M, Veiksina S, Uhlén S, Petrovska R, Mutule I, et al. (2005) Proteochemometric mapping of the interaction of organic compounds with melanocortin receptor subtypes. Mol Pharmacol 67: 50-59.
    • (2005) Mol Pharmacol , vol.67 , pp. 50-59
    • Lapinsh, M.1    Veiksina, S.2    Uhlén, S.3    Petrovska, R.4    Mutule, I.5
  • 23
    • 0035847119 scopus 로고    scopus 로고
    • PLS modeling of chimeric MS04/MSH-peptide and MC1/MC3-receptor interactions reveals a novel method for the analysis of ligand-receptor interactions
    • Prusis P, Muceniece R, Andersson P, Post C, Lundstedt T, et al. (2001) PLS modeling of chimeric MS04/MSH-peptide and MC1/MC3-receptor interactions reveals a novel method for the analysis of ligand-receptor interactions. Biochim Biophys Acta 1544: 350-357.
    • (2001) Biochim Biophys Acta , vol.1544 , pp. 350-357
    • Prusis, P.1    Muceniece, R.2    Andersson, P.3    Post, C.4    Lundstedt, T.5
  • 24
    • 33645023990 scopus 로고    scopus 로고
    • Rough set-based proteochemometrics modeling of G-protein-coupled receptorligand interactions
    • Strombergsson H, Prusis P, Midelfart H, Lapinsh M, Wikberg JE, et al. (2006) Rough set-based proteochemometrics modeling of G-protein-coupled receptorligand interactions. Proteins 63: 24-34.
    • (2006) Proteins , vol.63 , pp. 24-34
    • Strombergsson, H.1    Prusis, P.2    Midelfart, H.3    Lapinsh, M.4    Wikberg, J.E.5
  • 25
    • 34547782241 scopus 로고    scopus 로고
    • Proteochemometric modeling of antibody-antigen interactions using SPOT synthesised peptide arrays
    • Mandrika I, Prusis P, Yahorava S, Shikhagaie M, Wikberg JE (2007) Proteochemometric modeling of antibody-antigen interactions using SPOT synthesised peptide arrays. Protein Eng Des Sel 20: 301-307.
    • (2007) Protein Eng Des Sel , vol.20 , pp. 301-307
    • Mandrika, I.1    Prusis, P.2    Yahorava, S.3    Shikhagaie, M.4    Wikberg, J.E.5
  • 26
    • 34047224674 scopus 로고    scopus 로고
    • A look inside HIV resistance through retroviral protease interaction maps
    • Available, Accessed 2010 Apr 26 3
    • Kontijevskis A, Prusis P, Petrovska R, Yahorava S, Mutulis F, et al. (2007) A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol, Available: http://www.ploscompbiol.org/article/info%3Adoi% 2F10.1371%2Fjournal.pcbi.0030048 Accessed 2010 Apr 26 3.
    • (2007) PLoS Comput Biol
    • Kontijevskis, A.1    Prusis, P.2    Petrovska, R.3    Yahorava, S.4    Mutulis, F.5
  • 27
    • 42949131067 scopus 로고    scopus 로고
    • Proteochemometric modeling of HIV protease susceptibility
    • Available, Accessed 2010 Apr 26 9
    • Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JE (2008) Proteochemometric modeling of HIV protease susceptibility. BMC Bioinformatics 9. Available: http://www.biomedcentral.com/1471-2105/9/181 Accessed 2010 Apr 26 9.
    • (2008) BMC Bioinformatics , pp. 9
    • Lapins, M.1    Eklund, M.2    Spjuth, O.3    Prusis, P.4    Wikberg, J.E.5
  • 28
    • 0030221875 scopus 로고    scopus 로고
    • Multivariate design and modeling in QSAR
    • Eriksson L, Johansson E (1996) Multivariate design and modeling in QSAR. Chemom Intell Lab 34: 1-19.
    • (1996) Chemom Intell Lab , vol.34 , pp. 1-19
    • Eriksson, L.1    Johansson, E.2
  • 29
  • 30
    • 7244262081 scopus 로고    scopus 로고
    • Antivirogram or phenosense: A comparison of their reproducibility and an analysis of their correlation
    • Wang K, Samudrala R, Mittler JE (2004) Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation. Antivir Ther 9: 703-712.
    • (2004) Antivir Ther , vol.9 , pp. 703-712
    • Wang, K.1    Samudrala, R.2    Mittler, J.E.3
  • 31
    • 27844531602 scopus 로고    scopus 로고
    • Thymidine analogue mutation profiles: Factors associated with acquiring specific profiles and their impact on the virological response to therapy
    • Cozzi-Lepri A, Ruiz L, Loveday C, Phillips AN, Clotet B, et al. (2005) Thymidine analogue mutation profiles: factors associated with acquiring specific profiles and their impact on the virological response to therapy. Antivir Ther 10: 791-802.
    • (2005) Antivir Ther , vol.10 , pp. 791-802
    • Cozzi-Lepri, A.1    Ruiz, L.2    Loveday, C.3    Phillips, A.N.4    Clotet, B.5
  • 32
    • 70449384378 scopus 로고    scopus 로고
    • XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous Web services
    • Available, Accessed 2010 Apr 26 10
    • Wagener J, Spjuth O, Willighagen EL, Wikberg JE (2009) XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous Web services. BMC Bioinformatics, Available: http://www.biomedcentral. com/1471-2105/10/279 Accessed 2010 Apr 26 10.
    • (2009) BMC Bioinformatics
    • Wagener, J.1    Spjuth, O.2    Willighagen, E.L.3    Wikberg, J.E.4
  • 33
    • 78650739877 scopus 로고    scopus 로고
    • Available, Accessed 2010 Apr 26
    • HIV Drug Research Center. Available: http://www.hivdrc.org Accessed 2010 Apr 26.
    • HIV Drug Research Center
  • 34
    • 0037250521 scopus 로고    scopus 로고
    • Human immunodeficiency virus reverse transcriptase and protease sequence database
    • Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, et al. (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 31: 298-303.
    • (2003) Nucleic Acids Res , vol.31 , pp. 298-303
    • Rhee, S.Y.1    Gonzales, M.J.2    Kantor, R.3    Betts, B.J.4    Ravela, J.5
  • 35
    • 78650725622 scopus 로고    scopus 로고
    • Available, Accessed 1010 Jun 12
    • Release Notes for HIVdb, HIVseq, HIValg. Available: http://hivdb.stanford. edu/pages/asi/releaseNotes Accessed 1010 Jun 12.
    • Release Notes for HIVdb, HIVseq, HIValg
  • 36
    • 0032474777 scopus 로고    scopus 로고
    • New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids
    • Sandberg M, Eriksson L, Jonsson J, Sjöström M, Wold S (1998) New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J Med Chem 41: 2481-2491.
    • (1998) J Med Chem , vol.41 , pp. 2481-2491
    • Sandberg, M.1    Eriksson, L.2    Jonsson, J.3    Sjöström, M.4    Wold, S.5
  • 40
    • 0036083139 scopus 로고    scopus 로고
    • Orthogonal projections to partial least-squares (O-PLS)
    • Trygg J, Wold S (2002) Orthogonal projections to partial least-squares (O-PLS). J Chemometr 16: 119-28.
    • (2002) J Chemometr , vol.16 , pp. 119-128
    • Trygg, J.1    Wold, S.2


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