A new perspective on V3 phenotype prediction

AIDS Research and Human Retroviruses

Volumn 19, Issue 2, 2003, Pages 145-149

  Pillai, Satish ^a   Good, Benjamin ^b   Richman, Douglas ^a,b   Corbeil, Jacques ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b VETERANS AFFAIRS MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CXCR4;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; GENE SEQUENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; TECHNIQUE; VIRUS GENE; VIRUS STRAIN;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; HIV ENVELOPE PROTEIN GP120; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PHENOTYPE; PREDICTIVE VALUE OF TESTS; RECEPTORS, CCR5; RECEPTORS, CHEMOKINE; RECEPTORS, CYTOKINE; SOFTWARE;

EID: 0345505217     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/088922203762688658     Document Type: Article

References (14)

1. Wyatt R and Sodroski J: The HIV-1 envelope glycoproteins: Fusogens, antigens, and immunogens. Science 1998;280:1884-1888.
2. Fenyö EM, Schuitemaker H, Åsjö B, McKeating J, Sattentau Q, and EC Concerted Action on HIV Variability: The history of HIV-1 biological phenotypes past, present and future. In: Human Retroviruses and AIDS 1997: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences (Korber B, Hahn B, Foley B, Mellors JW, Leitner T, Myers G, McCutchan F, and Kuiken CL, eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 1997, pp. III-13-III-18.
3. Cheng-Mayer C, Quiroga M, Tung JW, Dina D, and Levy JA. Viral determinants of human immunodeficiency virus type 1 T-cell or macrophage tropism, cytopathogenicity, and CD4 antigen modulation. J Virol 1990;64:4390-4398.
4. Fouchier RAM, Groenink M, Kootstra NA, Tersmette M, Huisman HG, Miedema F, and Schuitemaker H. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 1992;66:3183-3187.
5. McDonald RA, Chang G, and Michael NL. Relationship between V3 genotype, biologic phenotype, tropism, and coreceptor use for primary isolates of human immunodeficiency virus type 1. J Hum Virol 2001;4:179-187.
6. Mjolsness E and DeCoste D. Machine learning for science: State of the art and future prospects. Science 2001;293:2051-2055.
7. Witten IH and Frank E. Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations. Morgan Kaufmann, San Francisco, 2000.
8. Hua S and Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 2001;17:721-728.
9. Resch W, Hoffman N, and Swanstrom R: Improved success phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 2001;288:51-62.
10. Thompson JD, Higgins DG, and Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
11. Quinlan JR. C4.5: Programs for Machine Learning. Morgan Kaufmann, San Francisco, 1993.
12. Vapnik V. The Nature of Statistical Learning Theory. Springer-Verlag, New York, 1995.
13. Lu Z, Berson JF, Chen Y, Turner JD, Zhang T, Sharron M, Jenks MH, Wang Z, Kim J, Rucker J, Hoxie JA, Peiper SC, and Doms RW. Evolution of HIV-1 coreceptor usage through interactions with distinct CCR5 and CXCR4 domains. Proc Natl Acad Sci USA 1997;94:6426-6431.
14. Rizzuto CD, Wyatt R, Hernandez-Ramos N, Sun Y, Kwong PD, Hendrickson WA, and Sodroski J. A conserved HIV gp120 glycoprotein structure involved in chemakine receptor binding. Science 1998;280:1949-1953.