-
1
-
-
0032577550
-
HIV entry and its inhibition
-
Chan DC, Kim PS, (1998) HIV entry and its inhibition. Cell 93: 681-684.
-
(1998)
Cell
, vol.93
, pp. 681-684
-
-
Chan, D.C.1
Kim, P.S.2
-
3
-
-
0025866185
-
Conformational changes induced in the human immunodeficiency virus envelope glycoprotein by soluble CD4 binding
-
Sattentau QJ, Moore JP, (1991) Conformational changes induced in the human immunodeficiency virus envelope glycoprotein by soluble CD4 binding. J Exp Med 174: 407-415.
-
(1991)
J Exp Med
, vol.174
, pp. 407-415
-
-
Sattentau, Q.J.1
Moore, J.P.2
-
4
-
-
16144365317
-
CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5
-
Trkola A, Dragic T, Arthos J, Binley JM, Olson WC, et al. (1996) CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5. Nature 384: 184-187.
-
(1996)
Nature
, vol.384
, pp. 184-187
-
-
Trkola, A.1
Dragic, T.2
Arthos, J.3
Binley, J.M.4
Olson, W.C.5
-
5
-
-
0026606727
-
Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule
-
Fouchier RA, Groenink M, Kootstra NA, Tersmette M, Huisman HG, et al. (1992) Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol 66: 3183-3187.
-
(1992)
J Virol
, vol.66
, pp. 3183-3187
-
-
Fouchier, R.A.1
Groenink, M.2
Kootstra, N.A.3
Tersmette, M.4
Huisman, H.G.5
-
6
-
-
0026754683
-
Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1
-
Shioda T, Levy JA, Cheng-Mayer C, (1992) Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A 89: 9434-9438.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 9434-9438
-
-
Shioda, T.1
Levy, J.A.2
Cheng-Mayer, C.3
-
7
-
-
0038637409
-
Predicting HIV-1 coreceptor usage with sequence analysis
-
Jensen MA, van 't Wout AB, (2003) Predicting HIV-1 coreceptor usage with sequence analysis. AIDS Rev 5: 104-112.
-
(2003)
AIDS Rev
, vol.5
, pp. 104-112
-
-
Jensen, M.A.1
van 't Wout, A.B.2
-
8
-
-
0033012398
-
Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease
-
Berger EA, Murphy PM, Farber JM, (1999) Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol 17: 657-700.
-
(1999)
Annu Rev Immunol
, vol.17
, pp. 657-700
-
-
Berger, E.A.1
Murphy, P.M.2
Farber, J.M.3
-
9
-
-
16044367526
-
The role of a mutant CCR5 allele in HIV-1 transmission and disease progression
-
Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, et al. (1996) The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 2: 1240-1243.
-
(1996)
Nat Med
, vol.2
, pp. 1240-1243
-
-
Huang, Y.1
Paxton, W.A.2
Wolinsky, S.M.3
Neumann, A.U.4
Zhang, L.5
-
10
-
-
27644510382
-
Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity
-
Dorr P, Westby M, Dobbs S, Griffin P, Irvine B, et al. (2005) Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity. Antimicrob Agents Chemother 49: 4721-4732.
-
(2005)
Antimicrob Agents Chemother
, vol.49
, pp. 4721-4732
-
-
Dorr, P.1
Westby, M.2
Dobbs, S.3
Griffin, P.4
Irvine, B.5
-
11
-
-
10744231634
-
Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences
-
Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, et al. (2003) Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol 77: 13376-13388.
-
(2003)
J Virol
, vol.77
, pp. 13376-13388
-
-
Jensen, M.A.1
Li, F.S.2
van 't Wout, A.B.3
Nickle, D.C.4
Shriner, D.5
-
12
-
-
0345505217
-
A new perspective on V3 phenotype prediction
-
Pillai S, Good B, Richman D, Corbeil J, (2003) A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses 19: 145-149.
-
(2003)
AIDS Res Hum Retroviruses
, vol.19
, pp. 145-149
-
-
Pillai, S.1
Good, B.2
Richman, D.3
Corbeil, J.4
-
13
-
-
0035884899
-
Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks
-
Resch W, Hoffman N, Swanstrom R, (2001) Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology 288: 51-62.
-
(2001)
Virology
, vol.288
, pp. 51-62
-
-
Resch, W.1
Hoffman, N.2
Swanstrom, R.3
-
14
-
-
36148931769
-
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
-
Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, et al. (2007) Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther 12: 1097-1106.
-
(2007)
Antivir Ther
, vol.12
, pp. 1097-1106
-
-
Sing, T.1
Low, A.J.2
Beerenwinkel, N.3
Sander, O.4
Cheung, P.K.5
-
15
-
-
33846623260
-
Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism
-
Whitcomb JM, Huang W, Fransen S, Limoli K, Toma J, et al. (2007) Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother 51: 566-575.
-
(2007)
Antimicrob Agents Chemother
, vol.51
, pp. 566-575
-
-
Whitcomb, J.M.1
Huang, W.2
Fransen, S.3
Limoli, K.4
Toma, J.5
-
16
-
-
84876004534
-
-
German AIDS Society. Available:Accessed 25 January 2013., Available
-
German AIDS Society (2008) Empfehlung zur Bestimmung des HIV-1-Korezeptor-Gebrauchs. Available:http://www.daignet.de/site-content/hiv-therapie/leitlinien-1/Leitlinien%20zur%20Topismus_Testung%20Stand%20Juni%202009.pdf Accessed 25 January 2013.
-
(2008)
Empfehlung zur Bestimmung des HIV-1-Korezeptor-Gebrauchs
-
-
-
17
-
-
79955483926
-
European guidelines on the clinical management of HIV-1 tropism testing
-
Vandekerckhove LP, Wensing AM, Kaiser R, Brun-Vézinet F, Clotet B, et al. (2011) European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect Dis May 11: 394-407.
-
(2011)
Lancet Infect Dis May
, vol.11
, pp. 394-407
-
-
Vandekerckhove, L.P.1
Wensing, A.M.2
Kaiser, R.3
Brun-Vézinet, F.4
Clotet, B.5
-
18
-
-
27744597054
-
Structure of a V3-containing HIV-1 gp120 core
-
Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, et al. (2005) Structure of a V3-containing HIV-1 gp120 core. Science 310: 1025-1028.
-
(2005)
Science
, vol.310
, pp. 1025-1028
-
-
Huang, C.C.1
Tang, M.2
Zhang, M.Y.3
Majeed, S.4
Montabana, E.5
-
19
-
-
34848868199
-
Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4
-
Huang CC, Lam SN, Acharya P, Tang M, Xiang SH, et al. (2007) Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science 317: 1930-1934.
-
(2007)
Science
, vol.317
, pp. 1930-1934
-
-
Huang, C.C.1
Lam, S.N.2
Acharya, P.3
Tang, M.4
Xiang, S.H.5
-
21
-
-
34047202703
-
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage
-
Sander O, Sing T, Sommer I, Low AJ, Cheung PK, et al. (2007) Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol 3: e58.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Sander, O.1
Sing, T.2
Sommer, I.3
Low, A.J.4
Cheung, P.K.5
-
22
-
-
0027265082
-
Analysis of heterogeneous viral populations by direct DNA sequencing
-
Leitner T, Halapi E, Scarlatti G, Rossi P, Albert J, et al. (1993) Analysis of heterogeneous viral populations by direct DNA sequencing. Biotechniques Jul;15: 120-127.
-
(1993)
Biotechniques Jul
, vol.15
, pp. 120-127
-
-
Leitner, T.1
Halapi, E.2
Scarlatti, G.3
Rossi, P.4
Albert, J.5
-
24
-
-
18144406581
-
Solving the protein sequence metric problem
-
Atchley WR, Zhao J, Fernandes AD, Druke T, (2005) Solving the protein sequence metric problem. Proc Natl Acad Sci U S A 102: 6395-6400.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 6395-6400
-
-
Atchley, W.R.1
Zhao, J.2
Fernandes, A.D.3
Druke, T.4
-
25
-
-
84875998803
-
-
Los Alamos HIV databases Available:Accessed 30 June 2011., Available
-
Los Alamos HIV databases (2012) Available:http://www.hiv.lanl.gov/ Accessed 30 June 2011.
-
(2012)
-
-
-
26
-
-
0035478854
-
Random Forests
-
Breiman L, (2001) Random Forests. Mach Learn 45: 5-32.
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
27
-
-
0036161259
-
Gene Selection for Cancer Classification using Support Vector Machines
-
Guyon I, Weston J, Barnhill S, Vapnik V, (2002) Gene Selection for Cancer Classification using Support Vector Machines. Mach Learn 46: 389-422.
-
(2002)
Mach Learn
, vol.46
, pp. 389-422
-
-
Guyon, I.1
Weston, J.2
Barnhill, S.3
Vapnik, V.4
-
28
-
-
85194972808
-
Regression shrinkage and selection via the lasso
-
Tibshirani R, (1996) Regression shrinkage and selection via the lasso. J Royal Statist Soc B 58: 267-288.
-
(1996)
J Royal Statist Soc B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
29
-
-
12144291059
-
Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy
-
Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, et al. (2004) Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. Aids 18: F1-9.
-
(2004)
Aids
, vol.18
-
-
Brumme, Z.L.1
Dong, W.W.2
Yip, B.3
Wynhoven, B.4
Hoffman, N.G.5
-
30
-
-
0028568650
-
Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales
-
Muñoz V, Serrano L, (1994) Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins Dec 20: 301-311.
-
(1994)
Proteins Dec
, vol.20
, pp. 301-311
-
-
Muñoz, V.1
Serrano, L.2
-
32
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci Jun;8: 275-282.
-
(1992)
Comput Appl Biosci Jun
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
33
-
-
0019025302
-
Characterization of multiple bends in proteins
-
Isogai Y, Némethy G, Rackovsky S, Leach SJ, Scheraga HA, (1980) Characterization of multiple bends in proteins. Biopolymers Jun;19: 1183-1210.
-
(1980)
Biopolymers Jun
, vol.19
, pp. 1183-1210
-
-
Isogai, Y.1
Némethy, G.2
Rackovsky, S.3
Leach, S.J.4
Scheraga, H.A.5
-
34
-
-
0018093765
-
Conformational preferences of amino acids in globular proteins
-
Levitt M, (1978) Conformational preferences of amino acids in globular proteins. Biochemistry Oct 3;17: 4277-4285.
-
(1978)
Biochemistry Oct 3
, vol.17
, pp. 4277-4285
-
-
Levitt, M.1
-
35
-
-
0015914842
-
Logical analysis of the mechanism of protein folding. I. Predictions of helices, loops and beta-structures from primary structure
-
Nagano K, (1973) Logical analysis of the mechanism of protein folding. I. Predictions of helices, loops and beta-structures from primary structure. J Mol Biol Apr 5;75: 401-420.
-
(1973)
J Mol Biol Apr 5
, vol.75
, pp. 401-420
-
-
Nagano, K.1
-
36
-
-
84987288517
-
Analysis of conformations of amino acid residues and prediction of backbone topography in proteins
-
Burgess AW, Ponnuswamy PK, Scheraga HA, (1974) Analysis of conformations of amino acid residues and prediction of backbone topography in proteins. Isr J Chem 12: 239-286.
-
(1974)
Isr J Chem
, vol.12
, pp. 239-286
-
-
Burgess, A.W.1
Ponnuswamy, P.K.2
Scheraga, H.A.3
-
37
-
-
0033613812
-
Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms
-
Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, et al. (1999) Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285: 1711-1733.
-
(1999)
J Mol Biol
, vol.285
, pp. 1711-1733
-
-
Word, J.M.1
Lovell, S.C.2
LaBean, T.H.3
Taylor, H.C.4
Zalis, M.E.5
-
38
-
-
77957271477
-
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage
-
Masso M, Vaisman II, (2010) Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage. BMC Bioinformatics 11: 494.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 494
-
-
Masso, M.1
Vaisman, I.I.2
-
39
-
-
0028802870
-
The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution
-
Vranken WF, Budesinsky M, Fant F, Boulez K, Borremans FA, (1995) The complete Consensus V3 loop peptide of the envelope protein gp120 of HIV-1 shows pronounced helical character in solution. FEBS Lett 374: 117-121.
-
(1995)
FEBS Lett
, vol.374
, pp. 117-121
-
-
Vranken, W.F.1
Budesinsky, M.2
Fant, F.3
Boulez, K.4
Borremans, F.A.5
-
40
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
41
-
-
0001720445
-
Numbering positions in HIV relative to HXB2CG
-
Korber B, Foley B, Kuiken C, Pillai S, Sorodski J, (1998) Numbering positions in HIV relative to HXB2CG. Human Retrovirus and AIDS III-102-111.
-
(1998)
Human Retrovirus and AIDS
-
-
Korber, B.1
Foley, B.2
Kuiken, C.3
Pillai, S.4
Sorodski, J.5
-
42
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
43
-
-
15544367670
-
A training algorithm for optimal margin classifiers
-
Accessed 30 June 2011., Available, 1992; Pittsburgh, Pennsylvania, United States: ACM. Available
-
Boser EB, Isabelle MG, Vladimir NV (1992) A training algorithm for optimal margin classifiers. In: Proceedings of the fifth annual workshop on Computational learning theory; 1992; Pittsburgh, Pennsylvania, United States: ACM. Available:http://dl.acm.org/citation.cfm?id=130401 Accessed 30 June 2011.
-
(1992)
In: Proceedings of the fifth annual workshop on Computational learning theory
-
-
Boser, E.B.1
Isabelle, M.G.2
Vladimir, N.V.3
-
44
-
-
84859549618
-
e1071: Misc Functions of the Department of Statistics (e1071)
-
Available:
-
Dimitriadou E, Hornik K, Leisch F, Meyer D, Weingessel A, (2005) e1071: Misc Functions of the Department of Statistics (e1071). TU Wien Available:http://CRAN.R-project.org/.
-
(2005)
TU Wien
-
-
Dimitriadou, E.1
Hornik, K.2
Leisch, F.3
Meyer, D.4
Weingessel, A.5
-
45
-
-
27544491192
-
ROCR: visualizing classifier performance in R
-
Sing T, Sander O, Beerenwinkel N, Lengauer T, (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
46
-
-
77954409264
-
Maraviroc in treatment-experienced patients with HIV-1 infection - experience from routine clinical practice
-
Reuter S, Braken P, Jensen B, Sierra-Aragon S, Oette M, et al. Maraviroc in treatment-experienced patients with HIV-1 infection- experience from routine clinical practice. Eur J Med Res 15: 231-237.
-
Eur J Med Res
, vol.15
, pp. 231-237
-
-
Reuter, S.1
Braken, P.2
Jensen, B.3
Sierra-Aragon, S.4
Oette, M.5
-
47
-
-
0023453329
-
Silhouettes: A Graphical Aid to the Interpretation and Validation of Cluster Analysis
-
Rousseeuw P, (1987) Silhouettes: A Graphical Aid to the Interpretation and Validation of Cluster Analysis. J Comput Appl Math 20: 53-65.
-
(1987)
J Comput Appl Math
, vol.20
, pp. 53-65
-
-
Rousseeuw, P.1
-
48
-
-
79954580509
-
-
Schrodinger LLC. Available: Accessed 30 June 2011., Available
-
Schrodinger LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1. Available:http://www.pymol.org Accessed 30 June 2011.
-
(2010)
The PyMOL Molecular Graphics System, Version 1.3r1
-
-
|