-
1
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B 57:289-300.
-
(1995)
J. R. Stat. Soc. Ser. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
2
-
-
0031849665
-
In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor
-
Carrillo, A., K. D. Stewart, H. L. Sham, D. W. Norbeck, W. E. Kohlbrenner, J. M. Leonard, D. J. Kempf, and A. Molla. 1998. In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor. J. Virol. 72:7532-7541.
-
(1998)
J. Virol.
, vol.72
, pp. 7532-7541
-
-
Carrillo, A.1
Stewart, K.D.2
Sham, H.L.3
Norbeck, D.W.4
Kohlbrenner, W.E.5
Leonard, J.M.6
Kempf, D.J.7
Molla, A.8
-
3
-
-
0027943157
-
Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases
-
Chen, Z., Y. Li, E. Chen, D. L. Hall, P. L. Darke, C. Culberson, J. A. Shafer, and L. C. Kuo. 1994. Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. J. Biol. Chem. 269:26344-26348.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 26344-26348
-
-
Chen, Z.1
Li, Y.2
Chen, E.3
Hall, D.L.4
Darke, P.L.5
Culberson, C.6
Shafer, J.A.7
Kuo, L.C.8
-
4
-
-
10344263394
-
Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type 1 protease inhibitor
-
Condra, J. H., D. J. Holder, W. A. Schleif, O. M. Blahy, R. M. Danovich, L. J. Gabryelski, D. J. Graham, D. Laird, J. C. Quintero, A. Rhodes, H. L. Robbins, E. Roth, M. Shivaprakash, T. Yang, J. A. Chodakewitz, P. J. Deutsch, R. Y. Leavitt, F. E. Massari, J. W. Mellors, K. E. Squires, R. T. Steigbigel, H. Teppler, and E. A. Emini. 1996. Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type 1 protease inhibitor. J. Virol. 70:8270-8276.
-
(1996)
J. Virol.
, vol.70
, pp. 8270-8276
-
-
Condra, J.H.1
Holder, D.J.2
Schleif, W.A.3
Blahy, O.M.4
Danovich, R.M.5
Gabryelski, L.J.6
Graham, D.J.7
Laird, D.8
Quintero, J.C.9
Rhodes, A.10
Robbins, H.L.11
Roth, E.12
Shivaprakash, M.13
Yang, T.14
Chodakewitz, J.A.15
Deutsch, P.J.16
Leavitt, R.Y.17
Massari, F.E.18
Mellors, J.W.19
Squires, K.E.20
Steigbigel, R.T.21
Teppler, H.22
Emini, E.A.23
more..
-
5
-
-
0028943992
-
In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors
-
Condra, J. H., W. A. Schleif, O. M. Blahy, L. J. Gabryelski, D. J. Graham, J. C. Quintero, A. Rhodes, H. L. Robbins, E. Roth, and M. Shivaprakash. 1995. In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature 374:569-571.
-
(1995)
Nature
, vol.374
, pp. 569-571
-
-
Condra, J.H.1
Schleif, W.A.2
Blahy, O.M.3
Gabryelski, L.J.4
Graham, D.J.5
Quintero, J.C.6
Rhodes, A.7
Robbins, H.L.8
Roth, E.9
Shivaprakash, M.10
-
6
-
-
0034867418
-
Replicative fitness in vivo of HIV-1 variants with multiple drug resistance-associated mutations
-
Devereux, H. L., V. C. Emery, M. A. Johnson, and C. Loveday. 2001. Replicative fitness in vivo of HIV-1 variants with multiple drug resistance-associated mutations. J. Med. Virol. 65:218-224.
-
(2001)
J. Med. Virol.
, vol.65
, pp. 218-224
-
-
Devereux, H.L.1
Emery, V.C.2
Johnson, M.A.3
Loveday, C.4
-
7
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Gobel, U., C. Sander, R. Schneider, and A. Valencia. 1994. Correlated mutations and residue contacts in proteins. Proteins 18:309-317.
-
(1994)
Proteins
, vol.18
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
8
-
-
0035887670
-
Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: Classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population
-
Gonzales, M. J., R. N. Machekano, and R. W. Shafer. 2001. Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population. J. Infect. Dis. 184:998-1006.
-
(2001)
J. Infect. Dis.
, vol.184
, pp. 998-1006
-
-
Gonzales, M.J.1
Machekano, R.N.2
Shafer, R.W.3
-
9
-
-
0029151345
-
Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure
-
Gulnik, S. V., L. I. Suvorov, B. Liu, B. Yu, B. Anderson, H. Mitsuya, and J. W. Erickson. 1995. Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. Biochemistry 34: 9282-9287.
-
(1995)
Biochemistry
, vol.34
, pp. 9282-9287
-
-
Gulnik, S.V.1
Suvorov, L.I.2
Liu, B.3
Yu, B.4
Anderson, B.5
Mitsuya, H.6
Erickson, J.W.7
-
10
-
-
0033921617
-
Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: A survey of over 6000 samples
-
Hertogs, K., S. Bloor, S. D. Kemp, C. Van den Eynde, T. M. Alcorn, R. Pauwels, M. Van Houtte, S. Staszewski, V. Miller, and B. A. Larder. 2000. Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: a survey of over 6000 samples. AIDS 14:1203-1210.
-
(2000)
AIDS
, vol.14
, pp. 1203-1210
-
-
Hertogs, K.1
Bloor, S.2
Kemp, S.D.3
Van den Eynde, C.4
Alcorn, T.M.5
Pauwels, R.6
Van Houtte, M.7
Staszewski, S.8
Miller, V.9
Larder, B.A.10
-
11
-
-
0028014288
-
Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor
-
Ho, D. D., T. Toyoshima, H. Mo, D. J. Kempf, D. Norbeck, C. M. Chen, N. E. Wideburg, S. K. Burt, J. W. Erickson, and M. K. Singh. 1994. Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor. J. Virol. 68:2016-2020.
-
(1994)
J. Virol.
, vol.68
, pp. 2016-2020
-
-
Ho, D.D.1
Toyoshima, T.2
Mo, H.3
Kempf, D.J.4
Norbeck, D.5
Chen, C.M.6
Wideburg, N.E.7
Burt, S.K.8
Erickson, J.W.9
Singh, M.K.10
-
12
-
-
0036203533
-
Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy
-
Kantor, R., W. J. Fessel, A. R. Zolopa, D. Israelski, N. Shulman, J. G. Montoya, M. Harbour, J. M. Schapiro, and R. W. Shafer. 2002. Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. Antimicrob. Agents Chemother. 46:1086-1092.
-
(2002)
Antimicrob. Agents Chemother.
, vol.46
, pp. 1086-1092
-
-
Kantor, R.1
Fessel, W.J.2
Zolopa, A.R.3
Israelski, D.4
Shulman, N.5
Montoya, J.G.6
Harbour, M.7
Schapiro, J.M.8
Shafer, R.W.9
-
13
-
-
0034909925
-
Identification of genotypic changes in human immunodeficiency virus protease that correlate with reduced susceptibility to the protease inhibitor lopinavir among viral isolates from protease inhibitor-experienced patients
-
Kempf, D. J., J. D. Isaacson, M. S. King, S. C. Brun, Y. Xu, K. Real, B. M. Bernstein, A. J. Japour, E. Sun, and R. A. Rode. 2001. Identification of genotypic changes in human immunodeficiency virus protease that correlate with reduced susceptibility to the protease inhibitor lopinavir among viral isolates from protease inhibitor-experienced patients. J. Virol. 75:7462-7469.
-
(2001)
J. Virol.
, vol.75
, pp. 7462-7469
-
-
Kempf, D.J.1
Isaacson, J.D.2
King, M.S.3
Brun, S.C.4
Xu, Y.5
Real, K.6
Bernstein, B.M.7
Japour, A.J.8
Sun, E.9
Rode, R.A.10
-
14
-
-
0027297096
-
Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
-
Korber, B. T., R. M. Farber, D. H. Wolpert, and A. S. Lapedes. 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90:7176-7180.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
15
-
-
0003507758
-
-
Los Alamos National Laboratory, Los Alamos, N.Mex.
-
Kuiken, C. L., B. Foley, B. H. Hahn, P. Marx, F. E. McCutchan, J. Mellors, J. I. Mullins, S. Wolanski, and B. Korber. 1999. Human retroviruses and AIDS: a compilation and analysis of nucleic and amino acid sequences. Los Alamos National Laboratory, Los Alamos, N.Mex.
-
(1999)
Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic and Amino Acid Sequences
-
-
Kuiken, C.L.1
Foley, B.2
Hahn, B.H.3
Marx, P.4
McCutchan, F.E.5
Mellors, J.6
Mullins, J.I.7
Wolanski, S.8
Korber, B.9
-
16
-
-
0034721944
-
Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
-
Larson, S. M., A. A. Di Nardo, and A. R. Davidson. 2000. Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol. 303:433-446.
-
(2000)
J. Mol. Biol.
, vol.303
, pp. 433-446
-
-
Larson, S.M.1
Di Nardo, A.A.2
Davidson, A.R.3
-
17
-
-
0036174439
-
Emergence of resistance to protease inhibitor amprenavir in human immunodeficiency virus type 1-infected patients: Selection of four alternative viral protease genotypes and influence of viral susceptibility to coadministered reverse transcriptase nucleoside inhibitors
-
Maguire, M., D. Shortino, A. Klein, W. Harris, V. Manohitharajah, M. Tisdale, R. Elston, J. Yeo, S. Randall, F. Xu, H. Parker, J. May, and W. Snowden. 2002. Emergence of resistance to protease inhibitor amprenavir in human immunodeficiency virus type 1-infected patients: selection of four alternative viral protease genotypes and influence of viral susceptibility to coadministered reverse transcriptase nucleoside inhibitors. Antimicrob. Agents Chemother. 46:731-738.
-
(2002)
Antimicrob. Agents Chemother.
, vol.46
, pp. 731-738
-
-
Maguire, M.1
Shortino, D.2
Klein, A.3
Harris, W.4
Manohitharajah, V.5
Tisdale, M.6
Elston, R.7
Yeo, J.8
Randall, S.9
Xu, F.10
Parker, H.11
May, J.12
Snowden, W.13
-
18
-
-
0032928065
-
Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1
-
Martinez-Picado, J., A. V. Savara, L. Sutton, and R. T. D'Aquila. 1999. Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1. J. Virol. 73:3744-3752.
-
(1999)
J. Virol.
, vol.73
, pp. 3744-3752
-
-
Martinez-Picado, J.1
Savara, A.V.2
Sutton, L.3
D'Aquila, R.T.4
-
19
-
-
15444377672
-
Ordered accumulation of mutations in HIV protease confers resistance to ritonavir
-
Molla, A., M. Korneyeva, Q. Gao, S. Vasavanonda, P. J. Schipper, H. M. Mo, M. Markowitz, T. Chernyavskiy, P. Niu, N. Lyons, A. Hsu, G. R. Granneman, D. D. Ho, C. A. Boucher, J. M. Leonard, D. W. Norbeck, and D. J. Kempf. 1996. Ordered accumulation of mutations in HIV protease confers resistance to ritonavir. Nat. Med. 2:760-766.
-
(1996)
Nat. Med.
, vol.2
, pp. 760-766
-
-
Molla, A.1
Korneyeva, M.2
Gao, Q.3
Vasavanonda, S.4
Schipper, P.J.5
Mo, H.M.6
Markowitz, M.7
Chernyavskiy, T.8
Niu, P.9
Lyons, N.10
Hsu, A.11
Granneman, G.R.12
Ho, D.D.13
Boucher, C.A.14
Leonard, J.M.15
Norbeck, D.W.16
Kempf, D.J.17
-
20
-
-
0031692748
-
Genotypic and phenotypic characterization of human immunodeficiency virus type 1 variants isolated from patients treated with the protease inhibitor nelfinavir
-
Patick, A. K., M. Duran, Y. Cao, D. Shugarts, M. R. Keller, E. Mazabel, M. Knowles, S. Chapman, D. R. Kuritzkes, and M. Markowitz. 1998. Genotypic and phenotypic characterization of human immunodeficiency virus type 1 variants isolated from patients treated with the protease inhibitor nelfinavir. Antimicrob. Agents Chemother. 42:2637-2644.
-
(1998)
Antimicrob. Agents Chemother.
, vol.42
, pp. 2637-2644
-
-
Patick, A.K.1
Duran, M.2
Cao, Y.3
Shugarts, D.4
Keller, M.R.5
Mazabel, E.6
Knowles, M.7
Chapman, S.8
Kuritzkes, D.R.9
Markowitz, M.10
-
21
-
-
0030317870
-
The effect of high-dose saquinavir on viral load and CD4+ T-cell counts in HIV-infected patients
-
Schapiro, J. M., M. A. Winters, F. Stewart, B. Efron, J. Norris, M. J. Kozal, and T. C. Merigan. 1996. The effect of high-dose saquinavir on viral load and CD4+ T-cell counts in HIV-infected patients. Ann. Intern. Med. 124:1039-1050.
-
(1996)
Ann. Intern. Med.
, vol.124
, pp. 1039-1050
-
-
Schapiro, J.M.1
Winters, M.A.2
Stewart, F.3
Efron, B.4
Norris, J.5
Kozal, M.J.6
Merigan, T.C.7
-
22
-
-
0029731556
-
Mutational anatomy of an HIV-1 protease variant conferring cross-resistance to protease inhibitors in clinical trials. Compensatory modulations of binding and activity
-
Schock, H. B., V. M. Garsky, and L. C. Kuo. 1996. Mutational anatomy of an HIV-1 protease variant conferring cross-resistance to protease inhibitors in clinical trials. Compensatory modulations of binding and activity. J. Biol. Chem. 271:31957-31963.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 31957-31963
-
-
Schock, H.B.1
Garsky, V.M.2
Kuo, L.C.3
-
23
-
-
0034483901
-
Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
-
Scott, W. R., and C. A. Schiffer. 2000. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Struct. Fold. Des. 8:1259-1265.
-
(2000)
Struct. Fold. Des.
, vol.8
, pp. 1259-1265
-
-
Scott, W.R.1
Schiffer, C.A.2
-
24
-
-
0033060308
-
Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors
-
Shafer, R. W., P. Hsu, A. K. Patick, C. Craig, and V. Brendel. 1999. Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors. J. Virol. 73:6197-6202.
-
(1999)
J. Virol.
, vol.73
, pp. 6197-6202
-
-
Shafer, R.W.1
Hsu, P.2
Patick, A.K.3
Craig, C.4
Brendel, V.5
-
25
-
-
0032947107
-
Human immunodeficiency virus reverse transcriptase and protease sequence database
-
Shafer, R. W., D. Stevenson, and B. Chan. 1999. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 27:348-352.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 348-352
-
-
Shafer, R.W.1
Stevenson, D.2
Chan, B.3
-
26
-
-
0032103187
-
Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients
-
Shafer, R. W., M. A. Winters, S. Palmer, and T. C. Merigan. 1998. Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients. Ann. Intern. Med. 128:906-911.
-
(1998)
Ann. Intern. Med.
, vol.128
, pp. 906-911
-
-
Shafer, R.W.1
Winters, M.A.2
Palmer, S.3
Merigan, T.C.4
-
27
-
-
0026344399
-
The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU
-
Spinelli, S., Q. Z. Liu, P. M. Alzari, P. H. Hirel, and R. J. Poljak. 1991. The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochimie 73:1391-1396.
-
(1991)
Biochimie
, vol.73
, pp. 1391-1396
-
-
Spinelli, S.1
Liu, Q.Z.2
Alzari, P.M.3
Hirel, P.H.4
Poljak, R.J.5
-
28
-
-
0036168452
-
Interference between D30N and L90M in selection and development of protease inhibitor-resistant human immunodeficiency virus type 1
-
Sugiura, W., Z. Matsuda, Y. Yokomaku, K. Hertogs, B. Larder, T. Oishi, A. Okano, T. Shiino, M. Tatsumi, M. Matsuda, H. Abumi, N. Takata, S. Shirahata, K. Yamada, H. Yoshikura, and Y. Nagai. 2002. Interference between D30N and L90M in selection and development of protease inhibitor-resistant human immunodeficiency virus type 1. Antimicrob. Agents Chemother. 46:708-715.
-
(2002)
Antimicrob. Agents Chemother.
, vol.46
, pp. 708-715
-
-
Sugiura, W.1
Matsuda, Z.2
Yokomaku, Y.3
Hertogs, K.4
Larder, B.5
Oishi, T.6
Okano, A.7
Shiino, T.8
Tatsumi, M.9
Matsuda, M.10
Abumi, H.11
Takata, N.12
Shirahata, S.13
Yamada, K.14
Yoshikura, H.15
Nagai, Y.16
-
29
-
-
0035910029
-
Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
-
Wang, W., and P. A. Kollman. 2001. Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc. Natl. Acad. Sci. USA 98:14937-14942.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14937-14942
-
-
Wang, W.1
Kollman, P.A.2
-
30
-
-
0027218692
-
Structure-based inhibitors of HIV-1 protease
-
Wlodawer, A., and J. W. Erickson. 1993. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:543-585.
-
(1993)
Annu. Rev. Biochem.
, vol.62
, pp. 543-585
-
-
Wlodawer, A.1
Erickson, J.W.2
-
31
-
-
0036145503
-
A potent human immunodeficiency virus type 1 protease inhibitor, UIC-94003 (TMC-126), and selection of a novel (A28S) mutation in the protease active site
-
Yoshimura, K., R. Kato, M. F. Kavlick, A. Nguyen, V. Maroun, K. Maeda, K. A. Hussain, A. K. Ghosh, S. V. Gulnik, J. W. Erickson, and H. Mitsuya. 2002. A potent human immunodeficiency virus type 1 protease inhibitor, UIC-94003 (TMC-126), and selection of a novel (A28S) mutation in the protease active site. J. Virol. 76:1349-1358.
-
(2002)
J. Virol.
, vol.76
, pp. 1349-1358
-
-
Yoshimura, K.1
Kato, R.2
Kavlick, M.F.3
Nguyen, A.4
Maroun, V.5
Maeda, K.6
Hussain, K.A.7
Ghosh, A.K.8
Gulnik, S.V.9
Erickson, J.W.10
Mitsuya, H.11
|