-
2
-
-
0031434606
-
Molecular mechanisms in retrovirus DNA integration
-
Asante-Appiah, E., and A. M. Skalka. 1997. Molecular mechanisms in retrovirus DNA integration. Antiviral Res. 36:139-156.
-
(1997)
Antiviral Res.
, vol.36
, pp. 139-156
-
-
Asante-Appiah, E.1
Skalka, A.M.2
-
3
-
-
0026019625
-
Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
-
Beese, L. S., and T. A. Steitz. 1991. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J. 10:25-33.
-
(1991)
EMBO J.
, vol.10
, pp. 25-33
-
-
Beese, L.S.1
Steitz, T.A.2
-
4
-
-
0023647997
-
Correct integration of retroviral DNA in vitro
-
Brown, P. O., B. Bowerman, H. E. Varmus, and J. M. Bishop. 1987. Correct integration of retroviral DNA in vitro. Cell. 49:347-356.
-
(1987)
Cell
, vol.49
, pp. 347-356
-
-
Brown, P.O.1
Bowerman, B.2
Varmus, H.E.3
Bishop, J.M.4
-
5
-
-
0030566832
-
The catalytic domain of human immunodeficiency virus integrase: Ordered active site in the F185H mutant
-
Bujacz, G., J. Alexandratos, Z. L. Qing, C. Clement-Mella, and A. Wlodawer. 1996. The catalytic domain of human immunodeficiency virus integrase: ordered active site in the F185H mutant. FEBS Lett. 398:175-178.
-
(1996)
FEBS Lett.
, vol.398
, pp. 175-178
-
-
Bujacz, G.1
Alexandratos, J.2
Qing, Z.L.3
Clement-Mella, C.4
Wlodawer, A.5
-
6
-
-
0028940992
-
Targeting retroviral integration
-
Bushman, F. 1995. Targeting retroviral integration. Science. 267:1443-1444.
-
(1995)
Science
, vol.267
, pp. 1443-1444
-
-
Bushman, F.1
-
7
-
-
0028225959
-
Human immunodeficiency virus type 1 integrase: Effect on viral replication of mutations at highly conserved residues
-
Cannon, P. M., W. Wilson, E. Byles, S. M. Kingsman, and A. J. Kingsman. 1994. Human immunodeficiency virus type 1 integrase: effect on viral replication of mutations at highly conserved residues. J. Virol. 68:4768-4775.
-
(1994)
J. Virol.
, vol.68
, pp. 4768-4775
-
-
Cannon, P.M.1
Wilson, W.2
Byles, E.3
Kingsman, S.M.4
Kingsman, A.J.5
-
8
-
-
0141878626
-
-
University of San Francisco, San Francisco, CA
-
Case, D. A., D. A. Pearlm, J. W. Caldwell, T. E. Cheatham 3rd, J. Wang, W. S. Ross, C. Simmerling, T. Darden, K. M. Merz, R. V. Stanton, and others. 2002. AMBER. Version 7. University of San Francisco, San Francisco, CA.
-
(2002)
AMBER. Version 7
-
-
Case, D.A.1
Pearlm, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.5
Ross, W.S.6
Simmerling, C.7
Darden, T.8
Merz, K.M.9
Stanton, R.V.10
-
11
-
-
0034682511
-
Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding
-
Chen, J. C., J. Krucinski, L. J. Miercke, J. S. Finer-Moore, A. H. Tang, A. D. Leavitt, and R. M. Stroud. 2000. Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding. Proc. Natl. Acad. Sci. USA. 97:8233-8238.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8233-8238
-
-
Chen, J.C.1
Krucinski, J.2
Miercke, L.J.3
Finer-Moore, J.S.4
Tang, A.H.5
Leavitt, A.D.6
Stroud, R.M.7
-
12
-
-
33846823909
-
Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
-
Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
13
-
-
0041488800
-
Small-molecule HIV-1 integrase inhibitors: The 2001-2002 update
-
Dayam, R., and N. Neamati. 2003. Small-molecule HIV-1 integrase inhibitors: the 2001-2002 update. Curr. Pharm. Des. 9:1789-1802.
-
(2003)
Curr. Pharm. Des.
, vol.9
, pp. 1789-1802
-
-
Dayam, R.1
Neamati, N.2
-
14
-
-
0029818017
-
The consistency of large concerted motions in proteins in molecular dynamics simulations
-
de Groot, B. L., D. M. van Aalten, A. Amadei, and H. J. Berendsen. 1996. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71:1707-1713.
-
(1996)
Biophys. J.
, vol.71
, pp. 1707-1713
-
-
Groot, B.L.1
Van Aalten, D.M.2
Amadei, A.3
Berendsen, H.J.4
-
16
-
-
0026740842
-
Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 in protein in vitro
-
Drelich, M., R. Wilhelm, and J. Mous. 1992. Identification of amino acid residues critical for endonuclease and integration activities of HIV-1 IN protein in vitro. Virology. 188:459-468.
-
(1992)
Virology.
, vol.188
, pp. 459-468
-
-
Drelich, M.1
Wilhelm, R.2
Mous, J.3
-
17
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, and others. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24:1999-2012.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
-
18
-
-
0028584269
-
Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
-
Dyda, F., A. B. Hickman, T. M. Jenkins, A. Engelman, R. Craigie, and D. R. Davies. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science. 266:1981-1986.
-
(1994)
Science
, vol.266
, pp. 1981-1986
-
-
Dyda, F.1
Hickman, A.B.2
Jenkins, T.M.3
Engelman, A.4
Craigie, R.5
Davies, D.R.6
-
19
-
-
0025600834
-
Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
-
Elber, R., and M. Karplus. 1990. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112:9161-9175.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
20
-
-
0026649557
-
Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro
-
Engelman, A., and R. Craigie. 1992. Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro. J. Virol. 66:6361-6369.
-
(1992)
J. Virol.
, vol.66
, pp. 6361-6369
-
-
Engelman, A.1
Craigie, R.2
-
21
-
-
0030988998
-
Structure-based mutagenesis of the catalytic domain of human immunodeficiency virus type 1 integrase
-
Engelman, A., Y. Liu, H. Chen, M. Farzan, and F. Dyda. 1997. Structure-based mutagenesis of the catalytic domain of human immunodeficiency virus type 1 integrase. J. Virol. 71:3507-3514.
-
(1997)
J. Virol.
, vol.71
, pp. 3507-3514
-
-
Engelman, A.1
Liu, Y.2
Chen, H.3
Farzan, M.4
Dyda, F.5
-
22
-
-
0347899425
-
ArchDB: Automated protein loop classification as a tool for structural genomics
-
Espadaler, J., N. Fernandez-Fuentes, A. Hermoso, E. Querol, F. X. Aviles, M. J. Sternberg, and B. Oliva. 2004. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res. (database issue) 32:D185-D188.
-
(2004)
Nucleic Acids Res. (Database Issue)
, vol.32
-
-
Espadaler, J.1
Fernandez-Fuentes, N.2
Hermoso, A.3
Querol, E.4
Aviles, F.X.5
Sternberg, M.J.6
Oliva, B.7
-
23
-
-
12944270496
-
HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase
-
Espeseth, A. S., P. Felock, A. Wolfe, M. Witmer, J. Grobler, N. Anthony, M. Egbertson, J. Y. Melamed, S. Young, T. Hamill, and others. 2000. HIV-1 integrase inhibitors that compete with the target DNA substrate define a unique strand transfer conformation for integrase. Proc. Natl. Acad. Sci. USA. 97:11244-112449.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 11244-112449
-
-
Espeseth, A.S.1
Felock, P.2
Wolfe, A.3
Witmer, M.4
Grobler, J.5
Anthony, N.6
Egbertson, M.7
Melamed, J.Y.8
Young, S.9
Hamill, T.10
-
24
-
-
0032189652
-
Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction
-
Esposito, D., and R. Craigie. 1998. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J. 17:5832-5843.
-
(1998)
EMBO J.
, vol.17
, pp. 5832-5843
-
-
Esposito, D.1
Craigie, R.2
-
25
-
-
0028821383
-
HIV-1 infection of nondividing cells: C-terminal tyrosine phosphorylation of the viral matrix protein is a key regulator
-
Gallay, P., S. Swingler, C. Aiken, and D. Trono. 1995. HIV-1 infection of nondividing cells: C-terminal tyrosine phosphorylation of the viral matrix protein is a key regulator. Cell. 80:379-388.
-
(1995)
Cell
, vol.80
, pp. 379-388
-
-
Gallay, P.1
Swingler, S.2
Aiken, C.3
Trono, D.4
-
26
-
-
0031949592
-
Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions
-
Gerton, J. L., S. Ohgi, M. Olsen, J. DeRisi, and P. O. Brown. 1998. Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions. J. Virol. 72:5046-5055.
-
(1998)
J. Virol.
, vol.72
, pp. 5046-5055
-
-
Gerton, J.L.1
Ohgi, S.2
Olsen, M.3
DeRisi, J.4
Brown, P.O.5
-
27
-
-
0033551443
-
The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity
-
Greenwald, J., V. Le, S. L. Butler, F. D. Bushman, and S. Choe. 1999. The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity. Biochemistry. 38:8892-8898.
-
(1999)
Biochemistry
, vol.38
, pp. 8892-8898
-
-
Greenwald, J.1
Le, V.2
Butler, S.L.3
Bushman, F.D.4
Choe, S.5
-
28
-
-
0031473847
-
SWISS-MODEL and the Swiss-PDBViewer: An environment for comparative protein modeling
-
Guex, N., and M. C. Peitsch. 1997. SWISS-MODEL and the Swiss-PDBViewer: an environment for comparative protein modeling. Electrophoresis. 18:2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
29
-
-
2642604727
-
Computer analysis of retroviral pol genes: Assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes
-
Johnson, M. S., M. A. McClure, D. F. Feng, J. Gray, and R. F. Doolittle. 1986. Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc. Natl. Acad. Sci. USA. 83:7648-7652.
-
(1986)
Proc. Natl. Acad. Sci. USA
, vol.83
, pp. 7648-7652
-
-
Johnson, M.S.1
McClure, M.A.2
Feng, D.F.3
Gray, J.4
Doolittle, R.F.5
-
30
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. Madura, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Klein, M.L.4
-
31
-
-
0026719238
-
Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases
-
Kulkosky, J., K. S. Jones, R. A. Katz, J. P. Mack, and A. M. Skalka. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331-2338.
-
(1992)
Mol. Cell. Biol.
, vol.12
, pp. 2331-2338
-
-
Kulkosky, J.1
Jones, K.S.2
Katz, R.A.3
Mack, J.P.4
Skalka, A.M.5
-
32
-
-
0027470432
-
Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro
-
Leavitt, A. D., L. Shiue, and H. E. Varmus. 1993. Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro. J. Biol. Chem. 268:2113-2119.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 2113-2119
-
-
Leavitt, A.D.1
Shiue, L.2
Varmus, H.E.3
-
33
-
-
0033063512
-
Molecular dynamics studies on the HIV-1 integrase catalytic domain
-
Lins, R. D., J. M. Briggs, T. P. Straatsma, H. A. Carlson, J. Greenwald, S. Choe, and J. A. McCammon. 1999. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys. J. 76:2999-3011.
-
(1999)
Biophys. J.
, vol.76
, pp. 2999-3011
-
-
Lins, R.D.1
Briggs, J.M.2
Straatsma, T.P.3
Carlson, H.A.4
Greenwald, J.5
Choe, S.6
McCammon, J.A.7
-
34
-
-
0024337080
-
The palindromic LTR-LTR junction of Moloney murine leukemia virus is not an efficient substrate for proviral integration
-
Lobel, L. I., J. E. Murphy, and S. P. Goff. 1989. The palindromic LTR-LTR junction of Moloney murine leukemia virus is not an efficient substrate for proviral integration. J. Virol. 63:2629-2637.
-
(1989)
J. Virol.
, vol.63
, pp. 2629-2637
-
-
Lobel, L.I.1
Murphy, J.E.2
Goff, S.P.3
-
35
-
-
0029633152
-
Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
-
Madura, J. D., J. M. Briggs, R. C. Wade, M. E. Davi, B. A. Luty, Ilin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. R. Scot, and others. 1995. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comput. Phys. Commun. 91:57-95.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 57-95
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davi, M.E.4
Luty, B.A.5
Ilin6
Antosiewicz, J.7
Gilson, M.K.8
Bagheri, B.9
Scot, L.R.10
-
36
-
-
0031557395
-
An automated classification of the structure of protein loops
-
Oliva, B., P. A. Bates, E. Querol, F. X. Aviles, and M. J. Sternberg. 1997. An automated classification of the structure of protein loops. J. Mol. Biol. 266:814-830.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 814-830
-
-
Oliva, B.1
Bates, P.A.2
Querol, E.3
Aviles, F.X.4
Sternberg, M.J.5
-
37
-
-
0032568959
-
Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction
-
Oliva, B., P. A. Bates, E. Querol, F. X. Aviles, and M. J. Sternberg. 1998. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J. Mol. Biol. 279:1193-1210.
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 1193-1210
-
-
Oliva, B.1
Bates, P.A.2
Querol, E.3
Aviles, F.X.4
Sternberg, M.J.5
-
38
-
-
0035984972
-
Targeting HIV: Old and new players
-
Pani, A., A. G. Loi, M. Mura, T. Marceddu, P. La Colla, and M. E. Marongiu. 2002. Targeting HIV: old and new players. Curr. Drug Targets Infect. Disord. 2:17-32.
-
(2002)
Curr. Drug Targets Infect. Disord.
, vol.2
, pp. 17-32
-
-
Pani, A.1
Loi, A.G.2
Mura, M.3
Marceddu, T.4
La Colla, P.5
Marongiu, M.E.6
-
40
-
-
36449006131
-
Modeling side chains in peptides and proteins: Application of locally enhanced sampling and simulated annealing methods to find minimum energy conformations
-
Roitberg, A., and R. Elber. 1991. Modeling side chains in peptides and proteins: application of locally enhanced sampling and simulated annealing methods to find minimum energy conformations. J. Chem. Phys. 95:9277-9287.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 9277-9287
-
-
Roitberg, A.1
Elber, R.2
-
41
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccitti, and H. J. Berendsen. 1977. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccitti, G.2
Berendsen, H.J.3
-
42
-
-
0034739559
-
Characterization of mutant HIV-1 integrase carrying amino acid changes in the catalytic domain
-
Sayasith, K., G. Sauve, and J. Yelle. 2000. Characterization of mutant HIV-1 integrase carrying amino acid changes in the catalytic domain. Mol. Cells. 10:525-532.
-
(2000)
Mol. Cells.
, vol.10
, pp. 525-532
-
-
Sayasith, K.1
Sauve, G.2
Yelle, J.3
-
44
-
-
1842607357
-
Discovery of a novel binding trench in HIV integrase
-
Schames, J. R., R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. Ni, and J. A. McCammon. 2004. Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47:1879-1881.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1879-1881
-
-
Schames, J.R.1
Henchman, R.H.2
Siegel, J.S.3
Sotriffer, C.A.4
Ni, H.5
McCammon, J.A.6
-
45
-
-
0033997592
-
Identification of critical amino acid residues in human immunodeficiency virus type 1 in required for efficient proviral DNA formation at steps prior to integration in dividing and nondividing cells
-
Tsurutani, N., M. Kubo, Y. Maeda, T. Ohashi, N. Yamamoto, M. Kannagi, and T. Masuda. 2000. Identification of critical amino acid residues in human immunodeficiency virus type 1 IN required for efficient proviral DNA formation at steps prior to integration in dividing and nondividing cells. J. Virol. 74:4795-4806.
-
(2000)
J. Virol.
, vol.74
, pp. 4795-4806
-
-
Tsurutani, N.1
Kubo, M.2
Maeda, Y.3
Ohashi, T.4
Yamamoto, N.5
Kannagi, M.6
Masuda, T.7
-
46
-
-
0035936692
-
Automated discovery of structural signatures of protein fold and function
-
Turcotte, M., S. H. Muggleton, and M. J, Sternberg. 2001. Automated discovery of structural signatures of protein fold and function. J. Mol. Biol. 306:591-605.
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 591-605
-
-
Turcotte, M.1
Muggleton, S.H.2
Sternberg, M.J.3
-
47
-
-
0031965842
-
Mutational scan of the human immunodeficiency virus type 2 integrase protein
-
van den Ent, F. M., A. Vos, and R. H. Plasterk. 1998. Mutational scan of the human immunodeficiency virus type 2 integrase protein. J. Virol. 72:3916-3924.
-
(1998)
J. Virol.
, vol.72
, pp. 3916-3924
-
-
Van Den Ent, F.M.1
Vos, A.2
Plasterk, R.H.3
-
48
-
-
0026668776
-
Mutational analysis of the integrase protein of human immunodeficiency virus type 2
-
van Gent, D. C., A. A. Groeneger, and R. H. Plasterk. 1992. Mutational analysis of the integrase protein of human immunodeficiency virus type 2. Proc. Natl. Acad. Sci. USA. 89:9598-9602.
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 9598-9602
-
-
Gent, D.C.1
Groeneger, A.A.2
Plasterk, R.H.3
-
49
-
-
0027179416
-
Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini
-
van Gent, D. C., A. A. Oude Groeneger, and R. H. Plasterk. 1993. Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini. Nucleic Acids Res. 21:3373-3377.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 3373-3377
-
-
Van Gent, D.C.1
Oude Groeneger, A.A.2
Plasterk, R.H.3
-
50
-
-
0026348879
-
Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNA termini mediated by the viral integrase protein
-
Vink, C., E. Yeheskiely, G. A. van der Marel, J. H. van Boom, and R. H. Plasterk. 1991. Site-specific hydrolysis and alcoholysis of human immunodeficiency virus DNA termini mediated by the viral integrase protein. Nucleic Acids Res. 19:6691-6698.
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 6691-6698
-
-
Vink, C.1
Yeheskiely, E.2
Van Der Marel, G.A.3
Van Boom, J.H.4
Plasterk, R.H.5
|