-
1
-
-
0026330796
-
HIV-1 DNA integration: Mechanism of viral DNA cleavage and DNA strand transfer
-
Engelman, A., Mizuuchi, K. and Craigie, R. (1991) HIV-1 DNA integration: mechanism of viral DNA cleavage and DNA strand transfer. Cell, 67, 1211-1221.
-
(1991)
Cell
, vol.67
, pp. 1211-1221
-
-
Engelman, A.1
Mizuuchi, K.2
Craigie, R.3
-
2
-
-
0037841763
-
Transcription start regions in the human genome are favored targets for MLV integration
-
Wu, X., Li, Y., Crise, B. and Burgess, S.M. (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1749-1751.
-
(2003)
Science
, vol.300
, pp. 1749-1751
-
-
Wu, X.1
Li, Y.2
Crise, B.3
Burgess, S.M.4
-
3
-
-
84896982583
-
Enhancers are major targets for murine leukemia virus vector integration
-
De Ravin, S.S., Su, L., Theobald, N., Choi, U., Macpherson, J.L., Poidinger, M., Symonds, G., Pond, S.M., Ferris, A.L., Hughes, S.H. et al. (2014) Enhancers are major targets for murine leukemia virus vector integration. J. Virol., 88, 4504-4513.
-
(2014)
J. Virol.
, vol.88
, pp. 4504-4513
-
-
De Ravin, S.S.1
Su, L.2
Theobald, N.3
Choi, U.4
MacPherson, J.L.5
Poidinger, M.6
Symonds, G.7
Pond, S.M.8
Ferris, A.L.9
Hughes, S.H.10
-
4
-
-
84898976913
-
MLV integration site selection is driven by strong enhancers and active promoters
-
LaFave, M.C., Varshney, G.K., Gildea, D.E., Wolfsberg, T.G., Baxevanis, A.D. and Burgess, S.M. (2014) MLV integration site selection is driven by strong enhancers and active promoters. Nucleic Acids Res., 42, 4257-4269.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 4257-4269
-
-
Lafave, M.C.1
Varshney, G.K.2
Gildea, D.E.3
Wolfsberg, T.G.4
Baxevanis, A.D.5
Burgess, S.M.6
-
5
-
-
0028584269
-
Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases
-
Dyda, F., Hickman, A.B., Jenkins, T.M., Engelman, A., Craigie, R. and Davies, D.R. (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
-
6
-
-
77949365510
-
Retroviral intasome assembly and inhibition of DNA strand transfer
-
Hare, S., Gupta, S.S., Valkov, E., Engelman, A. and Cherepanov, P. (2010) Retroviral intasome assembly and inhibition of DNA strand transfer. Nature, 464, 232-236.
-
(2010)
Nature
, vol.464
, pp. 232-236
-
-
Hare, S.1
Gupta, S.S.2
Valkov, E.3
Engelman, A.4
Cherepanov, P.5
-
7
-
-
0028034050
-
Characterization of the minimal DNA-binding domain of the HIV integrase protein
-
Lutzke, R.A., Vink, C. and Plasterk, R.H. (1994) Characterization of the minimal DNA-binding domain of the HIV integrase protein. Nucleic Acids Res., 22, 4125-4131.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4125-4131
-
-
Lutzke, R.A.1
Vink, C.2
Plasterk, R.H.3
-
8
-
-
2642604727
-
Computer analysis of retroviral pol genes: Assignment of enzymatic functions to specifc sequences and homologies with nonviral enzymes
-
Johnson, M.S., McClure, M.A., Feng, D.F., Gray, J. and Doolittle, R.F. (1986) Computer analysis of retroviral pol genes: assignment of enzymatic functions to specifc sequences and homologies with nonviral enzymes. Proc. Natl. Acad. Sci. U.S.A., 83, 7648-7652.
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 7648-7652
-
-
Johnson, M.S.1
McClure, M.A.2
Feng, D.F.3
Gray, J.4
Doolittle, R.F.5
-
9
-
-
0029145047
-
The DNA-binding domain of HIV-1 integrase has an SH3-like fold
-
Eijkelenboom, A.P., Lutzke, R.A., Boelens, R., Plasterk, R.H., Kaptein, R. and Hard, K. (1995) The DNA-binding domain of HIV-1 integrase has an SH3-like fold. Nat. Struct. Biol., 2, 807-810.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 807-810
-
-
Eijkelenboom, A.P.1
Lutzke, R.A.2
Boelens, R.3
Plasterk, R.H.4
Kaptein, R.5
Hard, K.6
-
10
-
-
0029116747
-
Solution structure of the DNA binding domain of HIV-1 integrase
-
Lodi, P.J., Ernst, J.A., Kuszewski, J., Hickman, A.B., Engelman, A., Craigie, R., Clore, G.M. and Gronenborn, A.M. (1995) Solution structure of the DNA binding domain of HIV-1 integrase. Biochemistry, 34, 9826-9833.
-
(1995)
Biochemistry
, vol.34
, pp. 9826-9833
-
-
Lodi, P.J.1
Ernst, J.A.2
Kuszewski, J.3
Hickman, A.B.4
Engelman, A.5
Craigie, R.6
Clore, G.M.7
Gronenborn, A.M.8
-
11
-
-
0034681303
-
Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase
-
Hyde, C.C., Bushman, F.D., Mueser, T.C. and Yang, Z.-N. (1999) Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase. J. Mol. Biol., 296, 535-538.
-
(1999)
J. Mol. Biol.
, vol.296
, pp. 535-538
-
-
Hyde, C.C.1
Bushman, F.D.2
Mueser, T.C.3
Yang, Z.-N.4
-
12
-
-
84901305093
-
Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction
-
Aiyer, S., Swapna, G.V., Malani, N., Aramini, J.M., Schneider, W.M., Plumb, M.R., Ghanem, M., Larue, R.C., Sharma, A., Studamire, B. et al. (2014) Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction. Nucleic Acids Res., 42, 5917-5928.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 5917-5928
-
-
Aiyer, S.1
Swapna, G.V.2
Malani, N.3
Aramini, J.M.4
Schneider, W.M.5
Plumb, M.R.6
Ghanem, M.7
Larue, R.C.8
Sharma, A.9
Studamire, B.10
-
13
-
-
84880392326
-
BET proteins promote effcient murine leukemia virus integration at transcription start sites
-
Sharma, A., Larue, R.C., Plumb, M.R., Malani, N., Male, F., Slaughter, A., Kessl, J.J., Shkriabai, N., Coward, E., Aiyer, S.S. et al. (2013) BET proteins promote effcient murine leukemia virus integration at transcription start sites. Proc. Natl. Acad. Sci. U.S.A., 110, 12036-12041.
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 12036-12041
-
-
Sharma, A.1
Larue, R.C.2
Plumb, M.R.3
Malani, N.4
Male, F.5
Slaughter, A.6
Kessl, J.J.7
Shkriabai, N.8
Coward, E.9
Aiyer, S.S.10
-
14
-
-
84888437641
-
The BET family of proteins targets Moloney murine leukemia virus integration near transcription start sites
-
De Rijck, J., de Kogel, C., Demeulemeester, J., Vets, S., El Ashkar, S., Malani, N., Bushman, F.D., Landuyt, B., Husson, S.J., Busschots, K. et al. (2013) The BET family of proteins targets Moloney murine leukemia virus integration near transcription start sites. Cell Rep., 5, 886-894.
-
(2013)
Cell Rep.
, vol.5
, pp. 886-894
-
-
De Rijck, J.1
De Kogel, C.2
Demeulemeester, J.3
Vets, S.4
El Ashkar, S.5
Malani, N.6
Bushman, F.D.7
Landuyt, B.8
Husson, S.J.9
Busschots, K.10
-
15
-
-
78149434355
-
The mechanism of retroviral integration from X-ray structures of its key intermediates
-
Maertens, G.N., Hare, S. and Cherepanov, P. (2010) The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature, 468, 326-329.
-
(2010)
Nature
, vol.468
, pp. 326-329
-
-
Maertens, G.N.1
Hare, S.2
Cherepanov, P.3
-
16
-
-
84868535547
-
Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA
-
Gupta, K., Curtis, J.E., Krueger, S., Hwang, Y., Cherepanov, P., Bushman, F.D. and Van Duyne, G.D. (2012) Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA. Structure, 20, 1918-1928.
-
(2012)
Structure
, vol.20
, pp. 1918-1928
-
-
Gupta, K.1
Curtis, J.E.2
Krueger, S.3
Hwang, Y.4
Cherepanov, P.5
Bushman, F.D.6
Van Duyne, G.D.7
-
17
-
-
67349135952
-
Identifying amino acid residues that contribute to the cellular-DNA binding site on retroviral integrase
-
Nowak, M.G., Sudol, M., Lee, N.E., Konsavage, W.M. Jr and Katzman, M. (2009) Identifying amino acid residues that contribute to the cellular-DNA binding site on retroviral integrase. Virology, 389, 141-148.
-
(2009)
Virology
, vol.389
, pp. 141-148
-
-
Nowak, M.G.1
Sudol, M.2
Lee, N.E.3
Konsavage, Jr.W.M.4
Katzman, M.5
-
18
-
-
84899865250
-
Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: Implications for the mechanism of target DNA binding
-
Serrao, E., Krishnan, L., Shun, M.C., Li, X., Cherepanov, P., Engelman, A. and Maertens, G.N. (2014) Integrase residues that determine nucleotide preferences at sites of HIV-1 integration: implications for the mechanism of target DNA binding. Nucleic Acids Res., 42, 5164-5176.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 5164-5176
-
-
Serrao, E.1
Krishnan, L.2
Shun, M.C.3
Li, X.4
Cherepanov, P.5
Engelman, A.6
Maertens, G.N.7
-
19
-
-
0026684601
-
Mutational analysis of N-linked glycosylation sites of the SU protein of Moloney murine leukemia virus
-
Felkner, R.H. and Roth, M.J. (1992) Mutational analysis of N-linked glycosylation sites of the SU protein of Moloney murine leukemia virus. J. Virol., 66, 4258-4264.
-
(1992)
J. Virol.
, vol.66
, pp. 4258-4264
-
-
Felkner, R.H.1
Roth, M.J.2
-
20
-
-
77956187416
-
The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium
-
Xiao, R., Anderson, S., Aramini, J., Belote, R., Buchwald, W.A., Ciccosanti, C., Conover, K., Everett, J.K., Hamilton, K., Huang, Y.J. et al. (2010) The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J. Struct. Biol., 172, 21-33.
-
(2010)
J. Struct. Biol.
, vol.172
, pp. 21-33
-
-
Xiao, R.1
Anderson, S.2
Aramini, J.3
Belote, R.4
Buchwald, W.A.5
Ciccosanti, C.6
Conover, K.7
Everett, J.K.8
Hamilton, K.9
Huang, Y.J.10
-
21
-
-
79952411326
-
Preparation of protein samples for NMR structure, function, and small-molecule screening studies
-
Acton, T.B., Xiao, R., Anderson, S., Aramini, J., Buchwald, W.A., Ciccosanti, C., Conover, K., Everett, J., Hamilton, K., Huang, Y.J. et al. (2011) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol., 493, 21-60.
-
(2011)
Methods Enzymol.
, vol.493
, pp. 21-60
-
-
Acton, T.B.1
Xiao, R.2
Anderson, S.3
Aramini, J.4
Buchwald, W.A.5
Ciccosanti, C.6
Conover, K.7
Everett, J.8
Hamilton, K.9
Huang, Y.J.10
-
22
-
-
0030095165
-
High-level production of uniformly (1)(5)N-and (1)(3)C-enriched fusion proteins in Escherichia coli
-
Jansson, M., Li, Y.C., Jendeberg, L., Anderson, S., Montelione, G.T. and Nilsson, B. (1996) High-level production of uniformly (1)(5)N-and (1)(3)C-enriched fusion proteins in Escherichia coli. J. Biomol. NMR., 7, 131-141.
-
(1996)
J. Biomol. NMR.
, vol.7
, pp. 131-141
-
-
Jansson, M.1
Li, Y.C.2
Jendeberg, L.3
Anderson, S.4
Montelione, G.T.5
Nilsson, B.6
-
23
-
-
20144387833
-
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium
-
Acton, T.B., Gunsalus, K.C., Xiao, R., Ma, L.C., Aramini, J., Baran, M.C., Chiang, Y.W., Climent, T., Cooper, B., Denissova, N.G. et al. (2005) Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol., 394, 210-243.
-
(2005)
Methods Enzymol.
, vol.394
, pp. 210-243
-
-
Acton, T.B.1
Gunsalus, K.C.2
Xiao, R.3
Ma, L.C.4
Aramini, J.5
Baran, M.C.6
Chiang, Y.W.7
Climent, T.8
Cooper, B.9
Denissova, N.G.10
-
24
-
-
0029400480
-
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
-
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 6, 277-293.
-
(1995)
J. Biomol. NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
Grzesiek, S.2
Vuister, G.W.3
Zhu, G.4
Pfeifer, J.5
Bax, A.6
-
25
-
-
0034923123
-
Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data
-
Moseley, H.N., Monleon, D. and Montelione, G.T. (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol., 339, 91-108.
-
(2001)
Methods Enzymol.
, vol.339
, pp. 91-108
-
-
Moseley, H.N.1
Monleon, D.2
Montelione, G.T.3
-
26
-
-
4344648451
-
Automated analysis of protein NMR assignments and structures
-
Baran, M.C., Huang, Y.J., Moseley, H.N. and Montelione, G.T. (2004) Automated analysis of protein NMR assignments and structures. Chem. Rev., 104, 3541-3556.
-
(2004)
Chem. Rev.
, vol.104
, pp. 3541-3556
-
-
Baran, M.C.1
Huang, Y.J.2
Moseley, H.N.3
Montelione, G.T.4
-
27
-
-
16244377434
-
An integrated platform for automated analysis of protein NMR structures
-
Huang, Y.J., Moseley, H.N., Baran, M.C., Arrowsmith, C., Powers, R., Tejero, R., Szyperski, T. and Montelione, G.T. (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol., 394, 111-141.
-
(2005)
Methods Enzymol.
, vol.394
, pp. 111-141
-
-
Huang, Y.J.1
Moseley, H.N.2
Baran, M.C.3
Arrowsmith, C.4
Powers, R.5
Tejero, R.6
Szyperski, T.7
Montelione, G.T.8
-
28
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Guntert, P., Mumenthaler, C. and Wuthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol., 273, 283-298.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wuthrich, K.3
-
29
-
-
0036873589
-
Protein NMR structure determination with automated NOE-identifcation in the NOESY spectra using the new software ATNOS
-
Herrmann, T., Guntert, P. and Wuthrich, K. (2002) Protein NMR structure determination with automated NOE-identifcation in the NOESY spectra using the new software ATNOS. J. Biomol. NMR, 24, 171-189.
-
(2002)
J. Biomol. NMR
, vol.24
, pp. 171-189
-
-
Herrmann, T.1
Guntert, P.2
Wuthrich, K.3
-
30
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54, 905-921.
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
-
31
-
-
33847079676
-
Evaluating protein structures determined by structural genomics consortia
-
Bhattacharya, A., Tejero, R. and Montelione, G.T. (2007) Evaluating protein structures determined by structural genomics consortia. Proteins, 66, 778-795.
-
(2007)
Proteins
, vol.66
, pp. 778-795
-
-
Bhattacharya, A.1
Tejero, R.2
Montelione, G.T.3
-
32
-
-
1442306656
-
Assignment validation software suite for the evaluation and presentation of protein resonance assignment data
-
Moseley, H.N., Sahota, G. and Montelione, G.T. (2004) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J. Biomol. NMR, 28, 341-355.
-
(2004)
J. Biomol. NMR
, vol.28
, pp. 341-355
-
-
Moseley, H.N.1
Sahota, G.2
Montelione, G.T.3
-
33
-
-
13644252170
-
Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics
-
Huang, Y.J., Powers, R. and Montelione, G.T. (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J. Am. Chem. Soc., 127, 1665-1674.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 1665-1674
-
-
Huang, Y.J.1
Powers, R.2
Montelione, G.T.3
-
34
-
-
42449090264
-
PROMALS3D: A tool for multiple protein sequence and structure alignments
-
Pei, J., Kim, B.H. and Grishin, N.V. (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res., 36, 2295-2300.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 2295-2300
-
-
Pei, J.1
Kim, B.H.2
Grishin, N.V.3
-
35
-
-
0032961270
-
ESPript: Analysis of multiple sequence alignments in PostScript
-
Gouet, P., Courcelle, E., Stuart, D.I. and Metoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308.
-
(1999)
Bioinformatics
, vol.15
, pp. 305-308
-
-
Gouet, P.1
Courcelle, E.2
Stuart, D.I.3
Metoz, F.4
-
36
-
-
0033988023
-
Second-site changes affect viability of amphotropic/ecotropic chimeric-enveloped MuLVs
-
O'Reilly, L. and Roth, M.J. (2000) Second-site changes affect viability of amphotropic/ecotropic chimeric-enveloped MuLVs. J. Virol., 74, 899-913.
-
(2000)
J. Virol.
, vol.74
, pp. 899-913
-
-
O'Reilly, L.1
Roth, M.J.2
-
37
-
-
0014322388
-
Enchancement of the infectivity of simian virus 40 deoxyribonucleic acid with diethylaminoethyl-dextran
-
McCutchan, J.H. and Pagano, J.S. (1968) Enchancement of the infectivity of simian virus 40 deoxyribonucleic acid with diethylaminoethyl-dextran. J. Natl. Cancer. Inst., 41, 351-357.
-
(1968)
J. Natl. Cancer. Inst.
, vol.41
, pp. 351-357
-
-
McCutchan, J.H.1
Pagano, J.S.2
-
38
-
-
0019507492
-
Isolation and properties of Moloney murine leukemia virus mutants; Use of a rapid assay for release of virion reverse transcriptase
-
Goff, S.P., Traktman, P. and Baltimore, D. (1981) Isolation and properties of Moloney murine leukemia virus mutants; use of a rapid assay for release of virion reverse transcriptase. J. Virol., 38, 239-248.
-
(1981)
J. Virol.
, vol.38
, pp. 239-248
-
-
Goff, S.P.1
Traktman, P.2
Baltimore, D.3
-
39
-
-
0031473847
-
SWISS-MODEL and the Swiss-PDBViewer: An environment for comparative protein modeling
-
Guex, N. and Peitsch, M.C. (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
-
40
-
-
0042622380
-
SWISS-MODEL: An automated protein homology-modeling server
-
Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003) SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
41
-
-
32144432437
-
The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
-
Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201.
-
(2006)
Bioinformatics
, vol.22
, pp. 195-201
-
-
Arnold, K.1
Bordoli, L.2
Kopp, J.3
Schwede, T.4
-
42
-
-
33646075470
-
Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling
-
Rai, B.K. and Fiser, A. (2006) Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling. Proteins, 63, 644-661.
-
(2006)
Proteins
, vol.63
, pp. 644-661
-
-
Rai, B.K.1
Fiser, A.2
-
43
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
44
-
-
77954065271
-
I-TASSER: A unifed platform for automated protein structure and function prediction
-
Roy, A., Kucukural, A. and Zhang, Y. (2010) I-TASSER: a unifed platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
45
-
-
84864460609
-
COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
-
Roy, A., Yang, J. and Zhang, Y. (2012) COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res., 40, W471-W477.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W471-W477
-
-
Roy, A.1
Yang, J.2
Zhang, Y.3
-
46
-
-
37349062680
-
Assessing model accuracy using the homology modeling automatically software
-
Bhattacharya, A., Wunderlich, Z., Monleon, D., Tejero, R. and Montelione, G.T. (2008) Assessing model accuracy using the homology modeling automatically software. Proteins, 70, 105-118.
-
(2008)
Proteins
, vol.70
, pp. 105-118
-
-
Bhattacharya, A.1
Wunderlich, Z.2
Monleon, D.3
Tejero, R.4
Montelione, G.T.5
-
47
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N.A., Sept, D., Joseph, S., Holst, M.J. and McCammon, J.A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U.S.A., 98, 10037-10041.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
48
-
-
84880736522
-
Development of an enzyme-linked immunosorbent assay based on the murine leukemia virus p30 capsid protein
-
Wu, D.T., Aiyer, S., Villanueva, R.A. and Roth, M.J. (2013) Development of an enzyme-linked immunosorbent assay based on the murine leukemia virus p30 capsid protein. J. Virol. Methods, 193, 332-336.
-
(2013)
J. Virol. Methods
, vol.193
, pp. 332-336
-
-
Wu, D.T.1
Aiyer, S.2
Villanueva, R.A.3
Roth, M.J.4
-
49
-
-
84857788410
-
MuLV in mutants responsive to HDAC inhibitors enhance transcription from unintegrated retroviral DNA
-
Schneider, W.M., Wu, D.T., Amin, V., Aiyer, S. and Roth, M.J. (2012) MuLV IN mutants responsive to HDAC inhibitors enhance transcription from unintegrated retroviral DNA. Virology, 426, 188-196.
-
(2012)
Virology
, vol.426
, pp. 188-196
-
-
Schneider, W.M.1
Wu, D.T.2
Amin, V.3
Aiyer, S.4
Roth, M.J.5
-
50
-
-
0022481618
-
Analysis of retroviral pol gene products with antisera raised against fusion proteins produced in Escherichia coli
-
Tanese, N., Roth, M.J. and Goff, S.P. (1986) Analysis of retroviral pol gene products with antisera raised against fusion proteins produced in Escherichia coli. J. Virol., 59, 328-340.
-
(1986)
J. Virol.
, vol.59
, pp. 328-340
-
-
Tanese, N.1
Roth, M.J.2
Goff, S.P.3
-
51
-
-
33749016024
-
Revealing domain structure through linker-scanning analysis of the murine leukemia virus (MuLV) RNase H and MuLV and human immunodefciency virus type 1 Integrase proteins
-
Puglia, J., Wang, T., Smith-Snyder, C., Cote, M., Scher, M., Pelletier, J., John, S., Jonsson, C. and Roth, M. (2006) Revealing domain structure through linker-scanning analysis of the murine leukemia virus (MuLV) RNase H and MuLV and human immunodefciency virus type 1 Integrase proteins. J. Virol., 80, 9497-9510.
-
(2006)
J. Virol.
, vol.80
, pp. 9497-9510
-
-
Puglia, J.1
Wang, T.2
Smith-Snyder, C.3
Cote, M.4
Scher, M.5
Pelletier, J.6
John, S.7
Jonsson, C.8
Roth, M.9
-
52
-
-
77649179682
-
A microscale protein NMR sample screening pipeline
-
Rossi, P., Swapna, G.V., Huang, Y.J., Aramini, J.M., Anklin, C., Conover, K., Hamilton, K., Xiao, R., Acton, T.B., Ertekin, A. et al. (2010) A microscale protein NMR sample screening pipeline. J. Biomol. NMR, 46, 11-22.
-
(2010)
J. Biomol. NMR
, vol.46
, pp. 11-22
-
-
Rossi, P.1
Swapna, G.V.2
Huang, Y.J.3
Aramini, J.M.4
Anklin, C.5
Conover, K.6
Hamilton, K.7
Xiao, R.8
Acton, T.B.9
Ertekin, A.10
-
53
-
-
84883463996
-
PDBStat: A universal restraint converter and restraint analysis software package for protein NMR
-
Tejero, R., Snyder, D., Mao, B., Aramini, J.M. and Montelione, G.T. (2013) PDBStat: a universal restraint converter and restraint analysis software package for protein NMR. J. Biomol. NMR, 56, 337-351.
-
(2013)
J. Biomol. NMR
, vol.56
, pp. 337-351
-
-
Tejero, R.1
Snyder, D.2
Mao, B.3
Aramini, J.M.4
Montelione, G.T.5
-
54
-
-
84883476906
-
Recommendations of the wwPDB NMR Validation Task Force
-
Montelione, G.T., Nilges, M., Bax, A., Guntert, P., Herrmann, T., Richardson, J.S., Schwieters, C.D., Vranken, W.F., Vuister, G.W., Wishart, D.S. et al. (2013) Recommendations of the wwPDB NMR Validation Task Force. Structure, 21, 1563-1570.
-
(2013)
Structure
, vol.21
, pp. 1563-1570
-
-
Montelione, G.T.1
Nilges, M.2
Bax, A.3
Guntert, P.4
Herrmann, T.5
Richardson, J.S.6
Schwieters, C.D.7
Vranken, W.F.8
Vuister, G.W.9
Wishart, D.S.10
-
55
-
-
77954288774
-
Dali server: Conservation mapping in 3D
-
Holm, L. and Rosenstrom, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38, W545-W549.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W545-W549
-
-
Holm, L.1
Rosenstrom, P.2
-
56
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy, H., Erez, E., Martz, E., Pupko, T. and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W529-W533
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
57
-
-
0026610767
-
Assessment of protein models with three-dimensional profles
-
Luthy, R., Bowie, J.U. and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profles. Nature, 356, 83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Luthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
58
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl, M.J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
59
-
-
0000243829
-
PROCHECK-a program to check the stereochemical quality of protein structures
-
Laskowski, R.A., Macarthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
60
-
-
0037441653
-
Structure validation by Calpha geometry: Phi, psi and Cbeta deviation
-
Lovell, S.C., Davis, I.W., Arendall, W.B. 3rd, de Bakker, P.I., Word, J.M., Prisant, M.G., Richardson, J.S. and Richardson, D.C. (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins, 50, 437-450.
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall, W.B.3
De Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
61
-
-
0037334017
-
An amino acid in the central catalytic domain of three retroviral integrases that affects target site selection in nonviral DNA
-
Harper, A.L., Sudol, M. and Katzman, M. (2003) An amino acid in the central catalytic domain of three retroviral integrases that affects target site selection in nonviral DNA. J. Virol., 77, 3838-3845.
-
(2003)
J. Virol.
, vol.77
, pp. 3838-3845
-
-
Harper, A.L.1
Sudol, M.2
Katzman, M.3
-
62
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
Swinger, K.K., Lemberg, K.M., Zhang, Y. and Rice, P.A. (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J., 22, 3749-3760.
-
(2003)
EMBO J.
, vol.22
, pp. 3749-3760
-
-
Swinger, K.K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
63
-
-
16244386233
-
Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses
-
Wu, X., Li, Y., Crise, B., Burgess, S.M. and Munroe, D.J. (2005) Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses. J. Virol., 79, 5211-5214.
-
(2005)
J. Virol.
, vol.79
, pp. 5211-5214
-
-
Wu, X.1
Li, Y.2
Crise, B.3
Burgess, S.M.4
Munroe, D.J.5
-
64
-
-
17844381584
-
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites
-
Holman, A.G. and Coffn, J.M. (2005) Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. Proc. Natl. Acad. Sci. U.S.A., 102, 6103-6107.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6103-6107
-
-
Holman, A.G.1
Coffn, J.M.2
-
65
-
-
79955769735
-
Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking
-
Bojja, R.S., Andrake, M.D., Weigand, S., Merkel, G., Yarychkivska, O., Henderson, A., Kummerling, M. and Skalka, A.M. (2011) Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking. J. Biol. Chem., 286, 17047-17059.
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 17047-17059
-
-
Bojja, R.S.1
Andrake, M.D.2
Weigand, S.3
Merkel, G.4
Yarychkivska, O.5
Henderson, A.6
Kummerling, M.7
Skalka, A.M.8
-
66
-
-
84874839394
-
Architecture and assembly of HIV integrase multimers in the absence of DNA substrates
-
Bojja, R.S., Andrake, M.D., Merkel, G., Weigand, S., Dunbrack, R.L. Jr and Skalka, A.M. (2013) Architecture and assembly of HIV integrase multimers in the absence of DNA substrates. J. Bio l. Chem., 288, 7373-7386.
-
(2013)
J. Bio L. Chem.
, vol.288
, pp. 7373-7386
-
-
Bojja, R.S.1
Andrake, M.D.2
Merkel, G.3
Weigand, S.4
Dunbrack, Jr.R.L.5
Skalka, A.M.6
-
67
-
-
0026085511
-
Mutational analysis of the carboxyl terminus of the Moloney murine leukemia virus integration protein
-
Roth, M.J. (1991) Mutational analysis of the carboxyl terminus of the Moloney murine leukemia virus integration protein. J. Virol., 65, 2141-2145.
-
(1991)
J. Virol.
, vol.65
, pp. 2141-2145
-
-
Roth, M.J.1
-
68
-
-
0035169289
-
Moloney murine leukemia virus integrase protein augments viral DNA synthesis in infected cells
-
Lai, L., Liu, H., Wu, X. and Kappes, J.C. (2001) Moloney murine leukemia virus integrase protein augments viral DNA synthesis in infected cells. J. Virol., 75, 11365-11372.
-
(2001)
J. Virol.
, vol.75
, pp. 11365-11372
-
-
Lai, L.1
Liu, H.2
Wu, X.3
Kappes, J.C.4
-
69
-
-
0029934077
-
Functional domains of Moloney murine leukemia virus integrase defned by mutation and complementation analysis
-
Jonsson, C.B., Donzella, G.A., Gaucan, E., Smith, C.M. and Roth, M.J. (1996) Functional domains of Moloney murine leukemia virus integrase defned by mutation and complementation analysis. J. Virol., 70, 4585-4597.
-
(1996)
J. Virol.
, vol.70
, pp. 4585-4597
-
-
Jonsson, C.B.1
Donzella, G.A.2
Gaucan, E.3
Smith, C.M.4
Roth, M.J.5
-
70
-
-
79955398402
-
Sequential deletion of the integrase (Gag-Pol) carboxyl terminus reveals distinct phenotypic classes of defective HIV-1
-
Mohammed, K.D., Topper, M.B. and Muesing, M.A. (2011) Sequential deletion of the integrase (Gag-Pol) carboxyl terminus reveals distinct phenotypic classes of defective HIV-1. J. Virol., 85, 4654-4666.
-
(2011)
J. Virol.
, vol.85
, pp. 4654-4666
-
-
Mohammed, K.D.1
Topper, M.B.2
Muesing, M.A.3
-
71
-
-
70450273192
-
Biochemical and virological analysis of the 18-residue C-terminal tail of HIV-1 integrase
-
Dar, M., Monel, B., Krishnan, L., Shun, M.-C., Nunzio, F., Helland, D. and Engelman, A. (2009) Biochemical and virological analysis of the 18-residue C-terminal tail of HIV-1 integrase. Retrovirology, 6, 94.
-
(2009)
Retrovirology
, vol.6
, pp. 94
-
-
Dar, M.1
Monel, B.2
Krishnan, L.3
Shun, M.-C.4
Nunzio, F.5
Helland, D.6
Engelman, A.7
-
72
-
-
33750214531
-
The discovery of endogenous retroviruses
-
Weiss, R.A. (2006) The discovery of endogenous retroviruses. Retrovirology, 3, 67.
-
(2006)
Retrovirology
, vol.3
, pp. 67
-
-
Weiss, R.A.1
-
73
-
-
34249952425
-
Human T-cell leukemia virus type 1 integration target sites in the human genome: Comparison with those of other retroviruses
-
Derse, D., Crise, B., Li, Y., Princler, G., Lum, N., Stewart, C., McGrath, C.F., Hughes, S.H., Munroe, D.J. and Wu, X. (2007) Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses. J. Virol., 81, 6731-6741.
-
(2007)
J. Virol.
, vol.81
, pp. 6731-6741
-
-
Derse, D.1
Crise, B.2
Li, Y.3
Princler, G.4
Lum, N.5
Stewart, C.6
McGrath, C.F.7
Hughes, S.H.8
Munroe, D.J.9
Wu, X.10
-
74
-
-
31944444349
-
Foamy virus vector integration sites in normal human cells
-
Trobridge, G.D., Miller, D.G., Jacobs, M.A., Allen, J.M., Kiem, H.-P., Kaul, R. and Russell, D.W. (2006) Foamy virus vector integration sites in normal human cells. Proc. Natl. Acad. Sci. U.S.A., 103, 1498-1503.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 1498-1503
-
-
Trobridge, G.D.1
Miller, D.G.2
Jacobs, M.A.3
Allen, J.M.4
Kiem, H.-P.5
Kaul, R.6
Russell, D.W.7
-
75
-
-
33846652601
-
LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro
-
Cherepanov, P. (2007) LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro. Nucleic Acids Res., 35, 113-124.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 113-124
-
-
Cherepanov, P.1
-
76
-
-
34249804819
-
Unique integration profles in a canine model of long-term repopulating cells transduced with gammaretrovirus, lentivirus, or foamy virus
-
Beard, B.C., Keyser, K.A., Trobridge, G.D., Peterson, L.J., Miller, D.G., Jacobs, M., Kaul, R. and Kiem, H.P. (2007) Unique integration profles in a canine model of long-term repopulating cells transduced with gammaretrovirus, lentivirus, or foamy virus. Hum. Gene Ther., 18, 423-434.
-
(2007)
Hum. Gene Ther.
, vol.18
, pp. 423-434
-
-
Beard, B.C.1
Keyser, K.A.2
Trobridge, G.D.3
Peterson, L.J.4
Miller, D.G.5
Jacobs, M.6
Kaul, R.7
Kiem, H.P.8
-
77
-
-
0024654338
-
A nucleoprotein complex mediates the integration of retroviral DNA
-
Bowerman, B., Brown, P.O., Bishop, J.M. and Varmus, H.E. (1989) A nucleoprotein complex mediates the integration of retroviral DNA. Genes Dev., 3, 469-478.
-
(1989)
Genes Dev.
, vol.3
, pp. 469-478
-
-
Bowerman, B.1
Brown, P.O.2
Bishop, J.M.3
Varmus, H.E.4
-
78
-
-
0027199982
-
Association of integrase, matrix, and reverse transcriptase antigens of human immunodefciency virus type 1 with viral nucleic acids following acute infection
-
Bukrinsky, M.I., Sharova, N., McDonald, T.L., Pushkarskaya, T., Tarpley, W.G. and Stevenson, M. (1993) Association of integrase, matrix, and reverse transcriptase antigens of human immunodefciency virus type 1 with viral nucleic acids following acute infection. Proc. Natl. Acad. Sci. U.S.A., 90, 6125-6129.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 6125-6129
-
-
Bukrinsky, M.I.1
Sharova, N.2
McDonald, T.L.3
Pushkarskaya, T.4
Tarpley, W.G.5
Stevenson, M.6
-
79
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe, N.M., Laskowski, R.A. and Thornton, J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
80
-
-
48849100166
-
Characterization of nuclear localization signals of the prototype foamy virus integrase
-
An, D.G., Hyun, U. and Shin, C.G. (2008) Characterization of nuclear localization signals of the prototype foamy virus integrase. J. G e n. Virol., 89, 1680-1684.
-
(2008)
J. G e N. Virol.
, vol.89
, pp. 1680-1684
-
-
An, D.G.1
Hyun, U.2
Shin, C.G.3
-
81
-
-
76849100334
-
Role of the 207-218 peptide region of Moloney murine leukemia virus integrase in enzyme catalysis
-
Acevedo, M.L., Arbildua, J.J., Monasterio, O., Toledo, H. and Leon, O. (2010) Role of the 207-218 peptide region of Moloney murine leukemia virus integrase in enzyme catalysis. Arch. Biochem. Biophys., 495, 28-34.
-
(2010)
Arch. Biochem. Biophys.
, vol.495
, pp. 28-34
-
-
Acevedo, M.L.1
Arbildua, J.J.2
Monasterio, O.3
Toledo, H.4
Leon, O.5
-
82
-
-
84910597493
-
HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort
-
Demeulemeester, J., Vets, S., Schrijvers, R., Madlala, P., De Maeyer, M., De Rijck, J., Ndung'u, T., Debyser, Z. and Gijsbers, R. (2014) HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort. Cell Host Microbe, 16, 651-662.
-
(2014)
Cell Host Microbe
, vol.16
, pp. 651-662
-
-
Demeulemeester, J.1
Vets, S.2
Schrijvers, R.3
Madlala, P.4
De Maeyer, M.5
De Rijck, J.6
Ndung'U, T.7
Debyser, Z.8
Gijsbers, R.9
-
83
-
-
0031718377
-
The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA
-
Gao, Y.G., Su, S.Y., Robinson, H., Padmanabhan, S., Lim, L., McCrary, B.S., Edmondson, S.P., Shriver, J.W. and Wang, A.H. (1998) The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nat. Struct. Biol., 5, 782-786.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 782-786
-
-
Gao, Y.G.1
Su, S.Y.2
Robinson, H.3
Padmanabhan, S.4
Lim, L.5
McCrary, B.S.6
Edmondson, S.P.7
Shriver, J.W.8
Wang, A.H.9
-
84
-
-
0037096967
-
DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus
-
Napoli, A., Zivanovic, Y., Bocs, C., Buhler, C., Rossi, M., Forterre, P. and Ciaramella, M. (2002) DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus. Nucleic Acids Res., 30, 2656-2662.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2656-2662
-
-
Napoli, A.1
Zivanovic, Y.2
Bocs, C.3
Buhler, C.4
Rossi, M.5
Forterre, P.6
Ciaramella, M.7
-
85
-
-
0032510217
-
The hyperthermophile chromosomal protein Sac7d sharply kinks DNA
-
Robinson, H., Gao, Y.G., McCrary, B.S., Edmondson, S.P., Shriver, J.W. and Wang, A.H. (1998) The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 202-205.
-
(1998)
Nature
, vol.392
, pp. 202-205
-
-
Robinson, H.1
Gao, Y.G.2
McCrary, B.S.3
Edmondson, S.P.4
Shriver, J.W.5
Wang, A.H.6
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