-
1
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
P.D. Adams, P.V. Afonine, G. Bunkóczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, and R.W. Grosse-Kunstleve PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkóczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
-
2
-
-
84860273177
-
Towards automated crystallographic structure refinement with phenix refine
-
P.V. Afonine, R.W. Grosse-Kunstleve, N. Echols, J.J. Headd, N.W. Moriarty, M. Mustyakimov, T.C. Terwilliger, A. Urzhumtsev, P.H. Zwart, and P.D. Adams Towards automated crystallographic structure refinement with phenix.refine Acta Crystallogr. D Biol. Crystallogr. 68 2012 352 367
-
(2012)
Acta Crystallogr. D Biol. Crystallogr.
, vol.68
, pp. 352-367
-
-
Afonine, P.V.1
Grosse-Kunstleve, R.W.2
Echols, N.3
Headd, J.J.4
Moriarty, N.W.5
Mustyakimov, M.6
Terwilliger, T.C.7
Urzhumtsev, A.8
Zwart, P.H.9
Adams, P.D.10
-
4
-
-
84881664828
-
Structure and function of the T-loop structural motif in noncoding RNAs
-
C.W. Chan, B. Chetnani, and A. Mondragon Structure and function of the T-loop structural motif in noncoding RNAs Wiley Interdiscip. Rev. RNA 4 2013 507 522
-
(2013)
Wiley Interdiscip. Rev. RNA
, vol.4
, pp. 507-522
-
-
Chan, C.W.1
Chetnani, B.2
Mondragon, A.3
-
5
-
-
84871957573
-
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
-
F.C. Chou, P. Sripakdeevong, S.M. Dibrov, T. Hermann, and R. Das Correcting pervasive errors in RNA crystallography through enumerative structure prediction Nat. Methods 10 2013 74 76
-
(2013)
Nat. Methods
, vol.10
, pp. 74-76
-
-
Chou, F.C.1
Sripakdeevong, P.2
Dibrov, S.M.3
Hermann, T.4
Das, R.5
-
7
-
-
80052036187
-
Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr)
-
A.P. Denmon, J. Wang, and E.P. Nikonowicz Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr) J. Mol. Biol. 412 2011 285 303
-
(2011)
J. Mol. Biol.
, vol.412
, pp. 285-303
-
-
Denmon, A.P.1
Wang, J.2
Nikonowicz, E.P.3
-
8
-
-
79956303529
-
Structures of the bacterial ribosome in classical and hybrid states of tRNA binding
-
J.A. Dunkle, L. Wang, M.B. Feldman, A. Pulk, V.B. Chen, G.J. Kapral, J. Noeske, J.S. Richardson, S.C. Blanchard, and J.H. Cate Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Science 332 2011 981 984
-
(2011)
Science
, vol.332
, pp. 981-984
-
-
Dunkle, J.A.1
Wang, L.2
Feldman, M.B.3
Pulk, A.4
Chen, V.B.5
Kapral, G.J.6
Noeske, J.7
Richardson, J.S.8
Blanchard, S.C.9
Cate, J.H.10
-
10
-
-
71549138669
-
The T box mechanism: TRNA as a regulatory molecule
-
N.J. Green, F.J. Grundy, and T.M. Henkin The T box mechanism: tRNA as a regulatory molecule FEBS Lett. 584 2010 318 324
-
(2010)
FEBS Lett.
, vol.584
, pp. 318-324
-
-
Green, N.J.1
Grundy, F.J.2
Henkin, T.M.3
-
11
-
-
84876907659
-
T box RNA decodes both the information content and geometry of tRNA to affect gene expression
-
J.C. Grigg, Y. Chen, F.J. Grundy, T.M. Henkin, L. Pollack, and A. Ke T box RNA decodes both the information content and geometry of tRNA to affect gene expression Proc. Natl. Acad. Sci. USA 110 2013 7240 7245
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 7240-7245
-
-
Grigg, J.C.1
Chen, Y.2
Grundy, F.J.3
Henkin, T.M.4
Pollack, L.5
Ke, A.6
-
12
-
-
0027234192
-
TRNA as a positive regulator of transcription antitermination in B subtilis
-
F.J. Grundy, and T.M. Henkin tRNA as a positive regulator of transcription antitermination in B. subtilis Cell 74 1993 475 482
-
(1993)
Cell
, vol.74
, pp. 475-482
-
-
Grundy, F.J.1
Henkin, T.M.2
-
13
-
-
0030901060
-
Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination
-
F.J. Grundy, S.E. Hodil, S.M. Rollins, and T.M. Henkin Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination J. Bacteriol. 179 1997 2587 2594
-
(1997)
J. Bacteriol.
, vol.179
, pp. 2587-2594
-
-
Grundy, F.J.1
Hodil, S.E.2
Rollins, S.M.3
Henkin, T.M.4
-
14
-
-
0033867256
-
TRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene
-
F.J. Grundy, J.A. Collins, S.M. Rollins, and T.M. Henkin tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene RNA 6 2000 1131 1141
-
(2000)
RNA
, vol.6
, pp. 1131-1141
-
-
Grundy, F.J.1
Collins, J.A.2
Rollins, S.M.3
Henkin, T.M.4
-
15
-
-
0036529579
-
Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: Disparity between conservation and functional requirements
-
F.J. Grundy, T.R. Moir, M.T. Haldeman, and T.M. Henkin Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements Nucleic Acids Res. 30 2002 1646 1655
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1646-1655
-
-
Grundy, F.J.1
Moir, T.R.2
Haldeman, M.T.3
Henkin, T.M.4
-
16
-
-
12344255940
-
Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene
-
F.J. Grundy, M.R. Yousef, and T.M. Henkin Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene J. Mol. Biol. 346 2005 73 81
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 73-81
-
-
Grundy, F.J.1
Yousef, M.R.2
Henkin, T.M.3
-
17
-
-
63849299263
-
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism
-
A. Gutiérrez-Preciado, T.M. Henkin, F.J. Grundy, C. Yanofsky, and E. Merino Biochemical features and functional implications of the RNA-based T-box regulatory mechanism Microbiol. Mol. Biol. Rev. 73 2009 36 61
-
(2009)
Microbiol. Mol. Biol. Rev.
, vol.73
, pp. 36-61
-
-
Gutiérrez-Preciado, A.1
Henkin, T.M.2
Grundy, F.J.3
Yanofsky, C.4
Merino, E.5
-
18
-
-
33747602081
-
RNA structural motifs: Building blocks of a modular biomolecule
-
D.K. Hendrix, S.E. Brenner, and S.R. Holbrook RNA structural motifs: building blocks of a modular biomolecule Q. Rev. Biophys. 38 2005 221 243
-
(2005)
Q. Rev. Biophys.
, vol.38
, pp. 221-243
-
-
Hendrix, D.K.1
Brenner, S.E.2
Holbrook, S.R.3
-
19
-
-
0026504685
-
Analysis of the Bacillus subtilis tyrS gene: Conservation of a regulatory sequence in multiple tRNA synthetase genes
-
T.M. Henkin, B.L. Glass, and F.J. Grundy Analysis of the Bacillus subtilis tyrS gene: conservation of a regulatory sequence in multiple tRNA synthetase genes J. Bacteriol. 174 1992 1299 1306
-
(1992)
J. Bacteriol.
, vol.174
, pp. 1299-1306
-
-
Henkin, T.M.1
Glass, B.L.2
Grundy, F.J.3
-
20
-
-
84861425552
-
Linking crystallographic model and data quality
-
P.A. Karplus, and K. Diederichs Linking crystallographic model and data quality Science 336 2012 1030 1033
-
(2012)
Science
, vol.336
, pp. 1030-1033
-
-
Karplus, P.A.1
Diederichs, K.2
-
21
-
-
4344596976
-
Crystallization of RNA and RNA-protein complexes
-
A. Ke, and J.A. Doudna Crystallization of RNA and RNA-protein complexes Methods 34 2004 408 414
-
(2004)
Methods
, vol.34
, pp. 408-414
-
-
Ke, A.1
Doudna, J.A.2
-
23
-
-
84878614233
-
A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders
-
J. Lehmann, F. Jossinet, and D. Gautheret A universal RNA structural motif docking the elbow of tRNA in the ribosome, RNAse P and T-box leaders Nucleic Acids Res. 41 2013 5494 5502
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 5494-5502
-
-
Lehmann, J.1
Jossinet, F.2
Gautheret, D.3
-
24
-
-
34447508216
-
Phaser crystallographic software
-
A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Cryst. 40 2007 658 674
-
(2007)
J. Appl. Cryst.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
25
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
C.W. Carter, R.M. Sweets, University of Virginia Charlottesville
-
Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode C.W. Carter, R.M. Sweets, Methods in Enzymology 1997 University of Virginia Charlottesville 307 326
-
(1997)
Methods in Enzymology
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
26
-
-
0029079497
-
Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis: Induction, repression and growth-rate regulation
-
H. Putzer, S. Laalami, A.A. Brakhage, C. Condon, and M. Grunberg-Manago Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis: induction, repression and growth-rate regulation Mol. Microbiol. 16 1995 709 718
-
(1995)
Mol. Microbiol.
, vol.16
, pp. 709-718
-
-
Putzer, H.1
Laalami, S.2
Brakhage, A.A.3
Condon, C.4
Grunberg-Manago, M.5
-
27
-
-
78650175123
-
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
-
N.J. Reiter, A. Osterman, A. Torres-Larios, K.K. Swinger, T. Pan, and A. Mondragón Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA Nature 468 2010 784 789
-
(2010)
Nature
, vol.468
, pp. 784-789
-
-
Reiter, N.J.1
Osterman, A.2
Torres-Larios, A.3
Swinger, K.K.4
Pan, T.5
Mondragón, A.6
-
28
-
-
0030795362
-
Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene
-
S.M. Rollins, F.J. Grundy, and T.M. Henkin Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene Mol. Microbiol. 25 1997 411 421
-
(1997)
Mol. Microbiol.
, vol.25
, pp. 411-421
-
-
Rollins, S.M.1
Grundy, F.J.2
Henkin, T.M.3
-
29
-
-
33749354360
-
Structure of the 70S ribosome complexed with mRNA and tRNA
-
M. Selmer, C.M. Dunham, F.V. Murphy 4th, A. Weixlbaumer, S. Petry, A.C. Kelley, J.R. Weir, and V. Ramakrishnan Structure of the 70S ribosome complexed with mRNA and tRNA Science 313 2006 1935 1942
-
(2006)
Science
, vol.313
, pp. 1935-1942
-
-
Selmer, M.1
Dunham, C.M.2
Murphy VI, F.V.3
Weixlbaumer, A.4
Petry, S.5
Kelley, A.C.6
Weir, J.R.7
Ramakrishnan, V.8
-
30
-
-
84872543206
-
A decade of riboswitches
-
A. Serganov, and E. Nudler A decade of riboswitches Cell 152 2013 17 24
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
31
-
-
43249097539
-
Iterative-build OMIT maps: Map improvement by iterative model building and refinement without model bias
-
T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.D. Adams, R.J. Read, P.H. Zwart, and L.W. Hung Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias Acta Crystallogr. D Biol. Crystallogr. 64 2008 515 524
-
(2008)
Acta Crystallogr. D Biol. Crystallogr.
, vol.64
, pp. 515-524
-
-
Terwilliger, T.C.1
Grosse-Kunstleve, R.W.2
Afonine, P.V.3
Moriarty, N.W.4
Adams, P.D.5
Read, R.J.6
Zwart, P.H.7
Hung, L.W.8
-
32
-
-
41649115061
-
Comparative genomic analysis of T-box regulatory systems in bacteria
-
A.G. Vitreschak, A.A. Mironov, V.A. Lyubetsky, and M.S. Gelfand Comparative genomic analysis of T-box regulatory systems in bacteria RNA 14 2008 717 735
-
(2008)
RNA
, vol.14
, pp. 717-735
-
-
Vitreschak, A.G.1
Mironov, A.A.2
Lyubetsky, V.A.3
Gelfand, M.S.4
-
33
-
-
79953233677
-
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA
-
J. Wang, and E.P. Nikonowicz Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA J. Mol. Biol. 408 2011 99 117
-
(2011)
J. Mol. Biol.
, vol.408
, pp. 99-117
-
-
Wang, J.1
Nikonowicz, E.P.2
-
34
-
-
77953716711
-
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA
-
J. Wang, T.M. Henkin, and E.P. Nikonowicz NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA Nucleic Acids Res. 38 2010 3388 3398
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 3388-3398
-
-
Wang, J.1
Henkin, T.M.2
Nikonowicz, E.P.3
-
35
-
-
0034897731
-
The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs
-
W.C. Winkler, F.J. Grundy, B.A. Murphy, and T.M. Henkin The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs RNA 7 2001 1165 1172
-
(2001)
RNA
, vol.7
, pp. 1165-1172
-
-
Winkler, W.C.1
Grundy, F.J.2
Murphy, B.A.3
Henkin, T.M.4
-
36
-
-
18844412633
-
Structural transitions induced by the interaction between tRNA(Gly) and the Bacillus subtilis glyQS T box leader RNA
-
M.R. Yousef, F.J. Grundy, and T.M. Henkin Structural transitions induced by the interaction between tRNA(Gly) and the Bacillus subtilis glyQS T box leader RNA J. Mol. Biol. 349 2005 273 287
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 273-287
-
-
Yousef, M.R.1
Grundy, F.J.2
Henkin, T.M.3
-
37
-
-
84881665997
-
Co-crystal structure of a T-box riboswitch stem i domain in complex with its cognate tRNA
-
J. Zhang, and A.R. Ferré-D'Amaré Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA Nature 500 2013 363 366
-
(2013)
Nature
, vol.500
, pp. 363-366
-
-
Zhang, J.1
Ferré-D'Amaré, A.R.2
|