-
1
-
-
24644443227
-
The functional genomics of noncoding RNA
-
Mattick JS (2005) The functional genomics of noncoding RNA. Science 309: 1527-1528.
-
(2005)
Science
, vol.309
, pp. 1527-1528
-
-
Mattick, J.S.1
-
2
-
-
24644505259
-
Fewer genes, more noncoding RNA
-
Claverie JM (2005) Fewer genes, more noncoding RNA. Science 309: 1529-1530.
-
(2005)
Science
, vol.309
, pp. 1529-1530
-
-
Claverie, J.M.1
-
3
-
-
0034676457
-
Functional genomic analysis of C. elegans chromosome I by systematic RNA interference
-
Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, et al. (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408: 325-330.
-
(2000)
Nature
, vol.408
, pp. 325-330
-
-
Fraser, A.G.1
Kamath, R.S.2
Zipperlen, P.3
Martinez-Campos, M.4
Sohrmann, M.5
-
6
-
-
84865187135
-
Determining {RNA} three-dimensional structures using low-resolution data
-
Parisien M, Major F (2012) Determining {RNA} three-dimensional structures using low-resolution data. J Struct Biol 179: 252-260.
-
(2012)
J Struct Biol
, vol.179
, pp. 252-260
-
-
Parisien, M.1
Major, F.2
-
7
-
-
61949315876
-
Protein structure determination in living cells by in-cell NMR spectroscopy
-
Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, et al. (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458: 102-105.
-
(2009)
Nature
, vol.458
, pp. 102-105
-
-
Sakakibara, D.1
Sasaki, A.2
Ikeya, T.3
Hamatsu, J.4
Hanashima, T.5
-
8
-
-
0033613919
-
A branch and bound algorithm for protein structure re-nement from sparse NMR data sets
-
Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE (1999) A branch and bound algorithm for protein structure re-nement from sparse NMR data sets. J Mol Biol 285: 1691-1710.
-
(1999)
J Mol Biol
, vol.285
, pp. 1691-1710
-
-
Standley, D.M.1
Eyrich, V.A.2
Felts, A.K.3
Friesner, R.A.4
McDermott, A.E.5
-
10
-
-
77953648210
-
On the significance of an RNA tertiary structure prediction
-
Hajdin CE, Ding F, Dokholyan NV,Weeks KM (2010) On the significance of an RNA tertiary structure prediction. RNA 16: 1340-1349.
-
(2010)
RNA
, vol.16
, pp. 1340-1349
-
-
Hajdin, C.E.1
Ding, F.2
Dokholyan, N.V.3
Weeks, K.M.4
-
12
-
-
0025831431
-
Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function
-
Wassarman DA, Steitz JA (1991) Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function. Mol Cell Biol 11: 3432-3445.
-
(1991)
Mol Cell Biol
, vol.11
, pp. 3432-3445
-
-
Wassarman, D.A.1
Steitz, J.A.2
-
13
-
-
70450285249
-
Evolution of 7SK RNA and its protein partners in Metazoa
-
Marz M, Donath A, Verstraete N, Nguyen VT, Stadler PF, et al. (2009) Evolution of 7SK RNA and its protein partners in Metazoa. Mol Biol Evol 26: 2821-2830.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2821-2830
-
-
Marz, M.1
Donath, A.2
Verstraete, N.3
Nguyen, V.T.4
Stadler, P.F.5
-
15
-
-
70349149051
-
New metrics for comparing and assessing discrepancies between RNA 3D structures and models
-
Parisien M, Cruz JA, Westhof E, Major F (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA 15: 1875-1885.
-
(2009)
RNA
, vol.15
, pp. 1875-1885
-
-
Parisien, M.1
Cruz, J.A.2
Westhof, E.3
Major, F.4
-
16
-
-
77955405123
-
Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
-
Jossinet F, Ludwig TE, Westhof E (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics.
-
(2010)
Bioinformatics
-
-
Jossinet, F.1
Ludwig, T.E.2
Westhof, E.3
-
17
-
-
84863522073
-
Towards 3D structure prediction of large RNA molecules: An integer programming framework to insert local 3D motifs in RNA secondary structure
-
Reinharz V, Major F, Waldispühl J (2012) Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 28: i207-i214.
-
(2012)
Bioinformatics
, vol.28
-
-
Reinharz, V.1
Major, F.2
Waldispühl, J.3
-
18
-
-
84856246110
-
Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
-
Kladwang W, Chou FC, Das R (2012) Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. J Am Chem Soc 134: 1404-1407.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 1404-1407
-
-
Kladwang, W.1
Chou, F.C.2
Das, R.3
-
19
-
-
84864953710
-
Automated 3D structure composition for large RNAs
-
Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, et al. (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res.
-
(2012)
Nucleic Acids Res
-
-
Popenda, M.1
Szachniuk, M.2
Antczak, M.3
Purzycka, K.J.4
Lukasiak, P.5
-
20
-
-
58249111738
-
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
-
Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, et al. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15: 189-199.
-
(2009)
RNA
, vol.15
, pp. 189-199
-
-
Jonikas, M.A.1
Radmer, R.J.2
Laederach, A.3
Das, R.4
Pearlman, S.5
-
22
-
-
34249894142
-
Small-angle X-ray scattering from RNA, proteins, and protein complexes
-
Lipfert J, Doniach S (2007) Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu Rev Biophys Biomol Struct 36: 307-327.
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 307-327
-
-
Lipfert, J.1
Doniach, S.2
-
23
-
-
0037039464
-
Exploring the folding landscape of a structured RNA
-
Russell R, Zhuang X, Babcock HP, Millett IS, Doniach S, et al. (2002) Exploring the folding landscape of a structured RNA. Proc Natl Acad Sci U S A 99: 155-160.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 155-160
-
-
Russell, R.1
Zhuang, X.2
Babcock, H.P.3
Millett, I.S.4
Doniach, S.5
-
25
-
-
40149085374
-
Extending the NMR spatial resolution limit for RNA by motional couplings
-
Zhang Q, Al-Hashimi HM (2008) Extending the NMR spatial resolution limit for RNA by motional couplings. Nat Methods 5: 243-245.
-
(2008)
Nat Methods
, vol.5
, pp. 243-245
-
-
Zhang, Q.1
Al-Hashimi, H.M.2
-
27
-
-
32044447209
-
RNA structure and RNA- protein interactions in purified yeast U6 snRNPs
-
Karaduman R, Fabrizio P, Hartmuth K, Urlaub H, Lührmann R (2006) RNA structure and RNA- protein interactions in purified yeast U6 snRNPs. J Mol Biol 356: 1248-1262.
-
(2006)
J Mol Biol
, vol.356
, pp. 1248-1262
-
-
Karaduman, R.1
Fabrizio, P.2
Hartmuth, K.3
Urlaub, H.4
Lührmann, R.5
-
28
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
-
(1999)
J Mol Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
30
-
-
80155177766
-
Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy
-
Bothe JR, Nikolova EN, Eichhorn CD, Chugh J, Hansen AL, et al. (2011) Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy. Nat Methods 8: 919-931.
-
(2011)
Nat Methods
, vol.8
, pp. 919-931
-
-
Bothe, J.R.1
Nikolova, E.N.2
Eichhorn, C.D.3
Chugh, J.4
Hansen, A.L.5
-
32
-
-
0000403125
-
Small-angle scattering. Information content and error analysis
-
Moore PB (1980) Small-angle scattering. information content and error analysis. J Appl Crystallogr 13: 168-175.
-
(1980)
J Appl Crystallogr
, vol.13
, pp. 168-175
-
-
Moore, P.B.1
-
33
-
-
38549083634
-
RNAJunction: A database of RNA junctions and kissing loops for threedimensional structural analysis and nanodesign
-
Bindewald E, Hayes R, Yingling YG, Kasprzak W, Shapiro BA (2008) RNAJunction: a database of RNA junctions and kissing loops for threedimensional structural analysis and nanodesign. Nucleic Acids Res 36: D392-D397.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Bindewald, E.1
Hayes, R.2
Yingling, Y.G.3
Kasprzak, W.4
Shapiro, B.A.5
-
34
-
-
67849122319
-
Web 3DNA - A web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
-
Zheng G, Lu XJ, Olson WK (2009) Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res 37: W240-W246.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Zheng, G.1
Lu, X.J.2
Olson, W.K.3
-
35
-
-
70349783815
-
A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements
-
Wang J, Zuo X, Yu P, Xu H, Starich MR, et al. (2009) A method for helical RNA global structure determination in solution using small-angle X-ray scattering and NMR measurements. J Mol Biol 393: 717-734.
-
(2009)
J Mol Biol
, vol.393
, pp. 717-734
-
-
Wang, J.1
Zuo, X.2
Yu, P.3
Xu, H.4
Starich, M.R.5
-
37
-
-
1442310610
-
Loops In Proteins (LIP) - A comprehensive loop database for homology modelling
-
Michalsky E, Goede A, Preissner R (2003) Loops In Proteins (LIP) - a comprehensive loop database for homology modelling. Protein Eng 16: 979-985.
-
(2003)
Protein Eng
, vol.16
, pp. 979-985
-
-
Michalsky, E.1
Goede, A.2
Preissner, R.3
-
38
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
Hastings W (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.1
-
39
-
-
0029185933
-
CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
-
Svergun D, Barberato C, Koch MHJ (1995) CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28: 768-773.
-
(1995)
J Appl Crystallogr
, vol.28
, pp. 768-773
-
-
Svergun, D.1
Barberato, C.2
Koch, M.H.J.3
-
40
-
-
35548950310
-
Automated de novo prediction of native-like RNA tertiary structures
-
Das R, Baker D (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A 104: 14664-14669.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 14664-14669
-
-
Das, R.1
Baker, D.2
-
41
-
-
76749092270
-
The WEKA data mining software: An update
-
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, et al. (2009) The WEKA data mining software: an update. SIGKDD Explor 11: 10-18.
-
(2009)
SIGKDD Explor
, vol.11
, pp. 10-18
-
-
Hall, M.1
Frank, E.2
Holmes, G.3
Pfahringer, B.4
Reutemann, P.5
-
42
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
43
-
-
0042161808
-
General plasmids for producing RNA in vitro transcripts with homogeneous ends
-
Walker SC, Avis JM, Conn GL (2003) General plasmids for producing RNA in vitro transcripts with homogeneous ends. Nucleic Acids Res 31: e82.
-
(2003)
Nucleic Acids Res
, vol.31
-
-
Walker, S.C.1
Avis, J.M.2
Conn, G.L.3
-
44
-
-
34248347847
-
Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg
-
Roessle MW, Kläring R, Ristau U, Robrahn B, Jahn D, et al. (2007) Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J Appl Crystallogr 40: s190-s194.
-
(2007)
J Appl Crystallogr
, vol.40
-
-
Roessle, M.W.1
Kläring, R.2
Ristau, U.3
Robrahn, B.4
Jahn, D.5
-
46
-
-
33645214738
-
ATSAS 2.1, a program package for small-angle scattering data analysis
-
Konarev PV, Petoukhov MV, Volkov VV, Svergun DI (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr 39: 277-286.
-
(2006)
J Appl Crystallogr
, vol.39
, pp. 277-286
-
-
Konarev, P.V.1
Petoukhov, M.V.2
Volkov, V.V.3
Svergun, D.I.4
-
47
-
-
0026910457
-
Determination of the regularization parameter in indirect-transform methods using perceptual criteria
-
Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25: 495-503.
-
(1992)
J Appl Crystallogr
, vol.25
, pp. 495-503
-
-
Svergun, D.I.1
-
48
-
-
62649139615
-
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering
-
Franke D, Svergun DI (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr 42: 342-346.
-
(2009)
J Appl Crystallogr
, vol.42
, pp. 342-346
-
-
Franke, D.1
Svergun, D.I.2
-
49
-
-
0035124442
-
Automated matching of high- and low-resolution structural models
-
Kozin MB, Svergun DI (2001) Automated matching of high- and low-resolution structural models. J Appl Crystallogr 34: 33-41.
-
(2001)
J Appl Crystallogr
, vol.34
, pp. 33-41
-
-
Kozin, M.B.1
Svergun, D.I.2
-
50
-
-
4544373206
-
Graphviz and Dynagraph - Static and dynamic graph drawing tools
-
Springer-Verlag
-
Ellson J, Gansner ER, Koutsofios E, North SC, Woodhull G (2003) Graphviz and Dynagraph - static and dynamic graph drawing tools. In: Graph Drawing Software. Springer-Verlag, 127-148.
-
(2003)
Graph Drawing Software
, pp. 127-148
-
-
Ellson, J.1
Gansner, E.R.2
Koutsofios, E.3
North, S.C.4
Woodhull, G.5
-
51
-
-
78549276115
-
Preformed protein-binding motifs in 7SK snRNA: Structural and thermodynamic comparisons with retroviral TAR
-
Durney MA, D'Souza VM (2010) Preformed protein-binding motifs in 7SK snRNA: Structural and thermodynamic comparisons with retroviral TAR. J Mol Biol 404: 555-567.
-
(2010)
J Mol Biol
, vol.404
, pp. 555-567
-
-
Durney, M.A.1
D'Souza, V.M.2
|