-
1
-
-
33645984848
-
Consensus folding of unaligned RNA sequences revisited
-
Bafna,V. et al. (2006) Consensus folding of unaligned RNA sequences revisited. J. Comput. Biol., 13, 283-295.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 283-295
-
-
Bafna, V.1
-
2
-
-
9244225713
-
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
-
Batey,R.T. et al. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
-
(2004)
Nature
, vol.432
, pp. 411-415
-
-
Batey, R.T.1
-
3
-
-
19244375613
-
Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation
-
Baumstark,T. et al. (1997) Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO J., 16, 599-610.
-
(1997)
EMBO J
, vol.16
, pp. 599-610
-
-
Baumstark, T.1
-
4
-
-
79955604950
-
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation
-
Blouin,S. et al. (2011) Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res., 39, 3373-3387.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 3373-3387
-
-
Blouin, S.1
-
5
-
-
11144330098
-
Natural and engineered nucleic acids as tools to explore biology
-
Breaker,R.R. (2004) Natural and engineered nucleic acids as tools to explore biology. Nature, 432, 838-845.
-
(2004)
Nature
, vol.432
, pp. 838-845
-
-
Breaker, R.R.1
-
6
-
-
77950494855
-
Computing folding pathways between RNA secondary structures
-
Dotu,I. et al. (2010) Computing folding pathways between RNA secondary structures. Nucleic Acids Res., 38, 1711-1722.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1711-1722
-
-
Dotu, I.1
-
7
-
-
0038476616
-
The riboswitch-mediated control of sulfur metabolism in bacteria
-
Epshtein,V. et al. (2003) The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci. USA, 100, 5052-5056.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5052-5056
-
-
Epshtein, V.1
-
8
-
-
0009955327
-
Reducing the conformation space in RNA structure prediction
-
German Research Center for Biotechnology, Braunschweig, Germany
-
Evers,D. and Giegerich,R. (2001) Reducing the conformation space in RNA structure prediction. In Proceedings of the German Conference on Bioinformatics. German Research Center for Biotechnology, Braunschweig, Germany, pp. 118-124.
-
(2001)
Proceedings of the German Conference on Bioinformatics
, pp. 118-124
-
-
Evers, D.1
Giegerich, R.2
-
9
-
-
0035257394
-
Design of multistable RNA molecules
-
Flamm,C. et al. (2001) Design of multistable RNA molecules. RNA, 7, 254-265.
-
(2001)
RNA
, vol.7
, pp. 254-265
-
-
Flamm, C.1
-
10
-
-
0036340121
-
Barrier trees of degenerate landscapes
-
Flamm,C. et al. (2002) Barrier trees of degenerate landscapes. Z. Phys. Chem., 216, 155-174.
-
(2002)
Z. Phys. Chem.
, vol.216
, pp. 155-174
-
-
Flamm, C.1
-
11
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier,S.M. et al. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA, 83, 9373-9377.
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 9373-9377
-
-
Freier, S.M.1
-
12
-
-
43049086258
-
Folding kinetics of large RNAs
-
Geis,M. et al. (2008) Folding kinetics of large RNAs. J. Mol. Biol., 379, 160-173.
-
(2008)
J. Mol. Biol.
, vol.379
, pp. 160-173
-
-
Geis, M.1
-
13
-
-
4544339512
-
Abstract shapes of RNA
-
Giegerich,R. et al. (2004) Abstract shapes of RNA. Nucleic Acids Res., 32, 4843-4851.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 4843-4851
-
-
Giegerich, R.1
-
14
-
-
0026335264
-
Nearest-neighbor parameters for G.U.
-
He,L. et al. (1991) Nearest-neighbor parameters for G.U mismatches. Biochemistry, 30, 11124-11132.
-
(1991)
Mismatches. Biochemistry
, vol.30
, pp. 11124-11132
-
-
He, L.1
-
15
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker,I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
-
16
-
-
5044242515
-
Alignment of RNA base pairing probability matrices
-
Hofacker,I.L. et al. (2004) Alignment of RNA base pairing probability matrices. Bioinformatics, 20, 2222-2227.
-
(2004)
Bioinformatics
, vol.20
, pp. 2222-2227
-
-
Hofacker, I.L.1
-
17
-
-
0345005029
-
Improved predictions of secondary structures for RNA
-
Jaeger,J.A. et al. (1989) Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA, 86, 7706-7710.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 7706-7710
-
-
Jaeger, J.A.1
-
18
-
-
79851499341
-
Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms
-
Lemay,J.F. et al. (2011) Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet., 7, e1001278.
-
(2011)
PLoS Genet
, vol.7
-
-
Lemay, J.F.1
-
19
-
-
33751162430
-
A method for rapid similarity analysis of RNA secondary structures
-
Liu,N. and Wang,T. (2006) A method for rapid similarity analysis of RNA secondary structures. BMC Bioinformatics, 7, 493.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 493
-
-
Liu, N.1
Wang, T.2
-
20
-
-
79551535532
-
Computing the partition function for kinetically trapped RNA secondary structures
-
Lorenz,W.A. and Clote,P. (2011) Computing the partition function for kinetically trapped RNA secondary structures. PLoS One, 6, e16178.
-
(2011)
PLoS One
, vol.6
-
-
Lorenz, W.A.1
Clote, P.2
-
21
-
-
0842334528
-
Adenine riboswitches and gene activation by disruption of a transcription terminator
-
Mandal,M. and Breaker,R.R. (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol., 11, 29-35.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 29-35
-
-
Mandal, M.1
Breaker, R.R.2
-
22
-
-
0038210214
-
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
-
Mandal,M. et al. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell, 113, 577-586.
-
(2003)
Cell
, vol.113
, pp. 577-586
-
-
Mandal, M.1
-
23
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H. et al. (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
-
24
-
-
18744396047
-
Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria
-
Mironov,A.S. et al. (2002) Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell, 111, 747-756.
-
(2002)
Cell
, vol.111
, pp. 747-756
-
-
Mironov, A.S.1
-
25
-
-
0032502487
-
Barrier heights between ground states in a model of RNA secondary structure
-
Morgan,S. and Higgs,P. (1998) Barrier heights between ground states in a model of RNA secondary structure. J. Phys. A: Math. Gen., 31, 3153-3170.
-
(1998)
J. Phys. A: Math. Gen.
, vol.31
, pp. 3153-3170
-
-
Morgan, S.1
Higgs, P.2
-
26
-
-
0034125274
-
Metrics on RNA secondary structures
-
Moulton,V. et al. (2000) Metrics on RNA secondary structures. J. Comput. Biol., 7, 277-292.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 277-292
-
-
Moulton, V.1
-
27
-
-
0030574258
-
Classification of RNAsecondary structures using the techniques of cluster analysis
-
Nakaya,A. et al. (1996) Classification of RNAsecondary structures using the techniques of cluster analysis. J. Theor. Biol., 183, 105-117.
-
(1996)
J. Theor. Biol.
, vol.183
, pp. 105-117
-
-
Nakaya, A.1
-
28
-
-
13444271576
-
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs
-
Noeske,J. et al. (2005) An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl Acad. Sci. USA, 102, 1372-1377.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 1372-1377
-
-
Noeske, J.1
-
29
-
-
0002213113
-
Algorithms for loop matchings
-
Nussinov,R. et al. (1978) Algorithms for loop matchings. SIAM J. App. Math., 35, 68-82.
-
(1978)
SIAM J. App. Math.
, vol.35
, pp. 68-82
-
-
Nussinov, R.1
-
30
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
Parisien,M. and Major,F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
-
(2008)
Nature
, vol.452
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
31
-
-
0016692310
-
Method for predicting RNA secondary structure
-
Pipas,J.M. and McMahon,J.E. (1975) Method for predicting RNA secondary structure. Proc. Natl Acad. Sci. USA, 72, 2017-2021.
-
(1975)
Proc. Natl Acad. Sci. USA
, vol.72
, pp. 2017-2021
-
-
Pipas, J.M.1
McMahon, J.E.2
-
32
-
-
34547116896
-
Conformational changes in the expression domain of the Escherichia coli thiM riboswitch
-
Rentmeister,A. et al. (2007) Conformational changes in the expression domain of the Escherichia coli thiM riboswitch. Nucleic Acids Res., 35, 3713-3722.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3713-3722
-
-
Rentmeister, A.1
-
33
-
-
0034698298
-
One sequence, two ribozymes: implications for the emergence of new ribozyme folds
-
Schultes,E.A. and Bartel,D.P. (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science, 289, 448-452.
-
(2000)
Science
, vol.289
, pp. 448-452
-
-
Schultes, E.A.1
Bartel, D.P.2
-
34
-
-
0025187499
-
Comparing multiple RNA secondary structures using tree comparisons
-
Shapiro,B.A. and Zhang,K.Z. (1990) Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci., 6, 309-318.
-
(1990)
Comput. Appl. Biosci.
, vol.6
, pp. 309-318
-
-
Shapiro, B.A.1
Zhang, K.Z.2
-
35
-
-
71449108155
-
Structural basis of ligand binding by a c-di-GMP riboswitch
-
Smith,K.D. et al. (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat. Struct. Mol. Biol., 16, 1218-1223.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1218-1223
-
-
Smith, K.D.1
-
36
-
-
32544440797
-
RNAshapes: an integrated RNA analysis package based on abstract shapes
-
Steffen,P. et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
-
(2006)
Bioinformatics
, vol.22
, pp. 500-503
-
-
Steffen, P.1
-
37
-
-
84873050372
-
An algorithm for the energy barrier problem without pseudoknots and temporary arcs
-
Thachuk,C. et al. (2010) An algorithm for the energy barrier problem without pseudoknots and temporary arcs. Pac. Symp. Biocomput., 15, 108-119.
-
(2010)
Pac. Symp. Biocomput.
, vol.15
, pp. 108-119
-
-
Thachuk, C.1
-
39
-
-
3543128223
-
Evaluating the predictability of conformational switching in RNA
-
Voss,B. et al. (2004) Evaluating the predictability of conformational switching in RNA. Bioinformatics, 20, 1573-1582.
-
(2004)
Bioinformatics
, vol.20
, pp. 1573-1582
-
-
Voss, B.1
-
40
-
-
34548454557
-
Structural features of metabolite-sensing riboswitches
-
Wakeman,C.A. et al. (2007) Structural features of metabolite-sensing riboswitches. Trends Biochem. Sci., 32, 415-424.
-
(2007)
Trends Biochem. Sci.
, vol.32
, pp. 415-424
-
-
Wakeman, C.A.1
-
41
-
-
0022380106
-
A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
-
Waterman,M.S. and Byers,T.H. (1985) A dynamic programming algorithm to find all solutions in a neighborhood of the optimum. Math. Biosci., 77, 179-188.
-
(1985)
Math. Biosci.
, vol.77
, pp. 179-188
-
-
Waterman, M.S.1
Byers, T.H.2
-
42
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
Wuchty,S. et al. (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49, 145-165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
-
43
-
-
32644434270
-
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
-
Yakovchuk,P. et al. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res., 34, 564-574.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 564-574
-
-
Yakovchuk, P.1
-
44
-
-
77957316730
-
A complexity-based method to compare RNA secondary structures and its application
-
Zhang,S. and Wang,T. (2010) A complexity-based method to compare RNA secondary structures and its application. J. Biomol. Struct. Dyn., 28, 247-258.
-
(2010)
J. Biomol. Struct. Dyn.
, vol.28
, pp. 247-258
-
-
Zhang, S.1
Wang, T.2
-
45
-
-
0000616205
-
RNA secondary structures and their prediction
-
Zuker,M. (1984) RNA secondary structures and their prediction. Bull. Math. Biol., 46, 591-621.
-
(1984)
Bull. Math. Biol.
, vol.46
, pp. 591-621
-
-
Zuker, M.1
-
46
-
-
0024477261
-
On finding all suboptimal foldings of an RNAmolecule
-
Zuker,M. (1989) On finding all suboptimal foldings of an RNAmolecule. Science, 244, 48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
47
-
-
0025731211
-
A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison
-
Zuker,M. et al. (1991) A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res., 19, 2707-2714.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 2707-2714
-
-
Zuker, M.1
|