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Volumn 27, Issue 21, 2011, Pages 2994-3001

Finding stable local optimal RNA secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 80054890160     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr510     Document Type: Article
Times cited : (17)

References (47)
  • 1
    • 33645984848 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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


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