메뉴 건너뛰기




Volumn 6, Issue 1, 2011, Pages

Computing the partition function for kinetically trapped RNA secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; ENTHALPY; GENE FUNCTION; GENETIC ALGORITHM; GENETIC VARIABILITY; HUMAN; MATHEMATICAL COMPUTING; PROCESS OPTIMIZATION; PROTEIN FOLDING; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; THERMODYNAMICS; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; INTERNET; NUCLEOTIDE SEQUENCE;

EID: 79551535532     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016178     Document Type: Article
Times cited : (33)

References (63)
  • 2
    • 0031576356 scopus 로고    scopus 로고
    • Programmed cell death by hok/sok of plasmid r1: Processing at the hok mRNA 3H-end triggers structural rearrangements that allow translation and antisense RNA binding
    • Franch T, Gultyaev AP, Gerdes K (1997) Programmed cell death by hok/sok of plasmid r1: Processing at the hok mRNA 3H-end triggers structural rearrangements that allow translation and antisense RNA binding. J Mol Biol 273: 38-51.
    • (1997) J Mol Biol , vol.273 , pp. 38-51
    • Franch, T.1    Gultyaev, A.P.2    Gerdes, K.3
  • 3
    • 0027173194 scopus 로고
    • The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms
    • Lecuyer K, Crothers D (1993) The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry 32(20): 5301-5311.
    • (1993) Biochemistry , vol.32 , Issue.20 , pp. 5301-5311
    • Lecuyer, K.1    Crothers, D.2
  • 4
    • 0038475911 scopus 로고    scopus 로고
    • Effect of transcription on folding of the Tetrahymena ribozyme
    • Heilman-Miller SL, Woodson SA (2003) Effect of transcription on folding of the Tetrahymena ribozyme. RNA 9: 722-733.
    • (2003) RNA , vol.9 , pp. 722-733
    • Heilman-Miller, S.L.1    Woodson, S.A.2
  • 5
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single stranded RNA
    • USA
    • Nussinov R, Jacobson AB (1980) Fast algorithm for predicting the secondary structure of single stranded RNA. Proceedings of the National Academy of Sciences, USA 77: 6309-6313.
    • (1980) Proceedings of the National Academy of Sciences , vol.77 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.B.2
  • 6
    • 0013693665 scopus 로고
    • RNA folding prediction: The continued need for interaction between biologists and mathematicians
    • Springer-Verlage
    • Zuker M (1986) RNA folding prediction: The continued need for interaction between biologists and mathematicians. In: Lectures on Mathematics in the Life Sciences. Springer-Verlage, volume 17: 87-124.
    • (1986) Lectures On Mathematics In the Life Sciences , vol.17 , pp. 87-124
    • Zuker, M.1
  • 7
    • 13444292041 scopus 로고    scopus 로고
    • An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model
    • Clote P (2005) An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J Comput Biol 12: 83-101.
    • (2005) J Comput Biol , vol.12 , pp. 83-101
    • Clote, P.1
  • 8
    • 33845372498 scopus 로고    scopus 로고
    • Combinatorics of saturated secondary structures of RNA
    • Clote P (2006) Combinatorics of saturated secondary structures of RNA. J Comput Biol 13: 1640-1657.
    • (2006) J Comput Biol , vol.13 , pp. 1640-1657
    • Clote, P.1
  • 9
  • 10
    • 0000765114 scopus 로고
    • On some new sequences generalizing the Catalan and Motzkin numbers
    • Stein PR, Waterman MS (1978) On some new sequences generalizing the Catalan and Motzkin numbers. Discrete Mathematics 26: 261-272.
    • (1978) Discrete Mathematics , vol.26 , pp. 261-272
    • Stein, P.R.1    Waterman, M.S.2
  • 11
    • 34248222805 scopus 로고    scopus 로고
    • Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model
    • Waldispuhl J, Clote P (2007) Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J Comput Biol 14: 190-215.
    • (2007) J Comput Biol , vol.14 , pp. 190-215
    • Waldispuhl, J.1    Clote, P.2
  • 12
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia T, J SantaLucia J, Burkard M, Kierzek R, Schroeder S, et al. (1999) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-35.
    • (1999) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia, J.J.2    Burkard, M.3    Kierzek, R.4    Schroeder, S.5
  • 14
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure
    • Mathews D, Sabina J, Zuker M, Turner D (1999) Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol 288: 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 15
    • 0037154101 scopus 로고    scopus 로고
    • Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops
    • Mathews DH, Turner DH (2002) Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry 41: 869-880.
    • (2002) Biochemistry , vol.41 , pp. 869-880
    • Mathews, D.H.1    Turner, D.H.2
  • 16
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding at elementary step resolution
    • Flamm C, Fontana W, Hofacker I, Schuster P (2000) RNA folding at elementary step resolution. RNA 6: 325-338.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1    Fontana, W.2    Hofacker, I.3    Schuster, P.4
  • 17
    • 23144463133 scopus 로고    scopus 로고
    • Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
    • Xayaphoummine A, Bucher T, Isambert H (2005) Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res 33: W605-W610.
    • (2005) Nucleic Acids Res , vol.33
    • Xayaphoummine, A.1    Bucher, T.2    Isambert, H.3
  • 20
    • 48449084225 scopus 로고    scopus 로고
    • Simulating RNA folding kinetics on approximated energy landscapes
    • Tang X, Thomas S, Tapia L, Giedroc DP, Amato NM (2008) Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol 381: 1055-1067.
    • (2008) J Mol Biol , vol.381 , pp. 1055-1067
    • Tang, X.1    Thomas, S.2    Tapia, L.3    Giedroc, D.P.4    Amato, N.M.5
  • 21
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie D (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comp Phys 22: 403-434.
    • (1976) J Comp Phys , vol.22 , pp. 403-434
    • Gillespie, D.1
  • 22
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D (1977) Exact stochastic simulation of coupled chemical reactions. J Comp Phys 22: 2340-2361.
    • (1977) J Comp Phys , vol.22 , pp. 2340-2361
    • Gillespie, D.1
  • 23
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty S, Fontana W, Hofacker I, Schuster P (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49: 145-164.
    • (1999) Biopolymers , vol.49 , pp. 145-164
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.3    Schuster, P.4
  • 27
    • 37249078871 scopus 로고    scopus 로고
    • Saddles and barrier in landscapes of generalized search operators
    • of Lecture Notes in Computer Science
    • Flamm C, Hofacker I, Stadler B, Stadler P (2007) Saddles and barrier in landscapes of generalized search operators. In: Foundations of Genetic Algorithms, Springer, volume 4436 of Lecture Notes in Computer Science. Pp 194-212.
    • (2007) Foundations of Genetic Algorithms, Springer , vol.4436 , pp. 194-212
    • Flamm, C.1    Hofacker, I.2    Stadler, B.3    Stadler, P.4
  • 29
    • 0035823067 scopus 로고    scopus 로고
    • RNA folding pathway functional intermediates: Their prediction and analysis
    • Shapiro BA, Bengali D, Kasprzak W, Wu JC (2001) RNA folding pathway functional intermediates: their prediction and analysis. J Mol Biol 312: 27-44.
    • (2001) J Mol Biol , vol.312 , pp. 27-44
    • Shapiro, B.A.1    Bengali, D.2    Kasprzak, W.3    Wu, J.C.4
  • 30
    • 70349290546 scopus 로고    scopus 로고
    • The jerky and knotty dynamics of RNA
    • Isambert H (2009) The jerky and knotty dynamics of RNA. Methods 49: 189-196.
    • (2009) Methods , vol.49 , pp. 189-196
    • Isambert, H.1
  • 31
    • 77950494855 scopus 로고    scopus 로고
    • Computing folding pathways between RNA secondary structures
    • Dotu I, Lorenz WA, VAN Hentenryck P, Clote P (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    Lorenz, W.A.2    Van, H.P.3    Clote, P.4
  • 32
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: Conformational statistics, folding kinetics, and ion electrostatics
    • Chen SJ (2008) RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys 37: 197-214.
    • (2008) Annu Rev Biophys , vol.37 , pp. 197-214
    • Chen, S.J.1
  • 33
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill J (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.1
  • 34
    • 33847262911 scopus 로고    scopus 로고
    • Robust prediction of consensus secondary structures using averaged base pairing probability matrices
    • Kiryu H, Kin T, Asai K (2007) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics 23: 434-441.
    • (2007) Bioinformatics , vol.23 , pp. 434-441
    • Kiryu, H.1    Kin, T.2    Asai, K.3
  • 35
    • 70349131635 scopus 로고    scopus 로고
    • Improved RNA secondary structure prediction by maximizing expected pair accuracy
    • Lu ZJ, Gloor JW, Mathews DH (2009) Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 15: 1805-1813.
    • (2009) RNA , vol.15 , pp. 1805-1813
    • Lu, Z.J.1    Gloor, J.W.2    Mathews, D.H.3
  • 36
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • Ding Y, Lawrence C (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31(24): 7280-7301.
    • (2003) Nucleic Acids Res , vol.31 , Issue.24 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.2
  • 37
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32: 0.
    • (2004) Nucleic Acids Res , vol.32 , pp. 0
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 38
    • 33748675254 scopus 로고    scopus 로고
    • An RNA gene expressed during cortical development evolved rapidly in humans
    • Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, et al. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172.
    • (2006) Nature , vol.443 , pp. 167-172
    • Pollard, K.S.1    Salama, S.R.2    Lambert, N.3    Lambot, M.A.4    Coppens, S.5
  • 39
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • Leontis N, Westhof E (2003) Tools for the automatic identification and classification of RNA base pairs. Nucl Acids Res 31(13): 3450-3460.
    • (2003) Nucl Acids Res , vol.31 , Issue.13 , pp. 3450-3460
    • Leontis, N.1    Westhof, E.2
  • 40
    • 0027434244 scopus 로고
    • Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure
    • Banerjee AR, JAEGER J, Turner D (1993) Thermal unfolding of a group I ribozyme: The low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32: 153-163.
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.2    Turner, D.3
  • 41
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngso RB, Pedersen CN (2000) RNA pseudoknot prediction in energy-based models. J Comput Biol 7: 409-427.
    • (2000) J Comput Biol , vol.7 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.2
  • 43
    • 26644439939 scopus 로고    scopus 로고
    • JViz.Rna-a Java tool for RNA secondary structure visualization
    • Wiese KC, Glen E, Vasudevan A (2005) JViz.Rna-a Java tool for RNA secondary structure visualization. IEEE Trans Nanobioscience 4: 212-218.
    • (2005) IEEE Trans Nanobioscience , vol.4 , pp. 212-218
    • Wiese, K.C.1    Glen, E.2    Vasudevan, A.3
  • 44
    • 58149179987 scopus 로고    scopus 로고
    • Pseudobase ++: An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
    • Taufer M, Licon A, Araiza R, Mireles D, Van Batenburg FH, et al. (2009) Pseudobase ++: An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Res 37: D127-D135.
    • (2009) Nucleic Acids Res , vol.37
    • Taufer, M.1    Licon, A.2    Araiza, R.3    Mireles, D.4    van Batenburg, F.H.5
  • 46
    • 0345005029 scopus 로고
    • Improved predictions of secondary structures for RNA
    • Jaeger JA, Turner DH, Zuker M (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    Turner, D.H.2    Zuker, M.3
  • 47
    • 0026335264 scopus 로고
    • Nearestneighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]
    • He L, Kierzek R, SantaLucia J, Jr., Walter AE, Turner DH (1991) Nearestneighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]. Biochemistry 30: 11124-11132.
    • (1991) Biochemistry , vol.30 , pp. 11124-11132
    • He, L.1    Kierzek, R.2    Santalucia Jr., J.3    Walter, A.E.4    Turner, D.H.5
  • 48
    • 0025900996 scopus 로고
    • Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
    • Peritz AE, Kierzek R, Sugimoto N, Turner DH (1991) Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. Biochemistry 30: 6428-6436.
    • (1991) Biochemistry , vol.30 , pp. 6428-6436
    • Peritz, A.E.1    Kierzek, R.2    Sugimoto, N.3    Turner, D.H.4
  • 49
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, et al. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 91: 9218-9222.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 9218-9222
    • Walter, A.E.1    Turner, D.H.2    Kim, J.3    Lyttle, M.H.4    Muller, P.5
  • 50
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25: 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 51
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Matthews D, Sabina J, Zuker M, Turner D (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
    • Matthews, D.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 52
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 55
    • 34248222805 scopus 로고    scopus 로고
    • Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model
    • Waldispuhl J, Clote P (2007) Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model. J Comput Biol 14: 190-215.
    • (2007) J Comput Biol , vol.14 , pp. 190-215
    • Waldispuhl, J.1    Clote, P.2
  • 56
    • 23144450198 scopus 로고    scopus 로고
    • RNALOSS: A web server for RNA locally optimal secondary structures
    • Clote P (2005) RNALOSS: a web server for RNA locally optimal secondary structures. Nucleic Acids Res 33: W600-W604.
    • (2005) Nucleic Acids Res , vol.33
    • Clote, P.1
  • 57
    • 0032502487 scopus 로고    scopus 로고
    • Barrier heights between ground states in a model of RNA secondary structure
    • Morgan S, 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
  • 58
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker I (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.1
  • 59
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen B, Hein J (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 31: 3423-3428.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 60
    • 14644430471 scopus 로고    scopus 로고
    • Probcons: Probabilistic consistency-based multiple sequence alignment
    • Do CB, Mahabhashyam MS, Brudno M, Batzoglou S (2005) Probcons: Probabilistic consistency-based multiple sequence alignment. Genome Res 15: 330-340.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 61
    • 23644448438 scopus 로고    scopus 로고
    • RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
    • Ding Y, Chan CY, Lawrence CE (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11: 1157-1166.
    • (2005) RNA , vol.11 , pp. 1157-1166
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 62
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews D, Disney M, Childs J, Schroeder S, Zuker M, et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101: 7287-7292.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7287-7292
    • Mathews, D.1    Disney, M.2    Childs, J.3    Schroeder, S.4    Zuker, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.