메뉴 건너뛰기




Volumn 30, Issue 14, 2014, Pages 2009-2017

Basin hopping graph: A computational framework to characterize RNA folding landscapes

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84904010364     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu156     Document Type: Article
Times cited : (36)

References (48)
  • 1
    • 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
  • 2
    • 0027050568 scopus 로고
    • In vitro recombination and terminal elongation of RNA by Qβ replicase
    • Biebricher, C.K. and Luce, R. (1992) In vitro recombination and terminal elongation of RNA by Qβ replicase. EMBO J., 38, 5129-5135.
    • (1992) EMBO J. , vol.38 , pp. 5129-5135
    • Biebricher, C.K.1    Luce, R.2
  • 3
    • 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., 1, 83-101.
    • (2005) J. Comput. Biol. , vol.1 , pp. 83-101
    • Clote, P.1
  • 4
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K. et al. (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
  • 5
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary structures
    • Das, R. and Baker, D. (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl Acad. Sci. USA, 104, 14664-14669.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 14664-14669
    • Das, R.1    Baker, D.2
  • 6
    • 0346888665 scopus 로고    scopus 로고
    • A statistical sampling algorithm for RNA secondary structure prediction
    • Ding, Y. and Lawrence, C. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7280-7301
    • Ding, Y.1    Lawrence, C.2
  • 7
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding, Y. et al. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32, W135-W141.
    • (2004) Nucleic Acids Res. , vol.32
    • Ding, Y.1
  • 8
    • 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
  • 9
    • 0000672765 scopus 로고    scopus 로고
    • Evolution of the potential energy surface with size for lennard-jones clusters
    • Doye, J.P. et al. (1999) Evolution of the potential energy surface with size for Lennard-Jones clusters. J. Chem. Phys., 111, 8417-8429.
    • (1999) J. Chem. Phys. , vol.111 , pp. 8417-8429
    • Doye, J.P.1
  • 10
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding kinetics at elementary step resolution
    • Flamm, C. et al. (2000) RNA folding kinetics at elementary step resolution. RNA, 6, 325-338.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1
  • 11
    • 0036340121 scopus 로고    scopus 로고
    • Barrier trees of degenerate landscapes
    • Flamm, C. et al. (2002) Barrier trees of degenerate landscapes. Z. Phys. Chem., 216, 155-173.
    • (2002) Z. Phys. Chem. , vol.216 , pp. 155-173
    • Flamm, C.1
  • 12
    • 84891741034 scopus 로고    scopus 로고
    • Combinatorics of locally optimal RNA secondary structures
    • Fusy, É. and Clote, P. (2012) Combinatorics of locally optimal RNA secondary structures. J. Math. Biology 68, 341-375.
    • (2012) J. Math. Biology , vol.68 , pp. 341-375
    • Fusy, É.1    Clote, P.2
  • 13
    • 10844231176 scopus 로고    scopus 로고
    • Efficiency of local search with multiple local optima
    • Garnier, J. and Kallel, L. (2000) Efficiency of local search with multiple local optima. SIAM J. Discrete Math., 15, 122-141.
    • (2000) SIAM J. Discrete Math. , vol.15 , pp. 122-141
    • Garnier, J.1    Kallel, L.2
  • 14
    • 0033200608 scopus 로고    scopus 로고
    • Energy landscapes, supergraphs, and "folding funnels" in spin systems
    • Garstecki, P. et al. (1999) Energy landscapes, supergraphs, and "folding funnels" in spin systems. Phys. Rev. E, 60, 3219-3226.
    • (1999) Phys. Rev. E , vol.60 , pp. 3219-3226
    • Garstecki, P.1
  • 15
    • 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
  • 16
    • 0000287314 scopus 로고    scopus 로고
    • Combinatorics of RNA secondary structures
    • Hofacker, I. et al. (1996) Combinatorics of RNA secondary structures. Discrete Appl. Math, 88, 207-237.
    • (1996) Discrete Appl. Math , vol.88 , pp. 207-237
    • Hofacker, I.1
  • 17
    • 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
  • 18
    • 0034612331 scopus 로고    scopus 로고
    • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
    • Isambert, H. and Siggia, E.D. (2000) Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6515-6520
    • Isambert, H.1    Siggia, E.D.2
  • 21
    • 0002631097 scopus 로고
    • Valley structures in the phase space of a finite 3D Ising spin glass with ±i interactions
    • Klotz, T. and Kobe, S. (1994) "Valley Structures" in the phase space of a finite 3D Ising spin glass with ±i interactions. J. Phys. A Math. Gen., 27, L95-L100.
    • (1994) J. Phys. A Math. Gen. , vol.27
    • Klotz, T.1    Kobe, S.2
  • 22
    • 79954633094 scopus 로고    scopus 로고
    • 2D projections of RNA folding landscapes
    • Grosse, I., et al. (eds)
    • Lorenz, R. et al. (2009) 2D projections of RNA folding landscapes. In: Grosse, I., et al. (eds) GCB.LNI. Vol. 157, pp. 11-20.
    • (2009) GCB.LNI , vol.157 , pp. 11-20
    • Lorenz, R.1
  • 23
    • 82055164092 scopus 로고    scopus 로고
    • ViennaRNA package 2.0
    • Lorenz, R. et al. (2011) ViennaRNA Package 2.0. Alg. Mol. Biol., 6, 26.
    • (2011) Alg. Mol. Biol. , vol.6 , pp. 26
    • Lorenz, R.1
  • 24
    • 79551535532 scopus 로고    scopus 로고
    • Computing the partition function for kinetically trapped RNA secondary structures
    • Lorenz, W. 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.1    Clote, P.2
  • 25
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. 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.1
  • 26
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D.H. 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.H.1
  • 27
    • 79952758719 scopus 로고    scopus 로고
    • NP-completeness of the energy barrier problem without pseudoknots and temporary arcs
    • Maňuch, J. et al. (2011) NP-completeness of the energy barrier problem without pseudoknots and temporary arcs. Nat. Comput., 10, 391-405.
    • (2011) Nat. Comput. , vol.10 , pp. 391-405
    • Maňuch, J.1
  • 28
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill, J.S. (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
  • 29
    • 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
  • 31
    • 0032486091 scopus 로고    scopus 로고
    • A toggle duplex in hepatitis delta virus selfcleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation
    • Perrotta, A.T. and Been, M.D. (1998) A toggle duplex in hepatitis delta virus selfcleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation. J. Mol. Biol., 279, 361-373.
    • (1998) J. Mol. Biol. , vol.279 , pp. 361-373
    • Perrotta, A.T.1    Been, M.D.2
  • 32
    • 36448947995 scopus 로고    scopus 로고
    • Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method
    • Ponty, Y. (2008) Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method. J. Math. Biol., 56, 107-127.
    • (2008) J. Math. Biol. , vol.56 , pp. 107-127
    • Ponty, Y.1
  • 33
    • 0036494672 scopus 로고    scopus 로고
    • Combinatorial landscapes
    • Reidys, C.M. and Stadler, P.F. (2002) Combinatorial landscapes. SIAM Rev., 44, 3-54.
    • (2002) SIAM Rev. , vol.44 , pp. 3-54
    • Reidys, C.M.1    Stadler, P.F.2
  • 34
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas, E. and Eddy, S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
    • (1999) J. Mol. Biol. , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 35
    • 80255140476 scopus 로고    scopus 로고
    • RNA and protein 3D structure modeling: Similarities and differences
    • Rother, K. et al. (2011) RNA and protein 3D structure modeling: similarities and differences. J. Mol. Model., 17, 2325-2336.
    • (2011) J. Mol. Model. , vol.17 , pp. 2325-2336
    • Rother, K.1
  • 36
    • 84857182503 scopus 로고    scopus 로고
    • Approximating the set of local minima in partial RNA folding landscapes
    • Sahoo, S. and Albrecht, A.A. (2012) Approximating the set of local minima in partial RNA folding landscapes. Bioinformatics, 28, 523-530.
    • (2012) Bioinformatics , vol.28 , pp. 523-530
    • Sahoo, S.1    Albrecht, A.A.2
  • 37
    • 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
  • 38
    • 0032739568 scopus 로고    scopus 로고
    • The lid method for exhaustive exploration of metastable states of complex systems
    • Sibani, P. et al. (1999) The lid method for exhaustive exploration of metastable states of complex systems. Comput. Phys. Commun., 116, 17-27.
    • (1999) Comput. Phys. Commun. , vol.116 , pp. 17-27
    • Sibani, P.1
  • 39
    • 63249135361 scopus 로고    scopus 로고
    • RNA structure prediction from evolutionary patterns of nucleotide composition
    • Smit, S. et al. (2009) RNA structure prediction from evolutionary patterns of nucleotide composition. Nucleic Acids Res., 37, 1378-1386.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1378-1386
    • Smit, S.1
  • 40
    • 34250880169 scopus 로고    scopus 로고
    • Evolutionary rates vary among rRNA structural elements
    • Smit, S. et al. (2007) Evolutionary rates vary among rRNA structural elements. Nucleic Acids Res., 35, 3339-3354.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3339-3354
    • Smit, S.1
  • 41
    • 48449084225 scopus 로고    scopus 로고
    • Simulating RNA folding kinetics on approximated energy landscapes
    • Tang, X. et al. (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
  • 42
    • 0034743153 scopus 로고    scopus 로고
    • Early events in RNA folding
    • Thirumalai, D. et al. (2001) Early events in RNA folding. Annu. Rev. Phys. Chem., 52, 751-762.
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 751-762
    • Thirumalai, D.1
  • 43
    • 84861946897 scopus 로고    scopus 로고
    • Decoding the energy landscape: Extracting structure, dynamics and thermodynamics
    • Wales, D.J. (2011) Decoding the energy landscape: extracting structure, dynamics and thermodynamics. Phil. Trans. R. Soc. A, 370, 2877-2899.
    • (2011) Phil. Trans. R. Soc. A , vol.370 , pp. 2877-2899
    • Wales, D.J.1
  • 44
    • 2442687677 scopus 로고    scopus 로고
    • Exact folding dynamics of RNA secondary structures
    • Wolfinger, M.T. et al. (2004) Exact folding dynamics of RNA secondary structures. J. Phys. A Math. Gen., 37, 4731-4741.
    • (2004) J. Phys. A Math. Gen. , vol.37 , pp. 4731-4741
    • Wolfinger, M.T.1
  • 45
    • 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
  • 46
    • 33846929128 scopus 로고    scopus 로고
    • Encoding folding paths of RNA switches
    • Xayaphoummine, A. et al. (2007) Encoding folding paths of RNA switches. Nucleic Acids Res., 35, 614-622.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 614-622
    • Xayaphoummine, A.1
  • 47
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 48
    • 0000616205 scopus 로고
    • RNA secondary structures and their prediction
    • Zuker, M. and Sankoff, D. (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    Sankoff, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.