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Volumn 28, Issue 12, 2012, Pages

Towards 3D structure prediction of large RNA molecules: An integer programming framework to insert local 3D motifs in RNA secondary structure

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84863522073     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts226     Document Type: Article
Times cited : (40)

References (29)
  • 1
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman, H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 2
    • 38549083634 scopus 로고    scopus 로고
    • RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
    • Bindewald, E. et al. (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res., 36, D392-D397.
    • (2008) Nucleic Acids Res , vol.36
    • Bindewald, E.1
  • 3
    • 79957851139 scopus 로고    scopus 로고
    • Sequence-based identification of 3D structural modules in RNA with RMDetect
    • Cruz, J.A. andWesthof, E. (2011) Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat. Meth., 8, 513-521.
    • (2011) Nat. Meth. , vol.8 , pp. 513-521
    • Cruz, J.A.1    Westhof, E.2
  • 4
    • 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
  • 5
    • 57049101474 scopus 로고    scopus 로고
    • Automated motif extraction and classification in RNA tertiary structures
    • Djelloul, M. and Denise, A. (2008) Automated motif extraction and classification in RNA tertiary structures. RNA, 14, 2489-2497.
    • (2008) RNA , vol.14 , pp. 2489-2497
    • Djelloul, M.1    Denise, A.2
  • 6
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA secondary structure prediction without physics-based models
    • Do, C.B. et al. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98.
    • (2006) Bioinformatics , vol.22
    • Do, C.B.1
  • 7
    • 67650930900 scopus 로고    scopus 로고
    • A probabilistic model of RNA conformational space
    • Frellsen, J. et al. (2009) A probabilistic model of RNA conformational space. PLoS Comput. Biol., 5, e1000406.
    • (2009) PLoS Comput. Biol. , vol.5
    • Frellsen, J.1
  • 8
    • 0035906639 scopus 로고    scopus 로고
    • Quantitative analysis of nucleic acid three-dimensional structures
    • Gendron, P. et al. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
    • (2001) J. Mol. Biol. , vol.308 , pp. 919-936
    • Gendron, P.1
  • 9
    • 67449156149 scopus 로고    scopus 로고
    • RNAsecondary structure analysis using the Vienna RNApackage
    • Chapter 12, Unit12.2
    • Hofacker, I.L. (2009) RNAsecondary structure analysis using the Vienna RNApackage. Curr. Protoc. Bioinform., Chapter 12, Unit12.2.
    • (2009) Curr. Protoc. Bioinform
    • Hofacker, I.L.1
  • 10
    • 84863502847 scopus 로고    scopus 로고
    • Houston, Texas: Gurobi Optimization, I. Gurobi optimizer version 4.5.1
    • Houston, Texas: Gurobi Optimization, I. (2011) Gurobi optimizer version 4.5.1.
    • (2011)
  • 11
    • 75849116392 scopus 로고    scopus 로고
    • Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
    • Jonikas, M.A. et al. (2009) Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics, 25, 3259-3266.
    • (2009) Bioinformatics , vol.25 , pp. 3259-3266
    • Jonikas, M.A.1
  • 12
    • 77955405123 scopus 로고    scopus 로고
    • Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
    • Jossinet, F. et al. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics, 26, 2057-2059.
    • (2010) Bioinformatics , vol.26 , pp. 2057-2059
    • Jossinet, F.1
  • 13
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • Laing, C. and Schlick, T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens. Matter, 22, 283101.
    • (2010) J. Phys. Condens. Matter , vol.22 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 14
    • 84856770808 scopus 로고    scopus 로고
    • Automated prediction of three-way junction topological families in RNA secondary structures
    • Lamiable, A. et al. (2012) Automated prediction of three-way junction topological families in RNA secondary structures. Comput. Biol. and Chem., 37, 1-5.
    • (2012) Comput. Biol. and Chem. , vol.37 , pp. 1-5
    • Lamiable, A.1
  • 15
    • 0036798116 scopus 로고    scopus 로고
    • RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire
    • Lemieux, S. and Major, F. (2002) RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res., 30, 4250-4263.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4250-4263
    • Lemieux, S.1    Major, F.2
  • 16
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: software for nucleic acid folding and hybridization
    • Markham, N.R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
    • (2008) Methods Mol. Biol. , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 17
    • 43749124906 scopus 로고    scopus 로고
    • RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA
    • Martinez, H.M. et al. (2008) RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J. Biomol. Struct. Dyn., 25, 669-683.
    • (2008) J. Biomol. Struct. Dyn. , vol.25 , pp. 669-683
    • Martinez, H.M.1
  • 18
    • 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
  • 19
    • 60849102148 scopus 로고    scopus 로고
    • Prediction of RNAsecondary structure with pseudoknots using integer programming
    • Poolsap, U. et al. (2009) Prediction of RNAsecondary structure with pseudoknots using integer programming. BMC Bioinformatics, 10(Suppl. 1), S38.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 1
    • Poolsap, U.1
  • 20
    • 77949447172 scopus 로고    scopus 로고
    • RNAstructure: software for RNA secondary structure prediction and analysis
    • Reuter, J.S. and Mathews, D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, 129.
    • (2010) BMC Bioinformatics , vol.11 , pp. 129
    • Reuter, J.S.1    Mathews, D.H.2
  • 21
    • 36448954303 scopus 로고    scopus 로고
    • FR3D: finding local and composite recurrent structural motifs in RNA 3D structures
    • Sarver, M. et al. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol., 56, 215-252.
    • (2008) J. Math. Biol. , vol.56 , pp. 215-252
    • Sarver, M.1
  • 22
    • 79959465715 scopus 로고    scopus 로고
    • IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
    • Sato, K. et al. (2011) IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics, 27, i85-i93.
    • (2011) Bioinformatics , vol.27
    • Sato, K.1
  • 23
    • 50549096615 scopus 로고    scopus 로고
    • iFoldRNA: three-dimensional RNA structure prediction and folding
    • Sharma, S. et al. (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
    • (2008) Bioinformatics , vol.24 , pp. 1951-1952
    • Sharma, S.1
  • 25
    • 65549163541 scopus 로고    scopus 로고
    • Frequency and isostericity of RNAbase pairs
    • Stombaugh, J. et al. (2009) Frequency and isostericity of RNAbase pairs. Nucleic Acids Res., 37, 2294-2312.
    • (2009) Nucleic Acids Res , vol.37 , pp. 2294-2312
    • Stombaugh, J.1
  • 26
    • 79959481959 scopus 로고    scopus 로고
    • A conditional random fields method for RNA sequencestructure relationship modeling and conformation sampling
    • Wang, Z. and Xu, J. (2011) A conditional random fields method for RNA sequencestructure relationship modeling and conformation sampling. Bioinformatics, 27, i102-i110.
    • (2011) Bioinformatics , vol.27
    • Wang, Z.1    Xu, J.2
  • 27
    • 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
  • 28
    • 79953222574 scopus 로고    scopus 로고
    • Rich parameterization improves rna structure prediction
    • Zakov, S. et al. (2011) Rich parameterization improves rna structure prediction. In RECOMB, pp. 546-562.
    • (2011) RECOMB , pp. 546-562
    • Zakov, S.1
  • 29
    • 79959437118 scopus 로고    scopus 로고
    • A folding algorithm for extended RNA secondary structures
    • Zu Siederdissen, C.H. et al. (2011) A folding algorithm for extended RNA secondary structures. Bioinformatics, 27, i129-i136.
    • (2011) Bioinformatics , vol.27
    • Zu Siederdissen, C.H.1


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