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Volumn 7, Issue 7, 2012, Pages

Conformational features of topologically classified RNA secondary structures

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84863616389     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039907     Document Type: Article
Times cited : (9)

References (37)
  • 1
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNAs
    • Storz G, (2002) An expanding universe of noncoding RNAs. Science 296: 1260-1263.
    • (2002) Science , vol.296 , pp. 1260-1263
    • Storz, G.1
  • 3
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: non-coding regulatory RNAs in bacteria
    • Gottesman S, (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends in Genetics 21: 399-404.
    • (2005) Trends in Genetics , vol.21 , pp. 399-404
    • Gottesman, S.1
  • 4
    • 0038187589 scopus 로고    scopus 로고
    • Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm
    • Repoila F, Majdalani N, Gottesman S, (2003) Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Molecular Microbiology 48: 855-861.
    • (2003) Molecular Microbiology , vol.48 , pp. 855-861
    • Repoila, F.1    Majdalani, N.2    Gottesman, S.3
  • 5
    • 0031588021 scopus 로고    scopus 로고
    • In vivo determination of RNA structure-function relationships: Analysis of the 790 loop in ribosomal RNA
    • Lee KS, Varma S, SantaLucia J, Cunningham PR, (1997) In vivo determination of RNA structure-function relationships: Analysis of the 790 loop in ribosomal RNA. Journal of molecular biology 269: 732-743.
    • (1997) Journal of Molecular Biology , vol.269 , pp. 732-743
    • Lee, K.S.1    Varma, S.2    SantaLucia, J.3    Cunningham, P.R.4
  • 8
    • 0019876473 scopus 로고
    • Optimal Computer Folding of Large Rna Sequences Using Thermodynamics and Auxiliary Information
    • Zuker M, Stiegler P, (1981) Optimal Computer Folding of Large Rna Sequences Using Thermodynamics and Auxiliary Information. Nucleic acids research 9: 133-148.
    • (1981) Nucleic Acids Research , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 9
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas E, Eddy SR, (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. Journal of molecular biology 285: 2053-2068.
    • (1999) Journal of Molecular Biology , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 10
    • 13244252326 scopus 로고    scopus 로고
    • Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
    • Reeder J, Giegerich R, (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC bioinformatics 5: 104.
    • (2004) BMC Bioinformatics , vol.5 , pp. 104
    • Reeder, J.1    Giegerich, R.2
  • 11
    • 78049458920 scopus 로고    scopus 로고
    • Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
    • Theis C, Janssen S, Giegerich R, (2010) Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. Algorithms in Bioinformatics 6293: 52-64.
    • (2010) Algorithms in Bioinformatics , vol.6293 , pp. 52-64
    • Theis, C.1    Janssen, S.2    Giegerich, R.3
  • 12
    • 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
  • 13
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • Dirks RM, Pierce NA, (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of computational chemistry 24: 1664-1677.
    • (2003) Journal of Computational Chemistry , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 14
    • 3042554001 scopus 로고    scopus 로고
    • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
    • Dirks RM, Pierce NA, (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of computational chemistry 25: 1295-1304.
    • (2004) Journal of Computational Chemistry , vol.25 , pp. 1295-1304
    • Dirks, R.M.1    Pierce, N.A.2
  • 16
    • 0041940818 scopus 로고    scopus 로고
    • Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
    • Akutsu T, (2000) Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Applied Mathematics 104: 45-62.
    • (2000) Discrete Applied Mathematics , vol.104 , pp. 45-62
    • Akutsu, T.1
  • 23
    • 52049083257 scopus 로고    scopus 로고
    • RNA STRAND: the RNA secondary structure and statistical analysis database
    • Andronescu M, Bereg V, Hoos HH, Condon A, (2008) RNA STRAND: the RNA secondary structure and statistical analysis database. BMC bioinformatics 9: 340.
    • (2008) BMC Bioinformatics , vol.9 , pp. 340
    • Andronescu, M.1    Bereg, V.2    Hoos, H.H.3    Condon, A.4
  • 28
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, et al. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic acids research 31: 3450-3460.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3450-3460
    • Yang, H.1    Jossinet, F.2    Leontis, N.3    Chen, L.4    Westbrook, J.5
  • 30
    • 48249125095 scopus 로고    scopus 로고
    • Structural principles from large RNAs
    • Holbrook SR, (2008) Structural principles from large RNAs. Annual review of biophysics 37: 445-464.
    • (2008) Annual Review of Biophysics , vol.37 , pp. 445-464
    • Holbrook, S.R.1
  • 31
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA, (2000) The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science 289: 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 32
  • 33
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare AR, Zhou K, Doudna JA, (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 34
    • 0033053643 scopus 로고    scopus 로고
    • A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes
    • Wadkins TS, Perrotta AT, Ferre-D'Amare AR, Doudna JA, Been MD, (1999) A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. Rna-a Publication of the Rna Society 5: 720-727.
    • (1999) Rna-a Publication of the Rna Society , vol.5 , pp. 720-727
    • Wadkins, T.S.1    Perrotta, A.T.2    Ferre-D'Amare, A.R.3    Doudna, J.A.4    Been, M.D.5
  • 35
    • 33744547883 scopus 로고    scopus 로고
    • Predicting RNA pseudoknot folding thermodynamics
    • Cao S, Chen SJ, (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic acids research 34: 2634-2652.
    • (2006) Nucleic Acids Research , vol.34 , pp. 2634-2652
    • Cao, S.1    Chen, S.J.2
  • 36
  • 37
    • 79956348656 scopus 로고    scopus 로고
    • Modeling Conserved Structure Patterns for Functional Noncoding RNA
    • Chen QF, Chen YPP, (2011) Modeling Conserved Structure Patterns for Functional Noncoding RNA. IEEE Transactions on Biomedical Engineering, 58(6): 1528-1533, 2011.
    • (2011) IEEE Transactions on Biomedical Engineering , vol.58 , Issue.6 , pp. 1528-1533
    • Chen, Q.F.1    Chen, Y.P.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.