메뉴 건너뛰기




Volumn 41, Issue 12, 2013, Pages 5978-5990

RNAlyzer - Novel approach for quality analysis of RNA structural models

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; STRUCTURE ANALYSIS;

EID: 84880248292     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt318     Document Type: Article
Times cited : (23)

References (30)
  • 1
    • 0003604405 scopus 로고    scopus 로고
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, NY
    • Gesteland, R.F., Cech, T.R. and Atkins, J.F. (2006) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, NY.
    • (2006) The RNA World
    • Gesteland, R.F.1    Cech, T.R.2    Atkins, J.F.3
  • 3
    • 70349149051 scopus 로고    scopus 로고
    • New metrics for comparing and assessing discrepancies between RNA 3D structures and models
    • Parisien, M., Cruz, J.A., Westhof, E. and Major, F. (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA, 15, 1875-1885.
    • (2009) RNA , vol.15 , pp. 1875-1885
    • Parisien, M.1    Cruz, J.A.2    Westhof, E.3    Major, F.4
  • 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
    • 44149101971 scopus 로고    scopus 로고
    • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
    • Ding, F., Sharma, S., Chalasani, P., Demidov, V.V., Broude, N.E. and Dokholyan, N.V. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
    • (2008) RNA , vol.14 , pp. 1164-1173
    • Ding, F.1    Sharma, S.2    Chalasani, P.3    Demidov, V.V.4    Broude, N.E.5    Dokholyan, N.V.6
  • 6
    • 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
  • 7
    • 58249111738 scopus 로고    scopus 로고
    • Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    • Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D. and Altman, R.B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
    • (2009) RNA , vol.15 , pp. 189-199
    • Jonikas, M.A.1    Radmer, R.J.2    Laederach, A.3    Das, R.4    Pearlman, S.5    Herschlag, D.6    Altman, R.B.7
  • 8
    • 0025678737 scopus 로고
    • Modeling of the three-dimensional architecture of group i catalytic introns based on comparative sequence analysis
    • Michel, F. and Westhof, E. (1990) Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
    • (1990) J. Mol. Biol. , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 9
    • 0032232529 scopus 로고    scopus 로고
    • MANIP: An interactive tool for modeling RNA
    • 255-257
    • Massire, C. and Westhof, E. (1998) MANIP: An interactive tool for modeling RNA. J. Mol. Graph. Model., 16, 197-205, 255-257.
    • (1998) J. Mol. Graph. Model. , vol.16 , pp. 197-205
    • Massire, C.1    Westhof, E.2
  • 10
    • 43749124906 scopus 로고    scopus 로고
    • RNA2D3D: A program for generating, viewing, and comparing three-dimensional models of RNA
    • Martinez, H.M., Maizel, J.V. Jr and Shapiro, B.A. (2008) RNA2D3D: A program for generating, viewing, and comparing three-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    Maizel, Jr.J.V.2    Shapiro, B.A.3
  • 11
    • 77955405123 scopus 로고    scopus 로고
    • Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
    • Jossinet, F., Ludwig, T.E. and Westhof, E. (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    Ludwig, T.E.2    Westhof, E.3
  • 12
    • 84873037275 scopus 로고    scopus 로고
    • Predicting RNA structure by multiple template homology modeling
    • Flores, S.C., Wan, Y., Russell, R. and Altman, R.B. (2010) Predicting RNA structure by multiple template homology modeling. Pac. Symp. Biocomput., 15, 216-227.
    • (2010) Pac. Symp. Biocomput. , vol.15 , pp. 216-227
    • Flores, S.C.1    Wan, Y.2    Russell, R.3    Altman, R.B.4
  • 13
    • 79959292152 scopus 로고    scopus 로고
    • ModeRNA: A tool for comparative modeling of RNA 3D structure
    • Rother, M., Rother, K., Puton, T. and Bujnicki, J.M. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4007-4022
    • Rother, M.1    Rother, K.2    Puton, T.3    Bujnicki, J.M.4
  • 14
    • 0036798116 scopus 로고    scopus 로고
    • RNA canonical and noncanonical base pairing types: A recognition method and complete repertoire
    • Lemieux, S. and Major, F. (2002) RNA canonical and noncanonical 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
    • 33646845815 scopus 로고    scopus 로고
    • Automated extraction and classification of RNA tertiary structure cyclic motifs
    • Lemieux, S. and Major, F. (2006) Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res., 34, 2340-2346.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2340-2346
    • Lemieux, S.1    Major, F.2
  • 17
    • 34548342932 scopus 로고    scopus 로고
    • A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships
    • Lisi, V. and Major, F. (2007) A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA, 13, 1537-1545.
    • (2007) RNA , vol.13 , pp. 1537-1545
    • Lisi, V.1    Major, F.2
  • 18
    • 57049151833 scopus 로고    scopus 로고
    • Annotation of tertiary interactions in RNA structures reveals variations and correlations
    • Xin, Y., Laing, C., Leontis, N.B. and Schlick, T. (2008) Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA, 14, 2465-2477.
    • (2008) RNA , vol.14 , pp. 2465-2477
    • Xin, Y.1    Laing, C.2    Leontis, N.B.3    Schlick, T.4
  • 20
    • 50549096615 scopus 로고    scopus 로고
    • IFoldRNA: Three-dimensional RNA structure prediction and folding
    • Sharma, S., Ding, F. and Dokholyan, N.V. (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
    • (2008) Bioinformatics , vol.24 , pp. 1951-1952
    • Sharma, S.1    Ding, F.2    Dokholyan, N.V.3
  • 22
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla, A. (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 24
    • 0000408083 scopus 로고
    • A mathematical procedure for superimposing atomic coordinates of proteins
    • McLachlan, A.D. (1972) A mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallogr., 28, 656-657.
    • (1972) Acta Crystallogr. , vol.28 , pp. 656-657
    • McLachlan, A.D.1
  • 25
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr., 32, 922-923.
    • (1976) Acta Crystallogr. , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 26
    • 0026077710 scopus 로고
    • The combination of symbolic and numerical computation for three-dimensional modeling of RNA
    • Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E. and Cedergren, R. (1991) The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science, 253, 1255-1260.
    • (1991) Science , vol.253 , pp. 1255-1260
    • Major, F.1    Turcotte, M.2    Gautheret, D.3    Lapalme, G.4    Fillion, E.5    Cedergren, R.6
  • 27
    • 0041417422 scopus 로고    scopus 로고
    • Building three-dimensional ribonucleic acid structures
    • Major, F. (2003) Building three-dimensional ribonucleic acid structures. Comput. Sci. Eng., 5, 44-53.
    • (2003) Comput. Sci. Eng. , vol.5 , pp. 44-53
    • Major, F.1
  • 28
    • 78649970557 scopus 로고    scopus 로고
    • Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch
    • Huang, L., Serganov, A. and Patel, D.J. (2010) Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol. Cell., 40, 774-786.
    • (2010) Mol. Cell. , vol.40 , pp. 774-786
    • Huang, L.1    Serganov, A.2    Patel, D.J.3
  • 29
    • 79952138382 scopus 로고    scopus 로고
    • Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA
    • Dibrov, S., McLean, J. and Hermann, T. (2011) Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA. Acta Crystallogr. D Biol. Crystallogr., 67, 97-104.
    • (2011) Acta Crystallogr. D Biol. Crystallogr. , vol.67 , pp. 97-104
    • Dibrov, S.1    McLean, J.2    Hermann, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.