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Volumn 26, Issue 21, 2010, Pages 2689-2697

R3D align: Global pairwise alignment of RNA 3D structures using local superpositions

Author keywords

[No Author keywords available]

Indexed keywords

RNA; RNA 16S;

EID: 77958470166     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq506     Document Type: Article
Times cited : (45)

References (27)
  • 1
    • 0000827467 scopus 로고
    • Abranch and bound algorithm for the maximum clique problem
    • Babel,L. and Tinhofer,G. (1990)Abranch and bound algorithm for the maximum clique problem. Math. Methods Oper. Res., 34, 207-217.
    • (1990) Math. Methods Oper. Res. , vol.34 , pp. 207-217
    • Babel, L.1    Tinhofer, G.2
  • 3
    • 0040389694 scopus 로고
    • Some heuristics for graph coloring
    • Nelson,R. andWilson,R.J. (eds) Longmans, New York
    • Biggs,N. (1990) Some heuristics for graph coloring. In Nelson,R. andWilson,R.J. (eds) Graph Colourings, Longmans, New York, pp. 87-96.
    • (1990) Graph Colourings , pp. 87-96
    • Biggs, N.1
  • 4
    • 69049103112 scopus 로고    scopus 로고
    • The RNA structure alignment ontology
    • Brown,J.W. et al. (2009) The RNA structure alignment ontology. RNA, 15, 1623-1631.
    • (2009) RNA , vol.15 , pp. 1623-1631
    • Brown, J.W.1
  • 5
    • 49549105830 scopus 로고    scopus 로고
    • RNA structure alignment by a unit-vector approach
    • Capriotti,E. and Marti-Renom,M.A. (2008) RNA structure alignment by a unit-vector approach. Bioinformatics, 24, i112-i118.
    • (2008) Bioinformatics , vol.24
    • Capriotti, E.1    Marti-Renom, M.A.2
  • 6
    • 48449106165 scopus 로고    scopus 로고
    • SARSA: a web tool for structural alignment of RNA using a structural alphabet
    • Chang,Y.F. et al. (2008) SARSA: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res., 36, W19-W24.
    • (2008) Nucleic Acids Res. , vol.36
    • Chang, Y.F.1
  • 7
    • 33747827586 scopus 로고    scopus 로고
    • NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
    • DeSantis, T.Z. Jr et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res., 34, W394-W399.
    • (2006) Nucleic Acids Res. , vol.34
    • DeSantis T.Z., Jr.1
  • 8
    • 27544504678 scopus 로고    scopus 로고
    • ARTS: alignment of RNA tertiary structures
    • Dror,O. et al. (2005) ARTS: alignment of RNA tertiary structures. Bioinformatics, 21 (Suppl. 2), ii47-ii53.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Dror, O.1
  • 9
    • 0344012516 scopus 로고    scopus 로고
    • RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
    • Duarte,C.M. et al. (2003) RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res., 31, 4755-4761.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4755-4761
    • Duarte, C.M.1
  • 10
    • 34547585553 scopus 로고    scopus 로고
    • DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
    • Ferre,F. et al. (2007) DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res., 35, W659-668.
    • (2007) Nucleic Acids Res. , vol.35
    • Ferre, F.1
  • 12
    • 0344011107 scopus 로고    scopus 로고
    • Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA
    • Hershkovitz,E. et al. (2003) Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. Nucleic Acids Res., 31, 6249-6257.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6249-6257
    • Hershkovitz, E.1
  • 13
    • 2942615089 scopus 로고    scopus 로고
    • The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
    • Klein D.J. et al. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141-177.
    • (2004) J. Mol. Biol. , vol.340 , pp. 141-177
    • Klein, D.J.1
  • 14
    • 6044275739 scopus 로고    scopus 로고
    • Basis for structural diversity in homologous RNAs
    • Krasilnikov,A.S. et al. (2004) Basis for structural diversity in homologous RNAs. Science, 306, 104-107.
    • (2004) Science , vol.306 , pp. 104-107
    • Krasilnikov, A.S.1
  • 15
    • 0037434709 scopus 로고    scopus 로고
    • Crystal structure of the specificity domain of ribonuclease P
    • Krasilnikov,A.S. et al. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature, 421, 760-764.
    • (2003) Nature , vol.421 , pp. 760-764
    • Krasilnikov, A.S.1
  • 16
    • 0014757386 scopus 로고
    • Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. andWunsch,C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 17
    • 0016502853 scopus 로고
    • Configurational statistics of polynucleotide chains. A single virtual bond treatment
    • Olson,W.K. (1975) Configurational statistics of polynucleotide chains. A single virtual bond treatment. Macromolecules, 8, 272-275.
    • (1975) Macromolecules , vol.8 , pp. 272-275
    • Olson, W.K.1
  • 18
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison
    • Ortiz,A.R. et al. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11, 2606-2621.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1
  • 19
    • 70349149051 scopus 로고    scopus 로고
    • New metrics for comparing and assessing discrepancies between RNA 3D structures and models
    • Parisien,M. et al. (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
  • 20
    • 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
  • 21
    • 27644491082 scopus 로고    scopus 로고
    • Structures of the bacterial ribosome at 3.5 A resolution
    • Schuwirth,B.S. et al. (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science, 310, 827-834.
    • (2005) Science , vol.310 , pp. 827-834
    • Schuwirth, B.S.1
  • 22
    • 33749354360 scopus 로고    scopus 로고
    • Structure of the 70S ribosome complexed with mRNA and tRNA
    • Selmer, M. et al. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942.
    • (2006) Science , vol.313 , pp. 1935-1942
    • Selmer, M.1
  • 23
    • 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
  • 24
    • 25144463996 scopus 로고    scopus 로고
    • Optimal protein structure alignment using maximum cliques
    • Strickland,D.M. et al. (2005) Optimal protein structure alignment using maximum cliques. Oper. Res., 53, 389-402.
    • (2005) Oper. Res. , vol.53 , pp. 389-402
    • Strickland, D.M.1
  • 25
    • 0034699518 scopus 로고    scopus 로고
    • Structure of the 30S ribosomal subunit
    • Wimberly,B.T. et al. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
    • (2000) Nature , vol.407 , pp. 327-339
    • Wimberly, B.T.1
  • 26
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • Yang,H. et al. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3450-3460
    • Yang, H.1
  • 27
    • 69849114530 scopus 로고    scopus 로고
    • Classification and energetic of the base-phosphate interactions in RNA
    • Zirbel,C.L. et al. (2009) Classification and energetic of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 4898-4918
    • Zirbel, C.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.