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Volumn 3, Issue 1, 2008, Pages 32-45

Computational RNA structure prediction

Author keywords

Comparative modeling; Computational biology; RNA; Secondary structure; Structure prediction; Tertiary structure

Indexed keywords

BIOACTIVITY; BIOINFORMATICS; FORECASTING; GENE EXPRESSION;

EID: 38949138481     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489308783329823     Document Type: Review
Times cited : (34)

References (150)
  • 1
    • 0030968993 scopus 로고    scopus 로고
    • RNA structures and folding: From conventional to new issues in structure predictions
    • Schuster P, Stadler PF, and Renner A. RNA structures and folding: from conventional to new issues in structure predictions. Curr Opin Struct Biol 1997; 7: 229-35.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 229-235
    • Schuster, P.1    Stadler, P.F.2    Renner, A.3
  • 2
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada C, Gardiner K, Marsh T, Pace N, and Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983; 35: 849-57.
    • (1983) Cell , vol.35 , pp. 849-857
    • Guerrier-Takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 3
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna JA and Cech TR. The chemical repertoire of natural ribozymes. Nature 2002; 418: 222-8.
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 4
    • 22744455135 scopus 로고    scopus 로고
    • Pseudoknots: RNA structures with diverse functions
    • Staple DW and Butcher SE. Pseudoknots: RNA structures with diverse functions. PLoS Biol 2005; 3: e213.
    • (2005) PLoS Biol , vol.3
    • Staple, D.W.1    Butcher, S.E.2
  • 5
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-97.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 6
    • 3242677639 scopus 로고    scopus 로고
    • siRNAs: Applications in functional genomics and potential as therapeutics
    • Dorsett Y and Tuschl T. siRNAs: applications in functional genomics and potential as therapeutics. Nat Rev Drug Discov 2004; 3: 318-29.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 318-329
    • Dorsett, Y.1    Tuschl, T.2
  • 7
    • 0033757940 scopus 로고    scopus 로고
    • Structural genomics of RNA
    • Doudha JA. Structural genomics of RNA. Nat Struct Biol 2000; 7 Suppl: 954-956.
    • (2000) Nat Struct Biol , vol.7 , Issue.SUPPL. , pp. 954-956
    • Doudha, J.A.1
  • 9
    • 0002556146 scopus 로고
    • Some molecular details of the secondary structure of ribonucleic acid
    • Fresco JR, Alberts BM, and Doty P. Some molecular details of the secondary structure of ribonucleic acid. Nature 1960; 188: 98-101.
    • (1960) Nature , vol.188 , pp. 98-101
    • Fresco, J.R.1    Alberts, B.M.2    Doty, P.3
  • 10
    • 0016146021 scopus 로고
    • Three-dimensional tertiary structure of yeast phenylalanine transfer RNA
    • Kim SH, Suddath FL, Quigley GJ, et al. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 1974; 185: 435-40.
    • (1974) Science , vol.185 , pp. 435-440
    • Kim, S.H.1    Suddath, F.L.2    Quigley, G.J.3
  • 11
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M and Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981; 9: 133-48.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 12
    • 0000616205 scopus 로고
    • RNA secondary structure and their prediction
    • Zuker M and Sankoff D. RNA secondary structure and their prediction. Bull Math Biol 1984; 46: 591-621.
    • (1984) Bull Math Biol , vol.46 , pp. 591-621
    • Zuker, M.1    Sankoff, D.2
  • 14
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • Nussinov R and Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 1980; 77: 63019-13.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 63019-63113
    • Nussinov, R.1    Jacobson, A.B.2
  • 15
    • 0025678737 scopus 로고
    • Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel F and Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 1990; 216: 585-610.
    • (1990) J Mol Biol , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 17
    • 0026742978 scopus 로고
    • The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
    • Berman HM, iOlson WK, Beveridge DL, et al. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 1992; 63: 751-9.
    • (1992) Biophys J , vol.63 , pp. 751-759
    • Berman, H.M.1    iOlson, W.K.2    Beveridge, D.L.3
  • 18
    • 0031305924 scopus 로고    scopus 로고
    • Three-dimensional comparative modeling of RNA
    • Zwieh C and Muller F. Three-dimensional comparative modeling of RNA. Nucleic Acids Symp Ser 1997: 69-71.
    • (1997) Nucleic Acids Symp Ser , pp. 69-71
    • Zwieh, C.1    Muller, F.2
  • 20
    • 85195242446 scopus 로고    scopus 로고
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003; 31: 3429-31.
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003; 31: 3429-31.
  • 21
    • 33747874580 scopus 로고    scopus 로고
    • CONTRAfold: RNA, secondary structure prediction without physics-based models
    • Do CB, Woods DA, and Batzoglou S. CONTRAfold: RNA, secondary structure prediction without physics-based models. Bioinformatics 2006; 22: e90-8.
    • (2006) Bioinformatics , vol.22
    • Do, C.B.1    Woods, D.A.2    Batzoglou, S.3
  • 22
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • Dowell RD and Eddy SR. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics 2006; 7: 400.
    • (2006) BMC Bioinformatics , vol.7 , pp. 400
    • Dowell, R.D.1    Eddy, S.R.2
  • 24
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D and Sali A. Protein structure prediction and structural genomics. Science 2001; 294: 93-6.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 26
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A and Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 27
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133-55.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 28
    • 0037249551 scopus 로고    scopus 로고
    • RNABase: An annotated database of RNA structures
    • Murthy VL and Rose GD. RNABase: an annotated database of RNA structures. Nucleic Acids Res 2003; 31: 502-4.
    • (2003) Nucleic Acids Res , vol.31 , pp. 502-504
    • Murthy, V.L.1    Rose, G.D.2
  • 29
    • 27644491082 scopus 로고    scopus 로고
    • Structures of the Bacterial Ribosome at 3.5 A Resolution
    • Schuwirth B, Borovinskaya M, Hau C, et al. Structures of the Bacterial Ribosome at 3.5 A Resolution. Science 2005; 310: 827-834.
    • (2005) Science , vol.310 , pp. 827-834
    • Schuwirth, B.1    Borovinskaya, M.2    Hau, C.3
  • 30
    • 22544453281 scopus 로고    scopus 로고
    • The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components
    • Gao H, Ayub MJ, Levin MJ, and Frank J. The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components. Proc Natl Acad Sci USA 2005; 102: 10206-11.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 10206-10211
    • Gao, H.1    Ayub, M.J.2    Levin, M.J.3    Frank, J.4
  • 31
    • 24644437810 scopus 로고    scopus 로고
    • RNA structure: Reading the ribosome
    • Noller HF. RNA structure: reading the ribosome. Science 2005; 309:1508-14.
    • (2005) Science , vol.309 , pp. 1508-1514
    • Noller, H.F.1
  • 32
    • 34250822304 scopus 로고    scopus 로고
    • RNA structure: Experimental analysis
    • Felden B. RNA structure: experimental analysis. Curr Opin Microbial 2007; 10: 286-91.
    • (2007) Curr Opin Microbial , vol.10 , pp. 286-291
    • Felden, B.1
  • 33
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature, and classification of RNA base pairs
    • Leontis NB and Westhof E. Geometric nomenclature, and classification of RNA base pairs. RNA 2001; 7: 499-512.
    • (2001) RNA , vol.7 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 34
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis NB, Stombaugh J, and Westhof E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 2002; 30: 3497-531.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3497-3531
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 35
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • Yang H, Jossinet F, Leontis N, et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res 2003; 31: 3450-60.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3450-3460
    • Yang, H.1    Jossinet, F.2    Leontis, N.3
  • 38
    • 85195236735 scopus 로고    scopus 로고
    • Hershkovitz E, Sapiro G, Tannenbaum A, and Williams LD. Statistical analysis of RNA backbone. IEEE/ACM Trans Comput Biol Bioinform 2006; 3: 33-46.
    • Hershkovitz E, Sapiro G, Tannenbaum A, and Williams LD. Statistical analysis of RNA backbone. IEEE/ACM Trans Comput Biol Bioinform 2006; 3: 33-46.
  • 43
    • 0346494941 scopus 로고    scopus 로고
    • SCOP. database in 2004: Refinements integrate structure and sequence family data
    • Database issue: D226-9
    • Andreeva A, Howorth D, Brenner SE, et al. SCOP. database in 2004: refinements integrate structure and sequence family data Nucleic Acids Res 2004; 32 Database issue: D226-9.
    • (2004) Nucleic Acids Res , pp. 32
    • Andreeva, A.1    Howorth, D.2    Brenner, S.E.3
  • 44
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25: 25-9.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 45
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Database issue: D138-41
    • Bateman A, Coin L, Durbin R, et al. The Pfam protein families database. Nucleic Acids Res 2004; 32 Database issue: D138-41.
    • (2004) Nucleic Acids Res , pp. 32
    • Bateman, A.1    Coin, L.2    Durbin, R.3
  • 46
    • 0037305939 scopus 로고    scopus 로고
    • Domains, motifs and clusters in the protein universe
    • Liu J and Rost B. Domains, motifs and clusters in the protein universe. Curr Opin Chem Biol 2003; 7: 5-11.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 5-11
    • Liu, J.1    Rost, B.2
  • 47
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • Tian W and Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 2003; 333. 863-82.
    • (2003) J Mol Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 48
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999; 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 50
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-401.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3401
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 51
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR and Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988; 85: 2444-8.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 52
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, and Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673-80.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 53
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5: 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 54
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32: 1792-7.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 55
    • 85195237517 scopus 로고    scopus 로고
    • Notredame C, Higgins DG, and Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000; 302: 205-17.
    • Notredame C, Higgins DG, and Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000; 302: 205-17.
  • 56
    • 85195238936 scopus 로고    scopus 로고
    • Hochsmann M, Voss B, and Giegerich R. Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform 2004; 1: 53-62.
    • Hochsmann M, Voss B, and Giegerich R. Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform 2004; 1: 53-62.
  • 57
    • 25444512062 scopus 로고    scopus 로고
    • A method for aligning RNA secondary structures and its application to RNA motif detection
    • Liu J, Wang JT, Hu J, and Tian B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 2005; 6: 89.
    • (2005) BMC Bioinformatics , vol.6 , pp. 89
    • Liu, J.1    Wang, J.T.2    Hu, J.3    Tian, B.4
  • 58
    • 24044519380 scopus 로고    scopus 로고
    • MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
    • Siebert S and Backofen R. MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 2005; 21: 3352-9.
    • (2005) Bioinformatics , vol.21 , pp. 3352-3359
    • Siebert, S.1    Backofen, R.2
  • 59
    • 33744477338 scopus 로고    scopus 로고
    • Local gapped subforest alignment and its application in finding RNA structural motifs
    • Jansson J, Hieu NT, and Sung WK. Local gapped subforest alignment and its application in finding RNA structural motifs. J Comput Biol 2006; 13: 702-18.
    • (2006) J Comput Biol , vol.13 , pp. 702-718
    • Jansson, J.1    Hieu, N.T.2    Sung, W.K.3
  • 60
    • 20744449966 scopus 로고    scopus 로고
    • Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
    • Matsui H, Sato K, and Sakakibara Y. Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics 2005; 21: 2611-7.
    • (2005) Bioinformatics , vol.21 , pp. 2611-2617
    • Matsui, H.1    Sato, K.2    Sakakibara, Y.3
  • 62
    • 33845986334 scopus 로고    scopus 로고
    • Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA
    • Freyhult EK, Bollback JP, and Gardner PP. Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Res 2007; 17: 117-25.
    • (2007) Genome Res , vol.17 , pp. 117-125
    • Freyhult, E.K.1    Bollback, J.P.2    Gardner, P.P.3
  • 63
    • 0037133945 scopus 로고    scopus 로고
    • Computational genomics of noncoding RNA genes
    • Eddy SR. Computational genomics of noncoding RNA genes. Cell 2002; 109: 137-40.
    • (2002) Cell , vol.109 , pp. 137-140
    • Eddy, S.R.1
  • 64
    • 0025095711 scopus 로고
    • Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA
    • Gautheret D, Major F, and Cedergren R. Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. Comput Appl Biosci 1990; 6: 325-31.
    • (1990) Comput Appl Biosci , vol.6 , pp. 325-331
    • Gautheret, D.1    Major, F.2    Cedergren, R.3
  • 65
    • 0035890840 scopus 로고    scopus 로고
    • RNAMotif, an RNA secondary structure definition and search algorithm
    • Macke TJ, Ecker DJ, Gutell RR, et al. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 2001; 29: 4724-35.
    • (2001) Nucleic Acids Res , vol.29 , pp. 4724-4735
    • Macke, T.J.1    Ecker, D.J.2    Gutell, R.R.3
  • 66
    • 0029986908 scopus 로고    scopus 로고
    • Palingol: A declarative programming language to describe nucleic acids' secondary structures and to scan sequence database
    • Billoud B, Kontic M, and Viari A. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database. Nucleic Acids Res 1996; 24: 1395-403.
    • (1996) Nucleic Acids Res , vol.24 , pp. 1395-1403
    • Billoud, B.1    Kontic, M.2    Viari, A.3
  • 67
    • 0033915990 scopus 로고    scopus 로고
    • PatSearch: A pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
    • Pesole G, Liuni S, and D'Souza M. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 2000; 16: 439-50.
    • (2000) Bioinformatics , vol.16 , pp. 439-450
    • Pesole, G.1    Liuni, S.2    D'Souza, M.3
  • 68
    • 4944232234 scopus 로고    scopus 로고
    • Pair hidden Markov models on tree structures
    • Sakakibara Y. Pair hidden Markov models on tree structures. Bioinformatics 2003; 19 Suppl 1: i232-40.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1 I232-40
    • Sakakibara, Y.1
  • 69
    • 0028593508 scopus 로고
    • Stochastic context-free grammars for tRNA modeling
    • Sakakibara Y, Brown M, Hughey R, et al. Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res 1994; 22: 5112-20.
    • (1994) Nucleic Acids Res , vol.22 , pp. 5112-5120
    • Sakakibara, Y.1    Brown, M.2    Hughey, R.3
  • 70
    • 0028272315 scopus 로고
    • RNA sequence analysis using covariance models
    • Eddy SR and Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res 1994; 22: 2079-88.
    • (1994) Nucleic Acids Res , vol.22 , pp. 2079-2088
    • Eddy, S.R.1    Durbin, R.2
  • 71
    • 0033582628 scopus 로고    scopus 로고
    • A computational screen for methylation guide snoRNAs in yeast
    • Lowe TM and Eddy SR. A computational screen for methylation guide snoRNAs in yeast. Science 1999; 283: 1168-71.
    • (1999) Science , vol.283 , pp. 1168-1171
    • Lowe, T.M.1    Eddy, S.R.2
  • 72
    • 2942544566 scopus 로고    scopus 로고
    • RSEARCH: Finding homologs of single structured RNA sequences
    • Klein RJ and Eddy SR. RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics 2003; 4: 44.
    • (2003) BMC Bioinformatics , vol.4 , pp. 44
    • Klein, R.J.1    Eddy, S.R.2
  • 74
    • 2942607685 scopus 로고    scopus 로고
    • A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
    • Eddy SR. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 2002; 3: 18.
    • (2002) BMC Bioinformatics , vol.3 , pp. 18
    • Eddy, S.R.1
  • 76
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff D. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J Appl Math 1985; 45: 810-825.
    • (1985) SIAM J Appl Math , vol.45 , pp. 810-825
    • Sankoff, D.1
  • 77
    • 0000228203 scopus 로고
    • Atlas of Protein Sequence and Structure
    • Dayhoff MO. Atlas of Protein Sequence and Structure. Natl. Biomed. Res. Found. 1978; 5: 345-352.
    • (1978) Natl. Biomed. Res. Found , vol.5 , pp. 345-352
    • Dayhoff, M.O.1
  • 78
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S and Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992; 89: 10915-9.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 79
    • 1542614592 scopus 로고    scopus 로고
    • Empirical models for substitution in ribosomal RNA
    • Smith AD, Lui TW, and Tillier ER. Empirical models for substitution in ribosomal RNA. Mol Biol Evol 2004; 21: 419-27.
    • (2004) Mol Biol Evol , vol.21 , pp. 419-427
    • Smith, A.D.1    Lui, T.W.2    Tillier, E.R.3
  • 80
    • 0141721420 scopus 로고    scopus 로고
    • RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences
    • Hudelot C, Gowri-Shankar V, Jow H, Rattray M, and Higgs PG. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol Phylogenel Evol 2003; 28: 241-52.
    • (2003) Mol Phylogenel Evol , vol.28 , pp. 241-252
    • Hudelot, C.1    Gowri-Shankar, V.2    Jow, H.3    Rattray, M.4    Higgs, P.G.5
  • 81
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP and Ranquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17: 754-5.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ranquist, F.2
  • 82
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F and Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinfomatics 2003; 19: 1572-4.
    • (2003) Bioinfomatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 84
    • 33744790273 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by free energy minimization
    • Mathews DH and Turner DH. Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol 2006; 16: 270-8.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 270-278
    • Mathews, D.H.1    Turner, D.H.2
  • 85
    • 85195242282 scopus 로고    scopus 로고
    • Ding Y. Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 2006; 12: 323-3-1.
    • Ding Y. Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 2006; 12: 323-3-1.
  • 86
    • 33746320475 scopus 로고    scopus 로고
    • Revolutions in RNA secondary structure prediction
    • Mathews DH. Revolutions in RNA secondary structure prediction. J Mol Biol 2006; 359: 526-32.
    • (2006) J Mol Biol , vol.359 , pp. 526-532
    • Mathews, D.H.1
  • 88
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science 1973; 181: 223-30.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 89
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, and Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288: 911-40.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 90
    • 3342977915 scopus 로고    scopus 로고
    • Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
    • Mathews DH. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA 2004; 10: 1178-90.
    • (2004) RNA , vol.10 , pp. 1178-1190
    • Mathews, D.H.1
  • 91
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty S, Fontana W, Hofacker IL, and Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999; 49: 145-65.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 93
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 1990; 29: 1105-19.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 94
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • van Batenburg FH, Gultyaev AP, and Pleij CW. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J Theor Biol 1959, 174: 269-80.
    • (1959) J Theor Biol , vol.174 , pp. 269-280
    • van Batenburg, F.H.1    Gultyaev, A.P.2    Pleij, C.W.3
  • 95
    • 0029061125 scopus 로고
    • The computer simulatiorr of RNA folding pathways using a genetic algorithm
    • Gultyaev AP, van Batenburg FH, and Pleij CW. The computer simulatiorr of RNA folding pathways using a genetic algorithm. J Mol Biol 1995; 250: 37-51.
    • (1995) J Mol Biol , vol.250 , pp. 37-51
    • Gultyaev, A.P.1    van Batenburg, F.H.2    Pleij, C.W.3
  • 96
    • 0035105948 scopus 로고    scopus 로고
    • The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation
    • Shapiro BA, Wit, JC, Bengali, D, and Potts MJ. The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation. Bioinformatics 2001; 17: 137-48.
    • (2001) Bioinformatics , vol.17 , pp. 137-148
    • Shapiro, B.A.1    Wit, J.C.2    Bengali, D.3    Potts, M.J.4
  • 97
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngso RB and Pedersen CN. RNA pseudoknot prediction in energy-based models. J Comput Biol 2000; 7: 409-27.
    • (2000) J Comput Biol , vol.7 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.2
  • 98
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • Rivas E and Eddy SR. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 1999; 285: 2053-68.
    • (1999) J Mol Biol , vol.285 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 99
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including, pseudoknots
    • Dirks RM and Pierce NA. A partition function algorithm for nucleic acid secondary structure including, pseudoknots. J Compur Chem 2003; 24: 1664-77.
    • (2003) J Compur Chem , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 100
    • 3042554001 scopus 로고    scopus 로고
    • An algorithm for computing nucleic acid base-pairing probabilities inciuding pseudoknots
    • Dirks RM and Pierce NA: An algorithm for computing nucleic acid base-pairing probabilities inciuding pseudoknots. J Comput Chem 2004; 25: 1295-304.
    • (2004) J Comput Chem , vol.25 , pp. 1295-1304
    • Dirks, R.M.1    Pierce, N.A.2
  • 101
    • 85195241027 scopus 로고    scopus 로고
    • Stochastic modeling of RNA pseudoknotted structures:. a grammatical approach
    • Sappl 1: i66-73
    • Cai L, Malmberg RI, and Wu Y. Stochastic modeling of RNA pseudoknotted structures:. a grammatical approach. Bioinformaticds 2003; 19 Sappl 1: i66-73.
    • (2003) Bioinformaticds , pp. 19
    • Cai, L.1    Malmberg, R.I.2    Wu, Y.3
  • 102
    • 33846900179 scopus 로고    scopus 로고
    • High sensitivity RNA pseudoknot prediction
    • Huang X, and Ali H. High sensitivity RNA pseudoknot prediction. Nucleic Acids Res 2007; 35: 656-63.
    • (2007) Nucleic Acids Res , vol.35 , pp. 656-663
    • Huang, X.1    Ali, H.2
  • 103
    • 0028823370 scopus 로고
    • An. interactive framework for RNA, secondary structure prediction- with a dynamical treatment of constraints
    • Gaspin C and Westhof E. An. interactive framework for RNA, secondary structure prediction- with a dynamical treatment of constraints. J Mol Biol 1995; 254: 163-74.
    • (1995) J Mol Biol , vol.254 , pp. 163-174
    • Gaspin, C.1    Westhof, E.2
  • 104
    • 13344262673 scopus 로고    scopus 로고
    • A comprehensive comparison of comparative RNA structure prediction approaches
    • Gardner PP and Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004; 5: 140.
    • (2004) BMC Bioinformatics , vol.5 , pp. 140
    • Gardner, P.P.1    Giegerich, R.2
  • 105
    • 0025721938 scopus 로고
    • Evolution of compensatory substitutions through G.U. intermediate state in Drosophila rRNA
    • Rousset F, Pelandakis M, and Solignac M. Evolution of compensatory substitutions through G.U. intermediate state in Drosophila rRNA. Proc Natl Acad Sci USA 1991; 88: 10032-6.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 10032-10036
    • Rousset, F.1    Pelandakis, M.2    Solignac, M.3
  • 106
    • 0029026878 scopus 로고
    • Maintenance of pre-mRNA secondary structure by epistatic selection
    • Kirby DA, Muse SV, and Stephan W. Maintenance of pre-mRNA secondary structure by epistatic selection. Proc Natl Acad Sci USA 1995; 92: 9047-51.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 9047-9051
    • Kirby, D.A.1    Muse, S.V.2    Stephan, W.3
  • 107
    • 0025832114 scopus 로고
    • Inferring consensus structure from nucleic acid sequences
    • Chiu DK and Kolodziejczak T. Inferring consensus structure from nucleic acid sequences. Comput Appl Biosci 1991; 7: 347-52.
    • (1991) Comput Appl Biosci , vol.7 , pp. 347-352
    • Chiu, D.K.1    Kolodziejczak, T.2
  • 108
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
    • Gutell RR, Power A, Hertz GZ, Putz EJ, and Stormo GD. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 1992; 20: 5785-95.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5785-5795
    • Gutell, R.R.1    Power, A.2    Hertz, G.Z.3    Putz, E.J.4    Stormo, G.D.5
  • 109
    • 33845362968 scopus 로고    scopus 로고
    • Measuring covariation in RNA alignments: Physical realism improves information measures
    • Lindgreen S, Gardner PP, and Krogh A. Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics 2006; 22: 2988-95.
    • (2006) Bioinformatics , vol.22 , pp. 2988-2995
    • Lindgreen, S.1    Gardner, P.P.2    Krogh, A.3
  • 110
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker IL, Fekete M, and Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol 2002; 319: 1059-66.
    • (2002) J Mol Biol , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 111
    • 0043123155 scopus 로고    scopus 로고
    • Pfold: RNA secondary structure prediction using stochastic context-free grammars
    • Knudsen B and Hein J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res 2003; 31: 3423-8.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3423-3428
    • Knudsen, B.1    Hein, J.2
  • 112
    • 3242880117 scopus 로고    scopus 로고
    • ILM: A web server for predicting RNA secondary structures with pseudoknots
    • Ruan J, Stormo GD, and Zhang W. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res 2004; 32: W146-9.
    • (2004) Nucleic Acids Res , vol.32
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 113
    • 0347724163 scopus 로고    scopus 로고
    • An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
    • Ruan J, Stormo GD, and Zhang W. An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 2004; 20: 58-66.
    • (2004) Bioinformatics , vol.20 , pp. 58-66
    • Ruan, J.1    Stormo, G.D.2    Zhang, W.3
  • 114
    • 23144449520 scopus 로고    scopus 로고
    • The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
    • Havgaard JH, Lyngso RB, and Gorodkin J. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res 2005; 33: W650-3.
    • (2005) Nucleic Acids Res , vol.33
    • Havgaard, J.H.1    Lyngso, R.B.2    Gorodkin, J.3
  • 116
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews DH and Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol 2002; 317: 191-203.
    • (2002) J Mol Biol , vol.317 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 117
    • 0037252550 scopus 로고    scopus 로고
    • Finding the common structure shared by two homologous RNAs
    • Perriquet O, Touzet H, and Dauchet M. Finding the common structure shared by two homologous RNAs. Bioinformatics 2003; 19: 108-16.
    • (2003) Bioinformatics , vol.19 , pp. 108-116
    • Perriquet, O.1    Touzet, H.2    Dauchet, M.3
  • 118
    • 3242882720 scopus 로고    scopus 로고
    • CARNAC: Folding families of related RNAs
    • Touzet H and Perriquet O. CARNAC: folding families of related RNAs. Nucleic Acids Res 2004; 32: W142-5.
    • (2004) Nucleic Acids Res , vol.32
    • Touzet, H.1    Perriquet, O.2
  • 119
    • 0025187499 scopus 로고
    • Comparing multiple RNA secondary structures using tree comparisons
    • Shapiro BA and Zhang KZ. Comparing multiple RNA secondary structures using tree comparisons. Comput Appl Biosci 1990; 6: 309-18.
    • (1990) Comput Appl Biosci , vol.6 , pp. 309-318
    • Shapiro, B.A.1    Zhang, K.Z.2
  • 121
    • 0032545158 scopus 로고    scopus 로고
    • Stepping through an RNA structure: A novel approach to conformational analysis
    • Duarte CM and Pyle AM. Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol 1998; 284: 1465-78.
    • (1998) J Mol Biol , vol.284 , pp. 1465-1478
    • Duarte, C.M.1    Pyle, A.M.2
  • 122
    • 36448954303 scopus 로고    scopus 로고
    • FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
    • in press
    • Sarver M, Zirbel CL, Stombaugh J, Mokdad A, and Leontis NB. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 2007; in press.
    • (2007) J Math Biol
    • Sarver, M.1    Zirbel, C.L.2    Stombaugh, J.3    Mokdad, A.4    Leontis, N.B.5
  • 123
    • 0033614014 scopus 로고    scopus 로고
    • Resolving the discrepancies among nucleic acid conformational analyses
    • Lu XJ and Olson WK. Resolving the discrepancies among nucleic acid conformational analyses. J Mol Biol 1999; 285: 1563-75.
    • (1999) J Mol Biol , vol.285 , pp. 1563-1575
    • Lu, X.J.1    Olson, W.K.2
  • 125
    • 0035906639 scopus 로고    scopus 로고
    • Quantitative analysis of nucleic acid three-dimensional structures
    • Gendron P, Lemieux S, and Major F. Quantitative analysis of nucleic acid three-dimensional structures. J Mol Biol 2001; 308: 919-36.
    • (2001) J Mol Biol , vol.308 , pp. 919-936
    • Gendron, P.1    Lemieux, S.2    Major, F.3
  • 126
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu XJ and Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 2003; 31: 5108-21.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 127
    • 27544504678 scopus 로고    scopus 로고
    • ARTS: Alignment of RNA tertiary structures
    • Dror O, Nussinov R, and Wolfson H. ARTS: alignment of RNA tertiary structures. Bioinformatics 2005; 21 Suppl 2: ii47-ii53.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Dror, O.1    Nussinov, R.2    Wolfson, H.3
  • 128
    • 33747834668 scopus 로고    scopus 로고
    • The ARTS web server for aligning RNA tertiary structures
    • Dror O, Nussinov R, and Wolfson HJ. The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res 2006; 34: W412-5.
    • (2006) Nucleic Acids Res , vol.34
    • Dror, O.1    Nussinov, R.2    Wolfson, H.J.3
  • 129
    • 34547566768 scopus 로고    scopus 로고
    • RNAbor: A web server for RNA structural neighbors
    • Freyhult E, Moulton V, and Clote P. RNAbor: a web server for RNA structural neighbors. Nucleic Acids Res 2007.35: W305-9
    • (2007) Nucleic Acids Res , vol.35
    • Freyhult, E.1    Moulton, V.2    Clote, P.3
  • 130
    • 85195237012 scopus 로고    scopus 로고
    • DLAL: A web server for RNA structural alignment using dihedral angles
    • in press
    • Ferre F, Lorenz WA, Ponty Y, and Clote P. DLAL: A web server for RNA structural alignment using dihedral angles. Nucleic Acids Res 2007; in press.
    • (2007) Nucleic Acids Res
    • Ferre, F.1    Lorenz, W.A.2    Ponty, Y.3    Clote, P.4
  • 131
    • 0347525829 scopus 로고    scopus 로고
    • Representation, searching and discovery of patterns of bases in complex RNA structures
    • Harrison AM, South DR, Willett P, and Artymiuk PJ. Representation, searching and discovery of patterns of bases in complex RNA structures. J Comput Aided Mol Des 2003; 17: 537-49.
    • (2003) J Comput Aided Mol Des , vol.17 , pp. 537-549
    • Harrison, A.M.1    South, D.R.2    Willett, P.3    Artymiuk, P.J.4
  • 132
    • 0344012516 scopus 로고    scopus 로고
    • RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
    • Duarte CM, Wadley LM, and Pyle AM. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res 2003; 31: 4755-61.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4755-4761
    • Duarte, C.M.1    Wadley, L.M.2    Pyle, A.M.3
  • 133
    • 13544255744 scopus 로고    scopus 로고
    • The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery
    • Wadley LM and Pyle AM. The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Res 2004; 32: 6650-9.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6650-6659
    • Wadley, L.M.1    Pyle, A.M.2
  • 135
    • 0032232180 scopus 로고    scopus 로고
    • MANIP: An interactive tool for modelling RNA
    • Massire C and Westhof E. MANIP: an interactive tool for modelling RNA. J Mol Graph Model 1998; 16: 197-205, 255-7.
    • (1998) J Mol Graph Model , vol.16 , Issue.197-205 , pp. 255-257
    • Massire, C.1    Westhof, E.2
  • 136
    • 85195238412 scopus 로고    scopus 로고
    • Jossinet F and Westhof E. Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 2005; 21: 3320-i.
    • Jossinet F and Westhof E. Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 2005; 21: 3320-i.
  • 137
    • 0345983583 scopus 로고    scopus 로고
    • Modeling unusual nucleic acid structures
    • Leontis N and SantaLucia J, Editors. American Chemical Society: Washington, DC
    • Macke TJ and Case D, Modeling unusual nucleic acid structures., In: Molecular Modeling of Nucleic Acids, Leontis N and SantaLucia J, Editors. American Chemical Society: Washington, DC. 1998; 379-393.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379-393
    • Macke, T.J.1    Case, D.2
  • 138
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham TE, 3rd and Young MA. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers 2000; 56: 232-56.
    • (2000) Biopolymers , vol.56 , pp. 232-256
    • Cheatham 3rd, T.E.1    Young, M.A.2
  • 139
    • 0041417422 scopus 로고    scopus 로고
    • Building three-dimensional ribonucleic acid structures
    • Major F. Building three-dimensional ribonucleic acid structures. Comput Sci Eng 2003; 5: 44-53.
    • (2003) Comput Sci Eng , vol.5 , pp. 44-53
    • Major, F.1
  • 140
    • 33748422686 scopus 로고    scopus 로고
    • The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation
    • Yingling YG and Shapiro BA. The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation. J Mol Graph Model 2006; 25: 261-74.
    • (2006) J Mol Graph Model , vol.25 , pp. 261-274
    • Yingling, Y.G.1    Shapiro, B.A.2
  • 141
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary structures
    • Das R and Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci USA 2007. 104: 14664-9.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 14664-14669
    • Das, R.1    Baker, D.2
  • 142
    • 30344483607 scopus 로고    scopus 로고
    • Free modeling with Rosetta in CASP6
    • Bradley P, Malmstrom L, Qian B, et al. Free modeling with Rosetta in CASP6. Proteins 2005; 61 (Suppl 7): 128-34.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 128-134
    • Bradley, P.1    Malmstrom, L.2    Qian, B.3
  • 143
    • 33645472732 scopus 로고    scopus 로고
    • The RNA Ontology Consortium: An open invitation to the RNA community
    • Leontis NB, Altman RB, Berman HK et al. The RNA Ontology Consortium: an open invitation to the RNA community. RNA 2006; 12: 533-41.
    • (2006) RNA , vol.12 , pp. 533-541
    • Leontis, N.B.1    Altman, R.B.2    Berman, H.K.3
  • 144
    • 33644874394 scopus 로고    scopus 로고
    • MODBASE: A database of annotated comparative protein structure models and associated resources
    • Pieper U, Eswar N, Davis FP, et al. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 2006; 34: D291-5.
    • (2006) Nucleic Acids Res , vol.34
    • Pieper, U.1    Eswar, N.2    Davis, F.P.3
  • 145
    • 33644874606 scopus 로고    scopus 로고
    • The SWISS-MODEL Repository: New features and functionalities
    • Kopp J and Schwede T. The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids Res 2006; 34: D315-8.
    • (2006) Nucleic Acids Res , vol.34
    • Kopp, J.1    Schwede, T.2
  • 146
    • 0043123167 scopus 로고    scopus 로고
    • Tools for comparative protein structure modeling and analysis
    • Eswar N, John B, Mirkovic N, et al. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 2003; 31: 3375-80.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3375-3380
    • Eswar, N.1    John, B.2    Mirkovic, N.3
  • 147
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, and Peitsch MC. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res 2003; 31: 3381-5.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 148
    • 33646272409 scopus 로고    scopus 로고
    • Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
    • Pedersen JS, Bejerano G, Siepel A, et al. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Comput Biol 2006; 2.
    • (2006) PLoS Comput Biol , pp. 2
    • Pedersen, J.S.1    Bejerano, G.2    Siepel, A.3
  • 150
    • 26644439939 scopus 로고    scopus 로고
    • JViz.Rna - a Java tool for RNA secondary structure visualization
    • Wiese KC, Glen E, and Vasudevan A. JViz.Rna - a Java tool for RNA secondary structure visualization. IEEE Trans Nanobioscience 2005; 4: 212-8.
    • (2005) IEEE Trans Nanobioscience , vol.4 , pp. 212-218
    • Wiese, K.C.1    Glen, E.2    Vasudevan, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.