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Volumn 39, Issue 10, 2011, Pages 4007-4022

ModeRNA: A tool for comparative modeling of RNA 3D structure

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSFER RNA;

EID: 79959292152     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1320     Document Type: Article
Times cited : (230)

References (72)
  • 1
    • 0003604405 scopus 로고    scopus 로고
    • 3 edn Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Gesteland, R.F., Cech, T.R. and Atkins, J.F. (2005) The RNA World, 3 edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (2005) The RNA World
    • Gesteland, R.F.1    Cech, T.R.2    Atkins, J.F.3
  • 5
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
    • Moult, J. (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol., 15, 285-289. (Pubitemid 40826447)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.SPEC. ISS. 3 , pp. 285-289
    • Moult, J.1
  • 6
    • 36349034517 scopus 로고    scopus 로고
    • Informatics challenges in structured RNA
    • DOI 10.1093/bib/bbm026, Special Issue: Current Progress in Bioinformatics: 2007
    • Laederach, A. (2007) Informatics challenges in structured RNA. Brief Bioinform., 8, 294-303. (Pubitemid 350142619)
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.5 , pp. 294-303
    • Laederach, A.1
  • 8
    • 0031020765 scopus 로고    scopus 로고
    • Protein evolution How far can sequences diverge?
    • Chothia, C. and Gerstein, M. (1997) Protein evolution. How far can sequences diverge? Nature, 385, 579, 581.
    • (1997) Nature , vol.385 , Issue.579 , pp. 581
    • Chothia, C.1    Gerstein, M.2
  • 9
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C. and Lesk, A.M. (1986) The relation between the divergence of sequence and structure in proteins. Embo J., 5, 823-826.
    • (1986) Embo J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 10
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin, N.V. (2001) Fold change in evolution of protein structures. J. Struct. Biol., 134, 167-185.
    • (2001) J. Struct. Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 11
    • 0036283048 scopus 로고    scopus 로고
    • Evolution and physics in comparative protein structure modeling
    • Fiser, A., Feig, M., Brooks, C.L. 3rd and Sali, A. (2002) Evolution and physics in comparative protein structure modeling. Acc. Chem. Res., 35, 413-421.
    • (2002) Acc. Chem. Res , vol.35 , pp. 413-421
    • Fiser, A.1    Feig, M.2    Brooks Iii, C.L.3    Sali, A.4
  • 12
    • 27544504678 scopus 로고    scopus 로고
    • ARTS: Alignment of RNA tertiary structures
    • DOI 10.1093/bioinformatics/bti1108
    • Dror, O., Nussinov, R. and Wolfson, H. (2005) ARTS: alignment of RNA tertiary structures. Bioinformatics, 21(Suppl 2), ii47-ii53. (Pubitemid 41535427)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Dror, O.1    Nussinov, R.2    Wolfson, H.3
  • 13
    • 6044275739 scopus 로고    scopus 로고
    • Basis for structural diversity in homologous RNAs
    • DOI 10.1126/science.1101489
    • Krasilnikov, A.S., Xiao, Y., Pan, T. and Mondragon, A. (2004) Basis for structural diversity in homologous RNAs. Science, 306, 104-107. (Pubitemid 39451948)
    • (2004) Science , vol.306 , Issue.5693 , pp. 104-107
    • Krasilnikov, A.S.1    Xiao, Y.2    Pan, T.3    Mondragon, A.4
  • 14
    • 33744807172 scopus 로고    scopus 로고
    • The building blocks and motifs of RNA architecture
    • DOI 10.1016/j.sbi.2006.05.009, PII S0959440X06000807
    • Leontis, N.B., Lescoute, A. and Westhof, E. (2006) The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol., 16, 279-287. (Pubitemid 43831653)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.3 , pp. 279-287
    • Leontis, N.B.1    Lescoute, A.2    Westhof, E.3
  • 15
    • 25144458057 scopus 로고    scopus 로고
    • Sequence to Structure (S2S): Display, manipulate and interconnect RNA data from sequence to structure
    • DOI 10.1093/bioinformatics/bti504
    • Jossinet, F. and Westhof, E. (2005) Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics, 21, 3320-3321. (Pubitemid 41418451)
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3320-3321
    • Jossinet, F.1    Westhof, E.2
  • 16
    • 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
  • 17
    • 0031305924 scopus 로고    scopus 로고
    • Three-dimensional comparative modeling of RNA
    • Zwieb, C. and Muller, F. (1997) Three-dimensional comparative modeling of RNA. Nucleic Acids Symp. Ser., 36, 69-71.
    • (1997) Nucleic Acids Symp. ser , vol.36 , pp. 69-71
    • Zwieb, C.1    Muller, F.2
  • 19
    • 0024974668 scopus 로고
    • Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs
    • Westhof, E., Romby, P., Romaniuk, P.J., Ebel, J.P., Ehresmann, C. and Ehresmann, B. (1989) Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs. J. Mol. Biol., 207, 417-431.
    • (1989) J. Mol. Biol , vol.207 , pp. 417-431
    • Westhof, E.1    Romby, P.2    Romaniuk, P.J.3    Ebel, J.P.4    Ehresmann, C.5    Ehresmann, B.6
  • 20
    • 0025340544 scopus 로고
    • Solution structure of human U1 snRNA Derivation of a possible three-dimensional model
    • Krol, A., Westhof, E., Bach, M., Luhrmann, R., Ebel, J.P. and Carbon, P. (1990) Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model. Nucleic Acids Res., 18, 3803-3811.
    • (1990) Nucleic Acids Res , vol.18 , pp. 3803-3811
    • Krol, A.1    Westhof, E.2    Bach, M.3    Luhrmann, R.4    Ebel, J.P.5    Carbon, P.6
  • 21
    • 0025678737 scopus 로고
    • Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610. (Pubitemid 120037393)
    • (1990) Journal of Molecular Biology , vol.216 , Issue.3 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 22
    • 16644372753 scopus 로고    scopus 로고
    • Atomic model of the Thermus thermophilus 70S ribosome developed in silico
    • Tung, C.S. and Sanbonmatsu, K.Y. (2004) Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophys. J., 87, 2714-2722.
    • (2004) Biophys. J , vol.87 , pp. 2714-2722
    • Tung, C.S.1    Sanbonmatsu, K.Y.2
  • 23
    • 1642499418 scopus 로고    scopus 로고
    • The three-dimensional architecture of the class I ligase ribozyme
    • DOI 10.1261/rna.5177504
    • Bergman, N.H., Lau, N.C., Lehnert, V., Westhof, E. and Bartel, D.P. (2004) The three-dimensional architecture of the class I ligase ribozyme. RNA, 10, 176-184. (Pubitemid 38129822)
    • (2004) RNA , vol.10 , Issue.2 , pp. 176-184
    • Bergman, N.H.1    Lau, N.C.2    Lehnert, V.3    Westhof, E.4    Bartel, D.P.5
  • 25
    • 0242362160 scopus 로고    scopus 로고
    • A "FRankenstein's Monster" Approach to Comparative Modeling: Merging the Finest Fragments of Fold-Recognition Models and Iterative Model Refinement Aided by 3D Structure Evaluation
    • DOI 10.1002/prot.10545
    • Kosinski, J., Cymerman, I.A., Feder, M., Kurowski, M.A., Sasin, J.M. and Bujnicki, J.M. (2003) A 'FRankenstein's monster' approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins, 53(Suppl 6), 369-379. (Pubitemid 37352195)
    • (2003) Proteins: Structure, Function and Genetics , vol.53 , Issue.SUPPL. 6 , pp. 369-379
    • Kosinski, J.1    Cymerman, I.A.2    Feder, M.3    Kurowski, M.A.4    Sasin, J.M.5    Bujnicki, J.M.6
  • 26
    • 30444446362 scopus 로고    scopus 로고
    • Protein-structure prediction by recombination of fragments
    • DOI 10.1002/cbic.200500235
    • Bujnicki, J.M. (2006) Protein-structure prediction by recombination of fragments. Chembiochem, 7, 19-27. (Pubitemid 43076278)
    • (2006) ChemBioChem , vol.7 , Issue.1 , pp. 19-27
    • Bujnicki, J.M.1
  • 28
    • 77249151455 scopus 로고    scopus 로고
    • Multiscale modeling of proteins
    • Tozzini, V. (2009) Multiscale modeling of proteins. Acc. Chem. Res., 43, 220-230.
    • (2009) Acc. Chem. Res , vol.43 , pp. 220-230
    • Tozzini, V.1
  • 30
    • 40449139010 scopus 로고    scopus 로고
    • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    • DOI 10.1038/nature06684, PII NATURE06684
    • Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55. (Pubitemid 351355097)
    • (2008) Nature , vol.452 , Issue.7183 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 31
    • 33646365635 scopus 로고    scopus 로고
    • Rigorous performance evaluation in protein structure modelling and implications for computational biology
    • DOI 10.1098/rstb.2005.1810
    • Moult, J. (2006) Rigorous performance evaluation in protein structure modelling and implications for computational biology. Philos. Trans. R Soc. Lond. B Biol. Sci., 361, 453-458. (Pubitemid 44870101)
    • (2006) Philosophical Transactions of the Royal Society B: Biological Sciences , vol.361 , Issue.1467 , pp. 453-458
    • Moult, J.1
  • 32
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali, A. and Blundell, T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815. (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 33
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • DOI 10.1093/nar/gkg520
    • Schwede, T., Kopp, J., Guex, N. and Peitsch, M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385. (Pubitemid 37442164)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 35
    • 28144441826 scopus 로고    scopus 로고
    • The bacterial ribosome as a target for antibiotics
    • DOI 10.1038/nrmicro1265, PII N1265
    • Poehlsgaard, J. and Douthwaite, S. (2005) The bacterial ribosome as a target for antibiotics. Nat. Rev. Microbiol., 3, 870-881. (Pubitemid 41693182)
    • (2005) Nature Reviews Microbiology , vol.3 , Issue.11 , pp. 870-881
    • Poehlsgaard, J.1    Douthwaite, S.2
  • 38
    • 1442310610 scopus 로고    scopus 로고
    • Loops In Proteins (LIP) - A comprehensive loop database for homology modelling
    • Michalsky, E., Goede, A. and Preissner, R. (2003) Loops In Proteins (LIP)-a comprehensive loop database for homology modelling. Protein Eng., 16, 979-985. (Pubitemid 38281748)
    • (2003) Protein Engineering , vol.16 , Issue.12 , pp. 979-985
    • Michalsky, E.1    Goede, A.2    Preissner, R.3
  • 40
    • 77950366829 scopus 로고    scopus 로고
    • Sequence-structure relationships in RNA loops: Establishing the basis for loop homology modeling
    • Schudoma, C., May, P., Nikiforova, V. and Walther, D. (2010) Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res., 38, 970-980.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 970-980
    • Schudoma, C.1    May, P.2    Nikiforova, V.3    Walther, D.4
  • 41
    • 25444455574 scopus 로고    scopus 로고
    • Full cyclic coordinate descent: Solving the protein loop closure problem in Calpha space
    • Boomsma, W. and Hamelryck, T. (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics, 6, 159.
    • (2005) BMC Bioinformatics , vol.6 , pp. 159
    • Boomsma, W.1    Hamelryck, T.2
  • 45
    • 38549138271 scopus 로고    scopus 로고
    • Smc5/6: A link between DNA repair and unidirectional replication?
    • DOI 10.1038/nrm2309, PII NRM2309
    • Murray, J.M. and Carr, A.M. (2008) Smc5/6: a link between DNA repair and unidirectional replication? Nat. Rev. Mol. Cell Biol., 9, 177-182. (Pubitemid 351158909)
    • (2008) Nature Reviews Molecular Cell Biology , vol.9 , Issue.2 , pp. 177-182
    • Murray, J.M.1    Carr, A.M.2
  • 47
    • 33745529250 scopus 로고    scopus 로고
    • Two conformations of a crystalline human tRNA synthetase-tRNA complex: Implications for protein synthesis
    • DOI 10.1038/sj.emboj.7601154, PII 7601154
    • Yang, X.L., Otero, F.J., Ewalt, K.L., Liu, J., Swairjo, M.A., Kohrer, C., Rajbhandary, U.L., Skene, R.J., McRee, D.E. and Schimmel, P. (2006) Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J., 25, 2919-2929. (Pubitemid 43980398)
    • (2006) EMBO Journal , vol.25 , Issue.12 , pp. 2919-2929
    • Yang, X.-L.1    Otero, F.J.2    Ewalt, K.L.3    Liu, J.4    Swairjo, M.A.5    Kohrer, C.6    Rajbhandary, U.L.7    Skene, R.J.8    McRee, D.E.9    Schimmel, P.10
  • 48
    • 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
  • 50
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • DOI 10.1093/nar/gkg529
    • Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460. (Pubitemid 37442176)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3450-3460
    • Yang, H.1    Jossinet, F.2    Leontis, N.3    Chen, L.4    Westbrook, J.5    Berman, H.6    Westhof, E.7
  • 51
    • 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., 216-227.
    • (2010) Pac. Symp. Biocomput. , pp. 216-227
    • Flores, S.C.1    Wan, Y.2    Russell, R.3    Altman, R.B.4
  • 52
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1    Kolbe, D.L.2    Eddy, S.R.3
  • 53
    • 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, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 55
    • 33745237318 scopus 로고    scopus 로고
    • The probable structure of the protamine-DNA complex
    • DOI 10.1016/j.jtbi.2005.12.015, PII S0022519305005473
    • Biegeleisen, K. (2006) The probable structure of the protamine-DNA complex. J. Theor. Biol., 241, 533-540. (Pubitemid 44038741)
    • (2006) Journal of Theoretical Biology , vol.241 , Issue.3 , pp. 533-540
    • Biegeleisen, K.1
  • 56
    • 77951643739 scopus 로고    scopus 로고
    • Atomic accuracy in predicting and designing noncanonical RNA structure
    • Das, R., Karanicolas, J. and Baker, D. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods, 7, 291-294.
    • (2010) Nat. Methods , vol.7 , pp. 291-294
    • Das, R.1    Karanicolas, J.2    Baker, D.3
  • 57
    • 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
  • 58
    • 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
  • 59
    • 38549083634 scopus 로고    scopus 로고
    • RNAJunction: A database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
    • DOI 10.1093/nar/gkm842
    • Bindewald, E., Hayes, R., Yingling, Y.G., Kasprzak, W. and Shapiro, B.A. (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res., 36, D392-D397. (Pubitemid 351149755)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Bindewald, E.1    Hayes, R.2    Yingling, Y.G.3    Kasprzak, W.4    Shapiro, B.A.5
  • 61
    • 38549140073 scopus 로고    scopus 로고
    • RNA FRABASE version 1.0: An engine with a database to search for the three-dimensional fragments within RNA structures
    • DOI 10.1093/nar/gkm786
    • Popenda, M., Blazewicz, M., Szachniuk, M. and Adamiak, R.W. (2008) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res., 36, D386-D391. (Pubitemid 351149754)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Popenda, M.1    Blazewicz, M.2    Szachniuk, M.3    Adamiak, R.W.4
  • 62
    • 0037271276 scopus 로고    scopus 로고
    • Fold recognition methods
    • Godzik, A. (2003) Fold recognition methods. Methods Biochem. Anal., 44, 525-546.
    • (2003) Methods Biochem. Anal , vol.44 , pp. 525-546
    • Godzik, A.1
  • 63
    • 44349140636 scopus 로고    scopus 로고
    • R-Coffee: A method for multiple alignment of non-coding RNA
    • Wilm, A., Higgins, D.G. and Notredame, C. (2008) R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36, e52.
    • (2008) Nucleic Acids Res , vol.36
    • Wilm, A.1    Higgins, D.G.2    Notredame, C.3
  • 64
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 65
    • 33749412683 scopus 로고    scopus 로고
    • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
    • Dowell, R.D. and Eddy, S.R. (2006) Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. BMC Bioinformatics, 7, 400.
    • (2006) BMC Bioinformatics , vol.7 , pp. 400
    • Dowell, R.D.1    Eddy, S.R.2
  • 66
    • 77954269050 scopus 로고    scopus 로고
    • Freiburg RNA Tools: A web server integrating IntaRNA, ExpaRNA and LosARNA
    • Smith, C., Heyne, S., Richter, A.S., Will, S. and Backofen, R. (2010) Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LosARNA. Nucleic Acids Res., 38, 373-377.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 373-377
    • Smith, C.1    Heyne, S.2    Richter, A.S.3    Will, S.4    Backofen, R.5
  • 67
    • 34249699636 scopus 로고    scopus 로고
    • Multiple structural alignment and clustering of RNA sequences
    • DOI 10.1093/bioinformatics/btm049
    • Torarinsson, E., Havgaard, J.H. and Gorodkin, J. (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics, 23, 926-932. (Pubitemid 47050578)
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 926-932
    • Torarinsson, E.1    Havgaard, J.H.2    Gorodkin, J.3
  • 68
    • 25444433586 scopus 로고    scopus 로고
    • Accelerated probabilistic inference of RNA structure evolution
    • Holmes, I. (2005) Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics, 6, 73.
    • (2005) BMC Bioinformatics , vol.6 , pp. 73
    • Holmes, I.1
  • 70
    • 0001962564 scopus 로고    scopus 로고
    • The molecular modeling toolkit: A new approach to molecular simulations
    • Hinsen, K. (2000) The molecular modeling toolkit: a new approach to molecular simulations. J. Comp. Chem., 21, 79-85.
    • (2000) J. Comp. Chem , vol.21 , pp. 79-85
    • Hinsen, K.1
  • 71
    • 27844442779 scopus 로고    scopus 로고
    • Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
    • DOI 10.1002/jcc.20312
    • Johnston, M.A., Galvan, I.F. and Villa-Freixa, J. (2005) Framework-based design of a new all-purpose molecular simulation application: the Adun simulator. J. Comput. Chem., 26, 1647-1659. (Pubitemid 41641694)
    • (2005) Journal of Computational Chemistry , vol.26 , Issue.15 , pp. 1647-1659
    • Johnston, M.A.1    Galvan, I.F.2    Villa-Freixa, J.3
  • 72
    • 33846103677 scopus 로고    scopus 로고
    • YUP: A molecular simulation program for coarse-grained and multiscaled models
    • Tan, R.K.Z., Petrov, A.S. and Harvey, S.C. (2006) YUP: A molecular simulation program for coarse-grained and multiscaled models. J Chem. Theory Comput., 2, 529-540.
    • (2006) J Chem. Theory Comput , vol.2 , pp. 529-540
    • Tan, R.K.Z.1    Petrov, A.S.2    Harvey, S.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.