메뉴 건너뛰기




Volumn 42, Issue D1, 2014, Pages

RNA Bricks - A database of RNA 3D motifs and their interactions

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER INTERFACE; DATA BASE; INFORMATION PROCESSING; INTERACTIONS WITH RNA; PRIORITY JOURNAL; PROTEIN DATA BANK; RNA BRICKS; RNA STRUCTURE; BASE PAIRING; COMPLEX FORMATION; CORRELATION COEFFICIENT; DOUBLE STRANDED DNA BREAK; GENE CLUSTER; HOMOLOGOUS RECOMBINATION; HUMAN; HYDROGEN BOND; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY; CHEMISTRY; INTERNET; NUCLEIC ACID DATABASE; NUCLEOTIDE MOTIF;

EID: 84891810008     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1084     Document Type: Article
Times cited : (69)

References (53)
  • 1
    • 0035423087 scopus 로고    scopus 로고
    • The kink-turn: A new RNA secondary structure motif
    • Klein, D.J., Schmeing, T.M., Moore, P.B. and Steitz, T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
    • (2001) EMBO J. , vol.20 , pp. 4214-4221
    • Klein, D.J.1    Schmeing, T.M.2    Moore, P.B.3    Steitz, T.A.4
  • 2
    • 0036760665 scopus 로고    scopus 로고
    • Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules
    • Leontis, N.B., Stombaugh, J. and Westhof, E. (2002) Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie, 84, 961-973.
    • (2002) Biochimie , vol.84 , pp. 961-973
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 3
    • 13544255744 scopus 로고    scopus 로고
    • The identification of novel RNA structural motifs using COMPADRES: An automated approach to structural discovery
    • Wadley, L.M. and Pyle, A.M. (2004) The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery. Nucleic Acids Res., 32, 6650-6659.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6650-6659
    • Wadley, L.M.1    Pyle, A.M.2
  • 4
    • 0038475947 scopus 로고    scopus 로고
    • On the occurrence of the T-loop RNA folding motif in large RNA molecules
    • Krasilnikov, A.S. (2003) On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA, 9, 640-643.
    • (2003) RNA , vol.9 , pp. 640-643
    • Krasilnikov, A.S.1
  • 5
    • 0036717041 scopus 로고    scopus 로고
    • Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs
    • Nagaswamy, U. and Fox, G.E. (2002) Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA, 8, 1112-1119.
    • (2002) RNA , vol.8 , pp. 1112-1119
    • Nagaswamy, U.1    Fox, G.E.2
  • 6
    • 84255189090 scopus 로고    scopus 로고
    • The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks
    • Butcher, S. and Pyle, A. (2011) The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Accounts Chem. Res., 44, 1302-1311.
    • (2011) Accounts Chem. Res. , vol.44 , pp. 1302-1311
    • Butcher, S.1    Pyle, A.2
  • 8
    • 80051989609 scopus 로고    scopus 로고
    • Understanding the transcriptome through RNA structure
    • Wan, Y., Kertesz, M. and Spitale, R. (2011) Understanding the transcriptome through RNA structure. Nat. Rev. Genet., 12, 641-655.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 641-655
    • Wan, Y.1    Kertesz, M.2    Spitale, R.3
  • 9
    • 84966380935 scopus 로고    scopus 로고
    • Comparative analysis of the higher-order structure of RNA
    • Russell, R. (ed.) Springer, New York
    • Gutell, R. (2013) Comparative analysis of the higher-order structure of RNA. In: Russell, R. (ed.), Biophysics of RNA Folding. Springer, New York, pp. 11-22.
    • (2013) Biophysics of RNA Folding , pp. 11-22
    • Gutell, R.1
  • 11
    • 77951796655 scopus 로고    scopus 로고
    • RNA FRABASE 2.0: An advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
    • Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E.K., Blazewicz, J. and Adamiak, R.W. (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinform., 11, 231.
    • (2010) BMC Bioinform. , vol.11 , pp. 231
    • Popenda, M.1    Szachniuk, M.2    Blazewicz, M.3    Wasik, S.4    Burke, E.K.5    Blazewicz, J.6    Adamiak, R.W.7
  • 12
    • 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
  • 13
    • 84859379964 scopus 로고    scopus 로고
    • RNA CoSSMos: Characterization of Secondary Structure Motifs-A searchable database of secondary structure motifs in RNA three-dimensional structures
    • Vanegas, P.L., Hudson, G.A., Davis, A.R., Kelly, S.C., Kirkpatrick, C.C. and Znosko, B.M. (2012) RNA CoSSMos: Characterization of Secondary Structure Motifs-A searchable database of secondary structure motifs in RNA three-dimensional structures. Nucleic Acids Res., 40, D439-D444.
    • (2012) Nucleic Acids Res. , vol.40
    • Vanegas, P.L.1    Hudson, G.A.2    Davis, A.R.3    Kelly, S.C.4    Kirkpatrick, C.C.5    Znosko, B.M.6
  • 14
    • 0035906639 scopus 로고    scopus 로고
    • Quantitative analysis of nucleic acid three-dimensional structures
    • Gendron, P., Lemieux, S. and Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
    • (2001) J. Mol. Biol. , vol.308 , pp. 919-936
    • Gendron, P.1    Lemieux, S.2    Major, F.3
  • 15
    • 38549083634 scopus 로고    scopus 로고
    • RNAJunction: A database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
    • 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.
    • (2008) Nucleic Acids Res. , vol.36
    • Bindewald, E.1    Hayes, R.2    Yingling, Y.G.3    Kasprzak, W.4    Shapiro, B.A.5
  • 16
    • 55549130811 scopus 로고    scopus 로고
    • Analysis and classification of RNA tertiary structures
    • Abraham, M., Dror, O., Nussinov, R. and Wolfson, H.J. (2008) Analysis and classification of RNA tertiary structures. RNA, 14, 2274-2289.
    • (2008) RNA , vol.14 , pp. 2274-2289
    • Abraham, M.1    Dror, O.2    Nussinov, R.3    Wolfson, H.J.4
  • 17
    • 27544504678 scopus 로고    scopus 로고
    • ARTS: Alignment of RNA tertiary structures
    • Dror, O., Nussinov, R. and Wolfson, H.J. (2005) ARTS: alignment of RNA tertiary structures. Bioinformatics, 21, 47-53.
    • (2005) Bioinformatics , vol.21 , pp. 47-53
    • Dror, O.1    Nussinov, R.2    Wolfson, H.J.3
  • 18
    • 84884679567 scopus 로고    scopus 로고
    • Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
    • Petrov, A.I., Zirbel, C.L. and Leontis, N.B. (2013) Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. RNA, 19, 1327-1340.
    • (2013) RNA , vol.19 , pp. 1327-1340
    • Petrov, A.I.1    Zirbel, C.L.2    Leontis, N.B.3
  • 19
    • 79960024822 scopus 로고    scopus 로고
    • WebFR3D-A server for finding, aligning and analyzing recurrent RNA 3D motifs
    • Petrov, A.I., Zirbel, C.L. and Leontis, N.B. (2011) WebFR3D-A server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res., 39, W50-W55.
    • (2011) Nucleic Acids Res. , vol.39
    • Petrov, A.I.1    Zirbel, C.L.2    Leontis, N.B.3
  • 22
    • 84879837060 scopus 로고    scopus 로고
    • Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2
    • Santos, N., Zhu, J., Donohue, J.P., Korostelev, A.A. and Noller, H.F. (2013) Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2. Structure, 21, 1258-1263.
    • (2013) Structure , vol.21 , pp. 1258-1263
    • Santos, N.1    Zhu, J.2    Donohue, J.P.3    Korostelev, A.A.4    Noller, H.F.5
  • 23
    • 77957350062 scopus 로고    scopus 로고
    • Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculum
    • Rupp, B. (2010) Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculum. J. Appl. Crystallogr., 43, 1242-1249.
    • (2010) J. Appl. Crystallogr. , vol.43 , pp. 1242-1249
    • Rupp, B.1
  • 24
    • 65249095696 scopus 로고    scopus 로고
    • RNA 3D structural motifs: Definition, identification, annotation, and database searching
    • Walter, N.G., Woodson, S.A. and Batey, R.T. (eds) Springer, Berlin Heidelberg
    • Nasalean, L., Stombaugh, J., Zirbel, C.L. and Leontis, N.B. (2009) RNA 3D structural motifs: definition, identification, annotation, and database searching. In: Walter, N.G., Woodson, S.A. and Batey, R.T. (eds), Non-Protein Coding RNAs. Springer, Berlin Heidelberg, pp. 1-26.
    • (2009) Non-Protein Coding RNAs , pp. 1-26
    • Nasalean, L.1    Stombaugh, J.2    Zirbel, C.L.3    Leontis, N.B.4
  • 25
    • 0036111645 scopus 로고    scopus 로고
    • The Computational Crystallography Toolbox: Crystallographic algorithms in a reusable software framework
    • Grosse-Kunstleve, R.W., Sauter, N.K., Moriarty, N.W. and Adams, P.D. (2002) The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Crystallogr., 35, 126-136.
    • (2002) J. Appl. Crystallogr. , vol.35 , pp. 126-136
    • Grosse-Kunstleve, R.W.1    Sauter, N.K.2    Moriarty, N.W.3    Adams, P.D.4
  • 26
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K., Denise, A. and Ponty, Y. (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 29
    • 40449086374 scopus 로고    scopus 로고
    • From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
    • Smit, S., Rother, K., Heringa, J. and Knight, R. (2008) From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. RNA, 14, 410-416.
    • (2008) RNA , vol.14 , pp. 410-416
    • Smit, S.1    Rother, K.2    Heringa, J.3    Knight, R.4
  • 30
    • 0014567146 scopus 로고
    • An algorithm for finding a fundamental set of cycles of a graph
    • Paton, K. (1969) An algorithm for finding a fundamental set of cycles of a graph. Commun. ACM, 12, 514-518.
    • (1969) Commun. ACM , vol.12 , pp. 514-518
    • Paton, K.1
  • 31
    • 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
  • 32
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I. and Thornton, J. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.1    Thornton, J.2
  • 33
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J.M., Lovell, S.C., Richardson, J.S. and Richardson, D.C. (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol., 285, 1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 34
    • 0043123152 scopus 로고    scopus 로고
    • Tools for the automatic identification and classification of RNA base pairs
    • Yang, H. (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
  • 35
    • 36448954303 scopus 로고    scopus 로고
    • FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
    • Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A. and Leontis, N.B. (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    Zirbel, C.L.2    Stombaugh, J.3    Mokdad, A.4    Leontis, N.B.5
  • 36
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis, N.B., Stombaugh, J. and Westhof, E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3497-3531
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3
  • 37
    • 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
  • 40
    • 0030498233 scopus 로고    scopus 로고
    • XdlMAPMAN and xdlDATAMAN-programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets
    • Kleywegt, G.J. and Jones, T.A. (1996) xdlMAPMAN and xdlDATAMAN-programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr., 52, 826-828.
    • (1996) Acta Crystallogr. D Biol. Crystallogr. , vol.52 , pp. 826-828
    • Kleywegt, G.J.1    Jones, T.A.2
  • 42
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • The UniProt Consortium.
    • The UniProt Consortium. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
    • (2013) Nucleic Acids Res. , vol.41
  • 43
    • 84876554720 scopus 로고    scopus 로고
    • Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking
    • Leontis, N.B. and Westhof, E Springer, Berlin
    • Leontis, N.B. and Zirbel, C.L. (2012) Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking. In: Leontis, N.B. and Westhof, E. (eds) , RNA 3D Structure Analysis and Prediction. Springer, Berlin, pp. 281-298.
    • (2012) RNA 3D Structure Analysis and Prediction , pp. 281-298
    • Leontis, N.B.1    Zirbel, C.L.2
  • 44
    • 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
  • 45
    • 84868035651 scopus 로고    scopus 로고
    • Visualizing group II intron catalysis through the stages of splicing
    • Marcia, M. and Pyle, A.M. (2012) Visualizing group II intron catalysis through the stages of splicing. Cell, 151, 497-507.
    • (2012) Cell , vol.151 , pp. 497-507
    • Marcia, M.1    Pyle, A.M.2
  • 46
    • 84876907659 scopus 로고    scopus 로고
    • T box RNA decodes both the information content and geometry of tRNA to affect gene expression
    • Grigg, J.C., Chen, Y., Grundy, F.J., Henkin, T.M., Pollack, L. and Ke, A. (2013) T box RNA decodes both the information content and geometry of tRNA to affect gene expression. Proc. Natl Acad. Sci. USA, 110, 7240-7245.
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 7240-7245
    • Grigg, J.C.1    Chen, Y.2    Grundy, F.J.3    Henkin, T.M.4    Pollack, L.5    Ke, A.6
  • 49
    • 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
  • 50
    • 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
  • 51
    • 84863365188 scopus 로고    scopus 로고
    • Template-based and template-free modeling of RNA 3D structure: Inspirations from protein structure modeling
    • Leontis, N.B. and Westhof, E. (eds) Springer, Berlin
    • Rother, K., Rother, M., Boniecki, M., Puton, T., Tomala, K., Lukasz, P. and Bujnicki, J.M. (2012) Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling. In: Leontis, N.B. and Westhof, E. (eds), RNA 3D Structure Analysis and Prediction. Springer, Berlin, pp. 67-90.
    • (2012) RNA 3D Structure Analysis and Prediction , pp. 67-90
    • Rother, K.1    Rother, M.2    Boniecki, M.3    Puton, T.4    Tomala, K.5    Lukasz, P.6    Bujnicki, J.M.7
  • 53
    • 58849160465 scopus 로고    scopus 로고
    • Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
    • Joosten, R.P., Womack, T., Vriend, G. and Bricogne, G. (2009) Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Crystallogr. D Biol. Crystallogr., 65, 176-185.
    • (2009) Acta Crystallogr. D Biol. Crystallogr. , vol.65 , pp. 176-185
    • Joosten, R.P.1    Womack, T.2    Vriend, G.3    Bricogne, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.