WebFR3D - A server for finding, aligning and analyzing recurrent RNA 3D motifs

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Petrov, Anton I ^a   Zirbel, Craig L ^a   Leontis, Neocles B ^a  

^a BOWLING GREEN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA;

ARTICLE; COMPUTER PROGRAM; GEOMETRY; INTERNET; MATHEMATICAL COMPUTING; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN MOTIF; RNA STRUCTURE; RNA THREE DIMENSIONAL MOTIF; WEBFR3D;

INTERNET; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; RNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 79960024822     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr249     Document Type: Article

References (24)

1. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
2. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R. and Schneider, B. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
3. Rabl, J., Leibundgut, M., Ataide, S.F., Haag, A. and Ban, N. (2011) Crystal structure of the eukaryotic 40 S ribosomal subunit in complex with initiation factor 1. Science, 331, 730-736.
4. Rangan, P., Masquida, B., Westhof, E. and Woodson, S.A. (2003) Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl Acad. Sci. USA, 100, 1574-1579. (Pubitemid 36254489)
5. Cruz, J.A. and Westhof, E. (2009) The dynamic landscapes of RNA architecture. Cell, 136, 604-609.
6. Leontis, N.B. and Westhof, E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300-308. (Pubitemid 36782455)
7. 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)
8. Nasalean, L., Stombaugh, J., Zirbel, C.L. and Leontis, N.B. (2009) In Walter, N.G., Woodson, S.A. and Batey, R.T. (eds), Non-Protein Coding RNAs, Vol. 13. Springer, Berlin Heidelberg, pp. 1-26.
9. 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. (Pubitemid 350172192)
10. 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 Bioinformatics, 11, 231.
11. Lai, C.-E., Tsai, M.-Y., Liu, Y.-C., Wang, C.-W., Chen, K.-T. and Lu, C.L. (2009) FASTR3D: a fast and accurate search tool for similar RNA 3D structures. Nucleic Acids Res., 37, W287-W295.
12. Kirillova, S., Tosatto, S.C. and Carugo, O. (2010) FRASS: the web-server for RNA structural comparison. BMC Bioinformatics, 11, 327.
13. Dror, O., Nussinov, R. and Wolfson, H.J. (2006) The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res., 34, W412-W415. (Pubitemid 44529804)
14. Ferre, F., Ponty, Y., Lorenz, W.A. and Clote, P. (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-W668.
15. Chang, Y.F., Huang, Y.L. and Lu, C.L. (2008) SARSA: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res., 36, W19-W24.
16. Capriotti, E. and Marti-Renom, M.A. (2009) SARA: a server for function annotation of RNA structures. Nucleic Acids Res., 37, W260-W265.
17. Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R., Brenner, S.E. and Holbrook, S.R. (2004) SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res., 32, D182-D184. (Pubitemid 38081634)
18. Rahrig, R.R., Leontis, N.B. and Zirbel, C.L. (2010) R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Bioinformatics, 26, 2689-2697.
19. Stombaugh, J., Zirbel, C., Westhof, E. and Leontis, N. (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res., 37, 2294-2312.
20. Leontis, N.B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512. (Pubitemid 32416808)
21. Hoehndorf, R., Batchelor, C., Bittner, T., Dumontier, M., Eilbeck, K., Knight, R., Mungall, C.J., Richardson, J.S., Stombaugh, J., Westhof, E. et al. (2011) The RNA Ontology (RNAO): an ontology for integrating RNA sequence and structure data. Appl. Ontol., 6, 53-89.
22. Zirbel, C.L., Sponer, J.E., Sponer, J., Stombaugh, J. and Leontis, N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
23. Richardson, J.S., Schneider, B., Murray, L.W., Kapral, G.J., Immormino, R.M., Headd, J.J., Richardson, D.C., Ham, D., Hershkovits, E., Williams, L.D. et al. (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA, 14, 465-481. (Pubitemid 351397812)
24. 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. (Pubitemid 351397805)