Skip to main content
SpringerLink
Log in

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

  • Conference paper
Bioinformatics Research and Applications (ISBRA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6674))

Included in the following conference series:

  • 1122 Accesses

Abstract

The recent interest in function of various RNA structures, reflected in the growth of solved RNA structures in PDB, calls for methods for effective and efficient similarity search in RNA structural databases. Here, we propose a method called SETTER (RNA SEcondary sTructure-based TERtiary structure similarity) based on partitioning of RNA structures into so-called generalized secondary structure units (GSSU). We introduce a fast similarity method exploiting RMSD-based algorithm allowing to assess distance to a pair of GSSU, and a method for aggregating these partial distances into a final distance corresponding to structural similarity of the examined RNA structures. Our algorithm yields not only the distance but also a superposition allowing to visualize the structural similarity. Comparative experiments show that our proposed method is competitive with the best existing solutions, both in terms of effectiveness and efficiency.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Baldi, P., Brunak, S.A., Chauvin, Y., Andersen, C.A.F., Nielsen, H.: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5), 412–424 (2000)

    Article  Google Scholar 

  2. Bartel, D.: MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116(2), 281–297 (2004)

    Article  Google Scholar 

  3. Bauer, R.A., Rother, K., Moor, P., Reinert, K., Steinke, T., Bujnicki, J.M., Preissner, R.: Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors. Algorithms 2(2), 692–709 (2009)

    Article  MathSciNet  Google Scholar 

  4. Berman, H.M., Westbrook, J.D., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Res. 28(1), 235–242 (2000)

    Article  Google Scholar 

  5. Brion, P., Westhof, E.: Hierarchy and dynamics of rna folding. Annual Review of Biophysics and Biomolecular Structure 26(1), 113–137 (1997)

    Article  Google Scholar 

  6. Capriotti, E., Marti-Renom, M.A.: Rna structure alignment by a unit-vector approach. Bioinformatics 118, i112–i118 (2008)

    Article  Google Scholar 

  7. Carter, R.J., Dubchak, I., Holbrook, S.R.: A computational approach to identify genes for functional RNAs in genomic sequences. Nucl. Acids Res. 29(19), 3928–3938 (2001)

    Google Scholar 

  8. Chang, Y.-F., Huang, Y.-L., Lu, C.L.: Sarsa: a web tool for structural alignment of rna using a structural alphabet. Nucleic Acids Res. 36(Web-Server-Issue), 19–24 (2008)

    Article  Google Scholar 

  9. Chworos, A., Severcan, I., Koyfman, A.Y., Weinkam, P., Oroudjev, E., Hansma, H.G., Jaeger, L.: Building programmable jigsaw puzzles with RNA. Science 306(5704), 2068–2072 (2004)

    Article  Google Scholar 

  10. Ditzler, M.A., Otyepka, M., Šponer, J., Walter, N.G.: Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Accounts of Chemical Research 43(1), 40–47 (2010)

    Article  Google Scholar 

  11. Dorsett, Y., Tuschl, T.: siRNAs: applications in functional genomics and potential as therapeutics. Nature Rev. Drug Discovery 3, 318–329 (2004)

    Article  Google Scholar 

  12. Doudna, J.A.: Structural genomics of RNA. Nat. Struct. Biol. 7 suppl., 954–956 (2000)

    Article  Google Scholar 

  13. Dror, O., Nussinov, R., Wolfson, H.: ARTS: alignment of RNA tertiary structures. Bioinformatics 21(suppl. 2) (September 2005)

    Google Scholar 

  14. Dror, O., Nussinov, R., Wolfson, H.J.: The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res. 34(Web Server issue) (July 2006)

    Google Scholar 

  15. Ferrè, F., Ponty, Y., Lorenz, W.A., Clote, P.: 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(Web-Server-Issue), 659–668 (2007)

    Article  Google Scholar 

  16. Hannon, G.J., Rivas, F.V., Murchison, E.P., Steitz, J.A.: The expanding universe of noncoding RNAs. Cold Spring Harb. Symp. Quant Biol. 71, 551–564 (2006)

    Article  Google Scholar 

  17. Hendrix, D.K., Brenner, S.E., Holbrook, S.R.: RNA structural motifs: building blocks of a modular biomolecule. Q. Rev. Biophys. 38(3), 221–243 (2005)

    Article  Google Scholar 

  18. Jaeger, L., Westhof, E., Leontis, N.B.: TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 29(2), 455–463 (2001)

    Article  Google Scholar 

  19. Kabsch, W.: A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 32(5), 922–923 (1976)

    Article  Google Scholar 

  20. Klosterman, P.S., Tamura, M., Holbrook, S.R., Brenner, S.E.: SCOR: a Structural Classification of RNA database. Nucleic Acids Res. 30(1), 392–394 (2002)

    Article  Google Scholar 

  21. Kolodny, R., Linial, N.: Approximate protein structural alignment in polynomial time. Proc. Natl. Acad. Sci. USA 101(33), 12201–12206 (2004)

    Article  Google Scholar 

  22. Leontis, N.B., Westhof, E.: Geometric nomenclature and classification of RNA base pairs. RNA 7(4), 499–512 (2001)

    Article  Google Scholar 

  23. Lu, X.-J., Olson, W.K.: 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols 3(7), 1213–1227 (2008)

    Article  Google Scholar 

  24. Lu, X.-J.J., Olson, W.K.: 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31(17), 5108–5121 (2003)

    Article  Google Scholar 

  25. Shapiro, B., Yingling, Y., Kasprzak, W., Bindewald, E.: Bridging the gap in RNA structure prediction. Current Opinion in Structural Biology 17(2), 157–165 (2007)

    Article  Google Scholar 

  26. Staple, D.W., Butcher, S.E.: Pseudoknots: RNA structures with diverse functions. PLoS Biology 3(6) (June 2005)

    Google Scholar 

  27. Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R., Brenner, S.E., Holbrook, S.R.: SCOR: Structural Classification of RNA, version 2.0. Nucleic Acids Res. 32(Database issue) (January 2004)

    Google Scholar 

  28. Wang, C.-W., Chen, K.-T., Lu, C.L.: iPARTS: an improved tool of pairwise alignment of rna tertiary structures. Nucleic Acids Res. 38(suppl.), W340–W347 (2010)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. FMP, Department of Software Engineering, Charles University in Prague, Malostranské nám. 25, 118 00, Prague, Czech Republic

    David Hoksza

  2. Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, Technická 5, 166 28, Prague, Czech Republic

    Daniel Svozil

Authors
  1. David Hoksza
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel Svozil
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, 77843-3112, College Station, TX, USA

    Jianer Chen

  2. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

  3. Department of Computer Science, Georgia State University, 30303, Atlanta, GA, USA

    Alexander Zelikovsky

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Hoksza, D., Svozil, D. (2011). SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. In: Chen, J., Wang, J., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2011. Lecture Notes in Computer Science(), vol 6674. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21260-4_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-21260-4_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-21259-8

  • Online ISBN: 978-3-642-21260-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation