PairAnalyzer: Extracting and Visualizing RNA Structure Elements Formed by Base Pairing

  • Daeho Lim
  • Kyungsook Han
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3036)


Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even for small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA, due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The algorithms were implemented in to a web-based program called PairAnalyzer. The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins. PairAnalyzer is accessible at


Base Pair Protein Data Bank Protein Data Bank File Base Pair Rule Mining Biological Data 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000)CrossRefGoogle Scholar
  2. 2.
    Tinoco, Jr.: The RNA World (R. F. Gesteland, J. F. Atkins, Eds.), pp. 603–607. Cold Spring Harbor Laboratory Press (1993)Google Scholar
  3. 3.
    McDonald, I.K., Thornton, J.M.: Satisfying Hydrogen Bonding Potential in Proteins. J. Mol.Biol. 238, 777–793 (1994)CrossRefGoogle Scholar
  4. 4.
    Stryer, L.: Biochemstry, 4th edn. W.H. Freeman, New York (1995)Google Scholar
  5. 5.
    Akmaev, V.R., Kelley, S.T., Stormo, G.D.: Phylogenetically enhanced statistical tools for RNA structure prediction. Bioinformatics 16, 501–512 (2000)CrossRefGoogle Scholar
  6. 6.
  7. 7.
    Kraulis, P.J.: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. Journal of Applied Crystallography 24, 946–950 (1991)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Daeho Lim
    • 1
  • Kyungsook Han
    • 1
  1. 1.School of Computer Science and EngineeringInha UniversityInchonKorea

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