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Representation, searching and discovery of patterns of bases in complex RNA structures

Harrison, A-M., South, D.R., Willett, P. and Artymiuk, P.J. (2004) Representation, searching and discovery of patterns of bases in complex RNA structures. Journal of Computer-Aided Molecular Design, 17 (8). pp. 537-549. ISSN 1573-4951

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Abstract

We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.

Item Type: Article
Copyright, Publisher and Additional Information: © 2003 Springer. This is an author produced version of a paper published in Journal of Computer-Aided Molecular Design. Uploaded in accordance with the publisher's self-archiving policy.
Keywords: graph theory, RNA structure representation, RNA tertiary structure, structural comparison
Academic Units: The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield)
The University of Sheffield > University of Sheffield Research Centres and Institutes > The Krebs Institute for Biomolecular Research (Sheffield)
The University of Sheffield > Faculty of Science (Sheffield) > School of Biological Sciences (Sheffield) > Department of Molecular Biology and Biotechnology (Sheffield)
Depositing User: Sherpa Assistant
Date Deposited: 24 Jan 2008 16:57
Last Modified: 08 Feb 2013 16:55
Published Version: http://dx.doi.org/10.1023/B:JCAM.0000004603.15856....
Status: Published
Publisher: Springer Netherlands
Refereed: Yes
Identification Number: 10.1023/B:JCAM.0000004603.15856.32
URI: http://eprints.whiterose.ac.uk/id/eprint/3592

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