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Modeling and Predicting RNA Three-Dimensional Structures

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RNA Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1269))

Abstract

Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis–Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structure databases. Further, we show how to take advantage of this knowledge to quickly and simply predict three-dimensional structures of large RNA molecules.

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Author information

Authors and Affiliations

  1. School of Computer Science, McGill University, 3480 University Street, Room 318, Montreal, QC, Canada, H3A 0E9

    Jérôme Waldispühl & Vladimir Reinharz

Authors
  1. Jérôme Waldispühl
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  2. Vladimir Reinharz
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Corresponding author

Correspondence to Jérôme Waldispühl .

Editor information

Editors and Affiliations

  1. Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research Council, University of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB), Rome, Italy

    Ernesto Picardi

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Waldispühl, J., Reinharz, V. (2015). Modeling and Predicting RNA Three-Dimensional Structures. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_6

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  • DOI: https://doi.org/10.1007/978-1-4939-2291-8_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2290-1

  • Online ISBN: 978-1-4939-2291-8

  • eBook Packages: Springer Protocols

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