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RNA Structure Prediction pp 263–285Cite as

RNA 3D Structure Comparison Using RNA-Puzzles Toolkit

Part of the Methods in Molecular Biology book series (MIMB,volume 2586)

Abstract

Computational modeling of RNA three-dimensional (3D) structure may help in unrevealing the molecular mechanisms of RNA molecules and in designing molecules with novel functions. An unbiased blind assessment to benchmark the computational modeling is required to understand the achievements and bottlenecks of the prediction, while a standard structure comparison protocol is necessary. RNA-Puzzles is a community-wide effort on the assessment of blind prediction of RNA tertiary structures. And RNA-Puzzles toolkit is a computational resource derived from RNA-Puzzles, which includes (i) decoy sets generated by different RNA 3D structure prediction methods; (ii) 3D structure normalization, analysis, manipulation, and visualization tools; and (iii) 3D structure comparison metric tools. In this chapter, we illustrate a standard RNA 3D structure prediction assessment protocol using the selected tools from RNA-Puzzles toolkit: rna-tools and RNA_assessment.

Key words

  • Structure comparison
  • RNA 3D structure prediction
  • Base pair
  • RNA-Puzzles

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  • DOI: 10.1007/978-1-0716-2768-6_16
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Acknowledgments

We thank Maciej Antczak, Tomasz Zok, Jakub Wiedemann, and Marta Szachniuk for collaboration in the RNA-Puzzles toolkit project. We also thank the authors of the libraries used in our programs. We thank Rhiju Das for the idea of “align all” and Wayne Dawson for sharing unpublished code for “clarna_play.” We would like to also acknowledge all users of our tools for valuable feedback.

Funding

M.M. was supported by the “Regenerative Mechanisms for Health-ReMedy” grant MAB/20172, carried out within the International Research Agendas Program of the Foundation for Polish Science cofinanced by the European Union under the European Regional Development Fund. Z.M. was supported by the Single Cell Gene Expression Atlas grant 108437/Z/15/Z from the Wellcome Trust.

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Authors and Affiliations

  1. ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Warsaw, Poland

    Marcin Magnus

  2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK

    Zhichao Miao

  3. Department of Anesthesiology, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China

    Zhichao Miao

Authors
  1. Marcin Magnus
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  2. Zhichao Miao
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Corresponding author

Correspondence to Zhichao Miao .

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Editors and Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Risa Karakida Kawaguchi

  2. Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan

    Junichi Iwakiri

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Magnus, M., Miao, Z. (2023). RNA 3D Structure Comparison Using RNA-Puzzles Toolkit. In: Karakida Kawaguchi, R., Iwakiri, J. (eds) RNA Structure Prediction. Methods in Molecular Biology, vol 2586. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2768-6_16

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  • DOI: https://doi.org/10.1007/978-1-0716-2768-6_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2767-9

  • Online ISBN: 978-1-0716-2768-6

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