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RNA Structure Determination pp 199–215Cite as

Automated RNA 3D Structure Prediction with RNAComposer

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1490))

Abstract

RNAs adopt specific structures to perform their activities and these are critical to virtually all RNA-mediated processes. Because of difficulties in experimentally assessing structures of large RNAs using NMR, X-ray crystallography, or cryo-microscopy, there is currently great demand for new high-resolution 3D structure prediction methods. Recently we reported on RNAComposer, a knowledge-based method for the fully automated RNA 3D structure prediction from a user-defined secondary structure. RNAComposer method is especially suited for structural biology users. Since our initial report in 2012, both servers, freely available at http://rnacomposer.ibch.poznan.pl and http://rnacomposer.cs.put.poznan.pl have been often visited. Therefore this chapter provides guidance for using RNAComposer and discusses points that should be considered when predicting 3D RNA structure. An application example presents current scope and limitations of RNAComposer.

*These authors contributed equally to this work.

Dedication: This work is dedicated to Professor David Shugar, one of the pioneers in the field of molecular biophysics, on the occasion of his 100th birthday anniversary.

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Acknowledgments

This work was supported by the National Science Center Poland [MAESTRO 2012/06/A/ST6/00384 (to R.W.A)] and Ministry of Science and Higher Education [0492/IP1/2013/72 (to K.J.P.)].

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    Authors and Affiliations

    1. European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland

      Marcin Biesiada, Marta Szachniuk, Jacek Blazewicz & Ryszard W. Adamiak

    2. Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

      Marcin Biesiada, Katarzyna J. Purzycka & Ryszard W. Adamiak

    3. Department of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

      Marta Szachniuk & Jacek Blazewicz

    Authors
    1. Marcin Biesiada
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    2. Katarzyna J. Purzycka
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    3. Marta Szachniuk
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    4. Jacek Blazewicz
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    5. Ryszard W. Adamiak
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    Corresponding author

    Correspondence to Ryszard W. Adamiak .

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    Editors and Affiliations

    1. Department of Chemistry and Center for RNA Biology, University of Rochester College of Arts and Sciences, Rochester, New York, USA

      Douglas H. Turner

    2. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA

      David H. Mathews

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    Biesiada, M., Purzycka, K.J., Szachniuk, M., Blazewicz, J., Adamiak, R.W. (2016). Automated RNA 3D Structure Prediction with RNAComposer. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Molecular Biology, vol 1490. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6433-8_13

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    • DOI: https://doi.org/10.1007/978-1-4939-6433-8_13

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    • Publisher Name: Humana Press, New York, NY

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