Automated RNA 3D Structure Prediction with RNAComposer

  • Marcin Biesiada
  • Katarzyna J. Purzycka
  • Marta Szachniuk
  • Jacek Blazewicz
  • Ryszard W. Adamiak
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

RNA tertiary structure RNA three-dimensional structure RNA modeling 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Marcin Biesiada
    • 1
    • 2
  • Katarzyna J. Purzycka
    • 2
  • Marta Szachniuk
    • 1
    • 3
  • Jacek Blazewicz
    • 1
    • 3
  • Ryszard W. Adamiak
    • 1
    • 2
  1. 1.European Center for Bioinformatics and Genomics, Institute of Computing SciencePoznan University of TechnologyPoznanPoland
  2. 2.Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
  3. 3.Department of Bioinformatics, Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland

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