Automated RNA 3D Structure Prediction with RNAComposer

Marcin Biesiada; Katarzyna J Purzycka; Marta Szachniuk; Jacek Blazewicz; Ryszard W Adamiak

doi:10.1007/978-1-4939-6433-8_13

Automated RNA 3D Structure Prediction with RNAComposer

Methods Mol Biol. 2016:1490:199-215. doi: 10.1007/978-1-4939-6433-8_13.

Authors

Marcin Biesiada^{1

2}, Katarzyna J Purzycka², Marta Szachniuk^{1

3}, Jacek Blazewicz^{1

3}, Ryszard W Adamiak^{4

5}

Affiliations

¹ European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
² Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
³ Department of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
⁴ European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland. adamiakr@ibch.poznan.pl.
⁵ Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. adamiakr@ibch.poznan.pl.

PMID: 27665601
DOI: 10.1007/978-1-4939-6433-8_13

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.

Keywords: RNA modeling; RNA tertiary structure; RNA three-dimensional structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Models, Molecular*
Nucleic Acid Conformation*
RNA / chemistry*
Software*
User-Computer Interface
Web Browser

Substances

RNA