Journal Article

Automated 3D structure composition for large RNAs

Mariusz Popenda, Marta Szachniuk, Maciej Antczak, Katarzyna J. Purzycka, Piotr Lukasiak, Natalia Bartol, Jacek Blazewicz and Ryszard W. Adamiak

in Nucleic Acids Research

Volume 40, issue 14, pages e112-e112
Published in print August 2012 | ISSN: 0305-1048
Published online April 2012 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gks339

More Like This

Show all results sharing these subjects:

  • Chemistry
  • Biochemistry
  • Bioinformatics and Computational Biology
  • Genetics and Genomics
  • Molecular and Cell Biology

GO

Show Summary Details

Preview

Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.

Journal Article.  6574 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.