Improved prediction of RNA tertiary structure with insights into native state dynamics

John Paul Bida, L. James Maher

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)385-393
Number of pages9
Issue number3
StatePublished - Mar 2012


  • Aptamer
  • Conformation
  • Monte Carlo
  • Noncanonical base-pairing
  • RNA tertiary structure prediction

ASJC Scopus subject areas

  • Molecular Biology


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