The identification of novel RNA structural motifs using COMPADRES: an automated approach to structural discovery

Nucleic Acids Res. 2004 Dec 17;32(22):6650-9. doi: 10.1093/nar/gkh1002. Print 2004.


Recurring RNA structural motifs are important sites of tertiary interaction and as such, are integral to RNA macromolecular structure. Although numerous RNA motifs have been classified and characterized, the identification of new motifs is of great interest. In this study, we discovered four new conformationally recurring motifs: the pi-turn, the Omega-turn, the alpha-loop and the C2'-endo mediated flipped adenosine motif. Not only do they have complex and interesting structures, but they participate in contacts of high biological significance. In a first for the RNA field, new motifs were discovered by a fully automated algorithm. This algorithm, COMPADRES, utilized a reduced representation of the RNA backbone and was highly successful at discerning unique structural relationships. This study also shows that recurring RNA substructures are not necessarily accompanied by consistent primary or secondary structure.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine / chemistry
  • Algorithms*
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA / chemistry*
  • Software*


  • RNA
  • Adenosine