title: A folding algorithm for extended RNA secondary structures.
abstract: BACKGROUND
  RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.
  
  
  RESULTS
  We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.
  
  
  BACKGROUND
  All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria. choener@tbi.inivie.ac.at
authors.forename: Christian
authors.initials: C
authors.lastname: Höner zu Siederdissen
authors.forename: Stephan H
authors.initials: SH
authors.lastname: Bernhart
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA