title: Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
abstract: BACKGROUND
  RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information.
  
  
  RESULTS
  We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are 'energetically favorable'. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms.
  
  
  METHODS
  The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http://www.tbi.univie.ac.at/bhg.html.
authors.affiliation: Institute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark.
authors.forename: Marcel
authors.initials: M
authors.lastname: Kucharík
authors.affiliation: Institute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark.
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.affiliation: Institute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, Univer
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: Institute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, DenmarkInstitute for Theoretical Chemistry and Research group BCB, Faculty of Computer Science, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria, Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark, Department of Computer Science & IZBI & iDiv & LIFE, Härtelstraße 16-18, D-04107 University of Leipzig, Max Planck Institute for Mathematics in the Sciences and Fraunhofer Institute IZI, Leipzig, Germany, Santa Fe Institute, Santa Fe, NM 87501, USA and Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark.
authors.forename: Jing
authors.initials: J
authors.lastname: Qin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D007700:Kinetics; D012313:RNA / Q000737:chemistry; D059370:RNA Folding
chemical_list: D012313:RNA