Basin Hopping Graph: A computational framework to characterize RNA folding landscapes

Marcel Kucharik, Ivo Hofacker, Peter Stadler, Jing Qin

Research output: Contribution to journalJournal articleResearchpeer-review


Motivation 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.

Availability The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from
Original languageEnglish
Issue number14
Pages (from-to)2009-2017
Publication statusPublished - 15. Jul 2014

Bibliographical note

tjek om den er med i BFI høst 2014, ellers skal den rykkes/atm


  • Algorithms
  • Computational Biology/methods
  • Kinetics
  • RNA Folding
  • RNA/chemistry


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