title: Predicting folding pathways between RNA conformational structures guided by RNA stacks.
abstract: BACKGROUND
  Accurately predicting low energy barrier folding pathways between conformational secondary structures of an RNA molecule can provide valuable information for understanding its catalytic and regulatory functions. Most existing heuristic algorithms guide the construction of folding pathways by free energies of intermediate structures in the next move during the folding. However due to the size and ruggedness of RNA energy landscape, energy-guided search can become trapped in local optima.
  
  
  RESULTS
  In this paper, we propose an algorithm that guides the construction of folding pathways through the formation and destruction of RNA stacks. Guiding the construction of folding pathways by coarse grained movements of RNA stacks can help reduce the search space and make it easier to jump out of local optima. RNAEAPath is able to find lower energy barrier folding pathways between secondary structures of conformational switches and outperforms the existing heuristic algorithms in most test cases.
  
  
  CONCLUSIONS
  RNAEAPath provides an alternate approach for predicting low-barrier folding pathways between RNA conformational secondary structures. The source code of RNAEAPath and the test data sets are available at http://genome.ucf.edu/RNAEAPath.
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Li
authors.forename: Shaojie
authors.initials: S
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics; D059370:RNA Folding; D013816:Thermodynamics
chemical_list: D012313:RNA