title: Structure clustering features on the Sfold Web server.
abstract: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure often lies outside of the cluster containing the structure determined by comparative sequence analysis. We have developed procedures to characterize and visualize the Boltzmann-weighted ensemble, and have made them available on the Sfold Web server. The new features on the Web server include clustering statistics, ensemble and cluster centroids, multi-dimensional scaling display and energy landscape representation of the Boltzmann-weighted ensemble.
  
  
  BACKGROUND
  http://sfold.wadsworth.org; http://www.bioinfo.rpi.edu/applications/sfold
  
  
  BACKGROUND
  chanc@wadsworth.org.
authors.affiliation: Bioinformatics Center, Wadsworth Center, New York State Department of Health, Albany, 12208, USA. chanc@wadsworth.org
authors.forename: Chi Yu
authors.initials: CY
authors.lastname: Chan
authors.forename: Charles E
authors.initials: CE
authors.lastname: Lawrence
authors.forename: Ye
authors.initials: Y
authors.lastname: Ding
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016000:Cluster Analysis; D003198:Computer Simulation; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000032:analysis* / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA