title: iFoldRNA v2: folding RNA with constraints.
abstract: A key to understanding RNA function is to uncover its complex 3D structure. Experimental methods used for determining RNA 3D structures are technologically challenging and laborious, which makes the development of computational prediction methods of substantial interest. Previously, we developed the iFoldRNA server that allows accurate prediction of short (<50 nt) tertiary RNA structures starting from primary sequences. Here, we present a new version of the iFoldRNA server that permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides. This substantial increase in the server capacity is achieved by utilization of experimental information such as base-pairing and hydroxyl-radical probing. We demonstrate a significant benefit provided by integration of experimental data and computational methods.
  
  
  METHODS
  http://ifoldrna.dokhlab.org
  
  
  BACKGROUND
  dokh@unc.eu.
authors.affiliation: Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: Andrey
authors.initials: A
authors.lastname: Krokhotin
authors.affiliation: Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Houlihan
authors.affiliation: Department of Biochemistry & Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: Nikolay V
authors.initials: NV
authors.lastname: Dokholyan
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D017665:Hydroxyl Radical / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D017665:Hydroxyl Radical; D012313:RNA