title: Vfold: a web server for RNA structure and folding thermodynamics prediction.
abstract: BACKGROUND
  The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies.
  
  
  RESULTS
  The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.
  
  
  CONCLUSIONS
  The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".
authors.affiliation: Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Peinan
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Department of Physics and Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America.
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen
mesh_terms: D030562:Databases, Protein; D006801:Humans; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D020871:RNA Stability; D012984:Software; D013816:Thermodynamics
chemical_list: D012313:RNA