title: TBI server: a web server for predicting ion effects in RNA folding.
abstract: BACKGROUND
  Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects.
  
  
  RESULTS
  The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects.
  
  
  CONCLUSIONS
  By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.
authors: Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA; Department of Physics, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China.
authors: Yuhong
authors: Y
authors: Zhu
authors: Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
authors: Zhaojian
authors: Z
authors: He
authors: Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
authors: Shi-Jie
authors: SJ
authors: Chen
mesh_terms: D000465:Algorithms; D006801:Humans; D020407:Internet; D007477:Ions; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D012984:Software
chemical_list: D007477:Ions; D012313:RNA