MCTBI: a web server for predicting metal ion effects in RNA structures
- 1Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- 2Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
- 3School of Science and Technology, Zhejiang International Studies University, Hangzhou 310012, China
- Corresponding author: chenshi{at}missouri.edu
Abstract
Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures.
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.060947.117.
- Received January 29, 2017.
- Accepted April 16, 2017.
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