MCTBI: a web server for predicting metal ion effects in RNA structures

Abstract

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures is 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, MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. The server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acids 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 would be important for understanding RNA functions and the rational design of RNA structures.