RBinds: A user-friendly server for RNA binding site prediction


RNA performs various biological functions by interacting with other molecules. The knowledge of RNA binding sites is essential for the understanding of RNA-protein or RNA-ligand complex structures and their mechanism. Here, we developed the RBinds, a user-friendly web server, to predict the RNA binding site using a simple graphical user interface. Some advanced features implemented in RBinds are (1) transforming the RNA structure to a network automatically; (2) analyzing the structural network properties to predict binding site; (3) constructing one annotated force-directed network; (4) providing visualization tool for users to scale and rotate the structure; (5) offering the related tools to predict or simulate RNA structures. RBinds web server is a reliable and user-friendly tool and facilitates the RNA binding site study without installing programs locally. See the Tutorial module for details.

Input an RNA tertiary structure in PDB format.



Example of the input RNA structure (Unbound RNA structure from RNAbenchmark1.0 database)
Example of the prediction result (nodes, edges, and sites)
 1. The "nodes" module contains the nucleotide names, closeness and degree values.
2. The "edges" module contains the information of connected nodes.
3. The "sites" module contains nucleotide name, closeness and degree values for predicted binding sites.
Zhao Group at Central China Normal University