Abstract
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 mechanisms. However, the RNA binding site prediction study requires tedious programming scripts and manual handling. One user-friendly bioinformatics tool for RNA binding site prediction has been missing. This limitation motivated us to develop 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 a 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. RBinds is freely accessible at http://zhaoserver.com.cn/RBinds/RBinds.html.