Tutorial

1. Home module

The Home module provides a brief introduction of the RBinds, an input box, an example of the input RNA structure, and an example of the corresponding prediction result. The input of RBinds is RNA tertiary structure in PDB format. The RNA tertiary structure can be downloaded from Protein Data Bank (PDB) database, or predicted by some RNA tertiary structure prediction computational methods, such as 3dRNA, Vflod3D, and iFoldRNA. Users can first upload the structure information and then click “Submit” to run the prediction task. If the user submits multiple RNA chains, RBinds will transform the RNAs into one network for binding site prediction. If the user submits RNA-ligand or RNA-protein complex information, RBinds will ignore the ligand or protein information. We also provide one input file example and one corresponding output file example for users to get familiar with the server.

After submitting the prediction task, the server will jump to the output page with the following results. See the Output example module for details.
(a) RNA binding site prediction results with the corresponding annotated force-directed network. Users can zoom the network by scrolling the mouse and drag the network for detailed network information. In the network, a node represents a single nucleotide. The radius of a node is proportional to the closeness value for the corresponding nucleotide. Users can get the nucleotide name, nucleotide number, closeness, and degree values if they put the mouse at the node. The edges represent non-covalent interactions between nucleotides. The information of predicted binding sites (red nodes) is listed in the table on the right. Moreover, users can zoom the network by scrolling the mouse and drag the network for particularly detailed network information.
(b) The statistical analysis of the closeness and degree calculation results can be downloaded separately. In the closeness/degree histogram, the X-axis shows closeness/degree values and the Y-axis shows the number of nucleotides.
(c) The prediction results can be downloaded with the following information. The “nodes” module contains the nucleotide names, closeness and degree values. The “edges” module contains the information of connected nodes. The “sites” module contains nucleotide name, closeness and degree values for predicted binding sites.

2. Visualization module

The RNA tertiary structure can be visualized in the Visualization part.
a. Users can upload an RNA tertiary structure in PDB format by clicking the "upload" button.
b. The visual area can be saved as a picture by clicking the “image” button.
c. Users can click on the visual area, and then hold down the left mouse button to rotate the RNA structure.
d. Users also can adjust the structure scale by scrolling the pulley on the mouse to facilitate the observation.
e. If an atom is clicked on the visual area, the name of the atom and the nucleotide which the atom belongs to can be displayed.
f. The key nucleotide can be highlighted in different colors by clicking “rainbow” and “red” buttons.
g. Users can display RNA structure in several different styles by clicking “spacefill”, “wire”, “ball&stick”, and “cartoons” buttons.

3. Links module

The Links module provides RNA tertiary structure prediction, docking, molecular dynamics, and other related useful RNA resources.

4. Output example module

The Output example module provides one tRNA prediction example.

5. Download RNA-protein benchmark

Users can download the RNA-protein benchmark that consists of 10 rigid docking complexes and 5 flexible docking complexes. The results show the average accuracy of 0.70 and 0.67 in rigid and flexible testing sets, respectively.