The Home module provides an introduction of the RNAPocket database.
The Search box consists of three parts: search box, a summary table of RNA clusters and a description table of RNA classification. The cluster table shows the cluster conclusion of two sequence identity cut-off, 0.80 (75 clusters), and 0.95 (94 clusters) respectively, and provides RMSD between presentative RNA and members for each cluster. Users can expand or collapse tables to see more or less content. The RNA description table is the result of the presentative RNAs classification based on their function and it provides users with the class name, function description, and members in the class. The two tables are designed to help users retrieve information using the pulldown search box easily. In the pulldown search box, users can select the object by sequence identity cutoff, RNA class, and presentative RNA PDB ID. For example, we fill in ‘0.80’, ‘riboswitch’, ‘1Y27’ in the three drop-down menus respectively, and it means we select an RNA structure whose PDB ID is 1Y27, and belongs to the riboswitch of the RLB75 dataset. Then a new page displays, it shows the detailed information for 1Y27. (1) A cluster table, (2) A comprehensive information table, (3) Sequence Preview. The introductions of the search results are as follow.
(1) Cluster table
A cluster table was made for showing the RMSD between presentative RNA (1Y27) and other members in this cluster.
(2) Comprehensive information table
A comprehensive information table consists of three sections: general information section provides the general information of 1Y27 structure including PDB ID, PubMed, method, resolution, organism, class, Nts, and a brief description; the interaction information section provides the sites and sequences in RNA which binds to ligands, and the functional groups in ligands which interacts with RNA; the pocket information section contains the geometrical information (volume, area, shape similarity score, effective radius, centroid, shape, rpd1, rpd2, and the secondary structural elements the pocket located), and the secondary structural elements which pockets located in. Users can click the blue ligand name or pocket ID in the table to check detail interaction graph of complexes and download the structure file of pockets in MRC format.
(3) Sequence Preview
A sequence map was generated to show the ligand binding sites, and motifs or function sites in a sequence by adding shadows in different colors. For motifs or function sites, users can click the shadow part to enter the RegRNA server for details.
In Visualization module, users can upload a molecule or pocket structure file in pdb format.Some functions are listed:
a. Users can click on the visual area, and then hold down the left mouse button to rotate the pocket structure.
b. Users also can adjust the structure scale by scrolling the pulley on the mouse to facilitate the observation.
c. If an atom is clicked on the visual area, the name of the atom and the residue which the atom belongs to can be displayed.
d. The visual area can be saved as a picture by clicking the "image" button or a pdb file by clicking the "pdb" button.
e. The size of the visual area can be adjusted by clicking the "big" and "small" buttons.
f. The key residues can be highlighted in different colors by clicking "rainbow" and "crimson" buttons.
g. Users can display pocket in several different styles by clicking "spacefill", "wire", "ball&stick", and "cartoons" buttons.
Three summary tables were provided in the download module. In the first table, users can download the RNA classification table (xlsx format) with the summary of the RNA classification and description based on function, all the pocket files of the RLB75 and RLB94 datasets (MRC format), and two RMSD tables (xlsx format) with RMSD information between presentative RNA and other members in the same cluster with 0.80 and 0.95 sequence identity cut-off. The second table is for the pockets of each RNA structure, users can download the pocket information table (xlsx format) and pocket structure files (MRC format) with structure information of all pockets of each of the RNA structure. These MRC format files can be visualized in UCSF Chimera. The third table is for the statistical analysis data. Users can download the RNA-ligand complexes general information involved in this study (xlsx format), RNA pocket topology information (xls format), RNA-ligand interaction information (xlsx format and RAR format), nine predicted structures involved used in structure modeling section and RPDescriptor program.
The Links module provides the other useful links of RNA 3D structure resources, sequence alignment, RNA modeling, molecular dynamics, molecular docking, and molecular visualization analysis. These useful websites would be helpful in RNA-related drug development and vaccine design.
The Tutorial module provides the introduction to use the RPocket and the abbreviation for the RPocket database.
Some statistical analysis was generated including: the motifs of binding sites, ligands functional groups involved in hydrogen bond interactions and non-bond contacts, the binding motifs of pockets on 2D topology, RNA pocket size distribution and pocket shape distribution. These statistical results could help researchers in the screening of small-molecule drugs.
The Contacts module provides emails for users to comment or ask questions.