Getting Started
Input data can be protein-RNA structure files in PDB format or PDB codes. The input structure should contain at least two chain identifiers forming the interface definition. One can query multiple structures in one run (maximum allowed 10 structures). Please follow the descriptions for the input format. Users could leave their email address; PrabHot will send the prediction results to the address. Titles also could be specified for the user to distinguish their different jobs. Private Key is set to protect your structure and analysis. Please refer to Figure 1.
Figure 1. Job submission.
The server will check the validity of the input structure, and once confirmed, process to the secend step to select the query protein and its RNA partners. If the selection is done, please click the button "submit" to run the job (Figure 2). Users will then be directed to the result page with job status. Book the link if you want to check your results later. However, the analysis could also be retrieved by user email or job ID in the result page.
Figure 2. Select the query protein and its partners.
PrabHot will return a list of residue ids which were predicted to be RNA-binding hot spots. The red residues in the query sequence are predicted hot spots. Users can download the results in text. By default, PrabHot predicts a interface residue to be in a hot spot when the associated score is higher than 0.5 but this cutoff is adjustable by the user. In order to visualize the 3D structures of the prediction resutls, users can click "View in 3D". (Figure 3)
Figure 3. Prediction results.
The information of the query job is shown at the top. The sturctures of the query protein and its RNA partners will be shown in Jsmol. Predicted hot spots are rendered in different colors from white to red, according to the probability from the lowest to the highest (Figure 4).
Figure 4. Prediction results and visulization.
Users can view the predicted hot spots with output scores listed at the bottom. Interactive operations are also provided (Figure 5).
Figure 5. Interactive operation.
An example Please follow the link to see an example.
