Web Browser Requirements
PrPDH requires a modern web browser with JavaScript and cookies enabled. To view the complex details, pop-ups must not be blocked. The following browsers have been thoroughly tested with PrPDH:
  • Mozilla Firefox, version 4 or above
  • Internet Explorer, versions 11 or above
  • Chrome, version 5 or above
The latest version of Firefox and Chrome is recommended for visualization.

Usage

1. Input

1). Two types of input formats are allowed for PrPDH: protein-DNA structural files from PDB (Protein Data Bank) or PDB IDs.
2). SPIDER2 is a sequence-based program to predict protein secondary structures. If this button is selected, it will produce a more precise prediction result by consuming more time.
3). If you do not know what chain contained in this complex, you can look up its PDB structural file. As there is usually more than one protein chain in a protein-DNA complex, one chain ID is needed each time.
4). Submission title and email address are optional for users.

Notes:

  • Only a protein-DNA complex with interactional interface is allowed for prediction.
  • PrPDH is not able to identify the structure with several models. We only keep the first model of structure for calculation. If you want to calculate a certain model specifically, please keep the model you need and remove others in the PDB file first.
  • The modified non-standard residues labeled as HETATM cannot be read by PrPDH.

Figure 1.

2. Submission

PrPDH runs tasks one by one. Multiple submitted tasks are queued for execution. If you submit the job mistakenly, the "Cancel" button is prepared for you to terminate the job in queue. Only the job in the queue can be canceled. Once the job is submitted, a table containing job information (job ID, created time, execution status and so on) can be returned. The result link is shown on the web page or sent to you (if you leave the email address).

3. Output

The predicted results will be displayed in a table. Meanwhile, we provide users with a visualized three-dimensional structure of protein-DNA complexes. It is executable to mark corresponding positions of predicted hot spots and non-hot spots on the visual structures. All prediction results can be download in tar.gz form.

4. Example

The example on the Server page provides a PDB ID (1TN9) and its chain (A) information. If you want to upload an example of PDB file, we also offer a download link here 1TN9.pdb. Upload the file and fill in the blank of chain "A". You can also use job ID and left email address to search for the task on the Server page. An example job ID is given.


Version
The current version number is 1.0 - Sep, 2018.