Prediction of protein-DNA binding affinity

PreDBA Help

Getting Started

Input data can be protein-DNA 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 5 structures). Please follow the descriptions for the input format. Users could leave their email address; PreDBA 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 DNA partner. 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 partner.

PreDBA will return the predicted Δ G value of the protein-DNA complex, which represents the protein-DNA binding affinity. (Figure 3)

Figure 3. Prediction results.

An example

Please follow the link to see an example.