about web server help people prc

Server for Determination of Potential DNA Binding Sites of Proteins
  1. In the web server page, you can either enter the PDB code and the chain ID or you may upload your own PDB file. The PDB file must be in the standard PDB file format. A sample PDB file can be found here.

     

  2. To refine the results by using conservation scores, you may either enter the PDB code and the chain ID to automatically get the conservations scores from ConSurf Server Database or you may upload your own conservation score data. A sample conservation score file can be found here.

    Conservation score submission is not necessary, but using conservation increases the selectivity and the precision of predictions.

     

  3. Conservation threshold, fast threshold, residue neighbourhood threshold, and GNM mode can be varied and the results can be observed. Explanation of these parameters can be seen on the web server page.
     
  4. If an e-mail address is given, the link to results will be sent to the given address.
     
  5. A sample input can be seen by clicking the sample button given in the web server page.
     
  6. When the processing is completed, you are automatically redirected to the results page.

    In this page, the parameters you have supplied can be seen on top.

The results obtained only by GNM can be seen as a table. These results are sorted according to fluctuation values in the chosen fast mode(s). The residue ID in the PDB file and the corresponding residue types are given.

Also, if the user has given conservation score data, the residues obtained above are filtered using the conservation threshold, which is also a parameter supplied at the web server page.

 


For questions and comments: "appserv AT prc.boun.edu.tr"