Welcome to the DUCK-BP online web server submit form!

DUCK-BP - Docking at University of Chicago using Knowledge-Based Potentials - is a suite of programs to perform docking and evaluation of the docking set. This version of DUCK-BP is custom-tailored for nucleic acid binding proteins. Here, the docking set is generated using FTdock. It is then scored using a contact matrix designed to recognize specific classes of nucleic acid binding proteins, like DNA or tRNA. [stats]

 1. Protein 
Please choose a protein 3D structure to dock against a nucleic acid.
Maximum 500 residues. Only the ATOM fields of the PDB file are recognized.

    

         

 2. Nucleic Acid 
Please choose the type of nucleic acid to dock against the protein.
The choice will set the nucleic acid 3D structure as well as the matrix used for scoring the docking poses.

    DUCK-BP scoring matrix:  

     tRNA-binding scoring matrix -- docking with modified PDB file 4TRA
     DNA-binding scoring matrix -- docking with modified PDB file 1A74


 3. Email Notification [optional] 
Please provide your email address so that the web server can notify you upon completion of the job. This field is optional. If left empty, you'll have to manually refresh your working directory to assess the job's completion, and bookmark it so that you can get to it at a later time.

    Email: 

 4. Job Packing [optional] 
Several docking processes can be packed on the same computer node to speed up the docking stage. However, because each docking job takes a lot of memory, it is possible that packing too many jobs on the same node can make the processes run out of memory, and therefore aborting the docking stage. In that case, one can run the docking jobs in a lower packing setting. The memory footprint of a docking job depends on the size of the protein, but not in an abvious way (doesn't correlate with neither the number of atoms, nor the surface, nor the volume of the protein).

    Choose the appropriate job packing:
    

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