DOCK Blaster:Prepare Input

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This is guide to how to prepare input for and run DOCK Blaster, a free web-based virtual screening service. We assume here that you have dealt with the important DOCK_Blaster:Preliminaries and have a target structure and some indication of the binding site in hand. Here we take up the question of how exactly to prepare the input so that DOCK Blaster will run successfully. Here is a brief overview. For more detail, please consult the separate articles containing a more detailed description.

Quick Overview

  • 1. Specify a target (PDB format).

The PDB file must have the following characteristics, to avoid confusing any of the programs used by DOCK Blaster.

    • a. only ATOM cards
    • b. chain identifier blank
    • c. there is a cofactor, you must
  • 2. Identify the binding site with a ligand or residues that form the site.
  • 3. Select a database to dock.
  • 4. Supply any positive controls (actives) you may have.
  • 5. Supply any negative controls (experimental decoys) you may have.
  • 6. Agree to the terms and click "I agree, DOCK!"

Sample Data

Sample data are available

  • DUD
  • Gold test set
  • other test sets
  • you can also generate your own sample decoy data



See also:

and the DOCK Blaster main page DOCK Blaster.


Each successful run of DOCK Blaster creates output in the Top Hits Collection (THC)