Difference between revisions of "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.
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Here we describe 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, possibly with additional information about actives and inactives for this target. For more detailed information, please consult the separate articles referenced herein.
  
 
== Quick Overview ==
 
== Quick Overview ==
 
*1. Specify a target (PDB format).
 
*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.
 
The PDB file must have the following characteristics, to avoid confusing any of the programs used by DOCK Blaster.
** a. only ATOM cards
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** a. only ATOM cards are allowed (HETATM are mapped to ATOM)
 
** b. chain identifier blank
 
** b. chain identifier blank
** c. there is a cofactor, you must  
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** c. if there is a cofactor, you must specify a cofactor file. With luck, your cofactor will be available in our co-factor dictionary. If not, you will have to prepare it yourself.
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** d. residue numbers must monotonically increase
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** e. disorder models must be resolved into a single choice for each atom
 +
** f. if you are docking to a metalloenzyme, special steps are requrired.
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** g. waters must be removed. Any structural waters should be "TIP" and not "HOH".
 +
** h. must be forgetting something, but what???
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If you do not have your own target, you may use some of our [[DOCK_Blaster:Sample_Data sample data]] or try one of our [[DOCK_Blaster:Tutorials tutorials]].
  
*2. Identify the binding site with a ligand or residues that form the site.
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*2. Specify the binding site.
*3. Select a database to dock.
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You may specify the binding site using a docked ligand in mol2 format, or residues bounding the binding site in PDB format. If you upload a mol2 file, it will be scored, redocked, and used in various other ways to evaluate the quality of the docking model. If you do not have a ligand (experimental or modeled) then you must specify at least 3 residues, the center of mass of which is at the center of the binding site.
*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!"
 
  
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*3. Specify your email address if you wish to receive status updates by email.
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*4. If you have actives and decoys, you may specify them in the fields provided. They will be docked and scored, and thus offer immediate feedback on the quality of the docking model.
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*5. If you wish to keep your calculation private, specify a PIN. The data you upload and produce will only be accessible with this PIN. If you wish to make your results available to anyone, leave the PIN blank
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*6. We recommend to write notes about the calculation in the memo field provided. This is particularly helpful if you launch many calculations. We recommend you keep a notebook, and note each Job ID down to keep track of your calculations.
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*7. If your target has a cofactor (other than a metal), you will need to specify a cofactor. Many cofactors are available from our co-factor dictionary. The cofactor must match all the atoms in your target structure or the calculation will not start.
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*8. Experts have the option to provide additional information to the docking calculation. No public documentation is available about this at this time. If you encounter problems with docking, we may provide an expert.tar file to help you work around weaknesses in the current design.
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*9. If you are happy with the input and the terms and conditions, you may click on "I agree. DOCK!" to submit the calculation.
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 +
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*10. If you do not have
 
== Sample Data ==
 
== Sample Data ==
 
Sample data are available
 
Sample data are available

Revision as of 22:36, 26 October 2006

Here we describe 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, possibly with additional information about actives and inactives for this target. For more detailed information, please consult the separate articles referenced herein.

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 are allowed (HETATM are mapped to ATOM)
    • b. chain identifier blank
    • c. if there is a cofactor, you must specify a cofactor file. With luck, your cofactor will be available in our co-factor dictionary. If not, you will have to prepare it yourself.
    • d. residue numbers must monotonically increase
    • e. disorder models must be resolved into a single choice for each atom
    • f. if you are docking to a metalloenzyme, special steps are requrired.
    • g. waters must be removed. Any structural waters should be "TIP" and not "HOH".
    • h. must be forgetting something, but what???

If you do not have your own target, you may use some of our DOCK_Blaster:Sample_Data sample data or try one of our DOCK_Blaster:Tutorials tutorials.

  • 2. Specify the binding site.

You may specify the binding site using a docked ligand in mol2 format, or residues bounding the binding site in PDB format. If you upload a mol2 file, it will be scored, redocked, and used in various other ways to evaluate the quality of the docking model. If you do not have a ligand (experimental or modeled) then you must specify at least 3 residues, the center of mass of which is at the center of the binding site.

  • 3. Specify your email address if you wish to receive status updates by email.
  • 4. If you have actives and decoys, you may specify them in the fields provided. They will be docked and scored, and thus offer immediate feedback on the quality of the docking model.
  • 5. If you wish to keep your calculation private, specify a PIN. The data you upload and produce will only be accessible with this PIN. If you wish to make your results available to anyone, leave the PIN blank
  • 6. We recommend to write notes about the calculation in the memo field provided. This is particularly helpful if you launch many calculations. We recommend you keep a notebook, and note each Job ID down to keep track of your calculations.
  • 7. If your target has a cofactor (other than a metal), you will need to specify a cofactor. Many cofactors are available from our co-factor dictionary. The cofactor must match all the atoms in your target structure or the calculation will not start.
  • 8. Experts have the option to provide additional information to the docking calculation. No public documentation is available about this at this time. If you encounter problems with docking, we may provide an expert.tar file to help you work around weaknesses in the current design.
  • 9. If you are happy with the input and the terms and conditions, you may click on "I agree. DOCK!" to submit the calculation.


  • 10. If you do not have

Sample Data

Sample data are available

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

FAQ

Credits

See also:

and the DOCK Blaster main page DOCK Blaster.


THC

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