DOCK Blaster: Difference between revisions

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[[Image:Dblogo.png|thumb|right|DOCK Blaster]]
[[Image:Dblogo.png|thumb|right|DOCK Blaster]]


DOCK Blaster is a free-to-use service for running docking screens, on the web at [http://blaster.docking.org http://blaster.docking.org].  **DOCK Blaster is currently in beta test, so you should contact John Irwin for access until it becomes public** To use DOCK Blaster you will need at least:
DOCK Blaster is a free-to-use service for running docking screens, on the web at [http://blaster.docking.org http://blaster.docking.org].  **DOCK Blaster is currently in beta test, so you should contact John Irwin for access until it becomes public**


* The structure of the target in PDB format (preferred) or mol2 format
To use DOCK Blaster you will need the structure of a protein target and an indication of the binding site you wish to target.  
* A specification of the binding site, which may be one of:
There are two ways to do this:
** A docked ligand in mol2 format, which is also used to test the docking parameterization
** "hot spots", in PDB format, which may be based on one or more ligands.
** Atoms of residues forming the binding site. The center of inertia of these atoms should coincide with where you expect the ligand to go.


{{TOCright}}
* If your target is in the PDB, you may simply specify the PDB code, in the [http://blaster.docking.org/parser.shtml Parser].


That's really all you need to get started.  If the target you wish to screen is already in the PDB, you may simply specify its PDB code, and DOCK Blaster will attempt to do the rest.
* If your target is not in the PDB, or you edited a PDB file, use the [http://blaster.docking.org/start.shtml Preparer].
** Upload the target in PDB format (preferred) or mol2 format
** Specify the binding site using
*** a docked ligand in mol2 format (preferred) or
*** "hot spots", in PDB format
*** atoms of residues forming the binding site, the center of inertia of which be where you expect the ligand to go.


If you do not have a particular project in mind, and you are just curious about DOCK Blaster, you can simply use the "I'm feeling lucky" option, and we will pick a target for you.
{{TOCright}}


If you would like to try one of the examples featured in our forthcoming paper, take a look at the [[DOCK Blaster:Sample_Data | sample data]] to experiment.
If you do not have a particular target in mind and are simply curious about DOCK Blaster, you may select "I'm feeling lucky", and we will pick a target for you from the PDB. To try one of the examples featured in our (forthcoming) DOCK Blaster paper, consult the [[DOCK Blaster:Sample_Data | sample data]].


To learn more about DOCK Blaster, please consult the topics below.
To learn more please consult the topics below.


== Before you get started ==
== Before you get started ==

Revision as of 18:25, 12 February 2009

DOCK Blaster

DOCK Blaster is a free-to-use service for running docking screens, on the web at http://blaster.docking.org. **DOCK Blaster is currently in beta test, so you should contact John Irwin for access until it becomes public**

To use DOCK Blaster you will need the structure of a protein target and an indication of the binding site you wish to target. There are two ways to do this:

  • If your target is in the PDB, you may simply specify the PDB code, in the Parser.
  • If your target is not in the PDB, or you edited a PDB file, use the Preparer.
    • Upload the target in PDB format (preferred) or mol2 format
    • Specify the binding site using
      • a docked ligand in mol2 format (preferred) or
      • "hot spots", in PDB format
      • atoms of residues forming the binding site, the center of inertia of which be where you expect the ligand to go.

If you do not have a particular target in mind and are simply curious about DOCK Blaster, you may select "I'm feeling lucky", and we will pick a target for you from the PDB. To try one of the examples featured in our (forthcoming) DOCK Blaster paper, consult the sample data.

To learn more please consult the topics below.

Before you get started

Preparation and Docking

Understanding the Results

Other information


To cite DOCK Blaster, please reference Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, 49(23), 6789-6801

For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists [1]. We welcome your feedback about DOCK Blaster. Please send bug reports to support at docking.org. Please send opinions to comments at docking.org.

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