DOCK Blaster: Difference between revisions

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[[Image:Dblogo.png|thumb|right|DOCK Blaster]]
#REDIRECT [[Category:DOCK Blaster]]
 
DOCK Blaster is a free service for running docking screens, on the web at [http://blaster.docking.org http://blaster.docking.org]. DOCK Blaster was developed in the [[Shoichet Lab]] at [[UCSF]] during the years 2000-2009. The service became public in August 2009, and a paper was published in J Med Chem in September 2009.  The current version is 1.0.1.
 
= What you need to start =
To use DOCK Blaster you will need the structure of a protein target and an indication of the binding site.  There are three ways to do this:
 
* If your target is in the PDB, you may simply specify the PDB code, in the [http://blaster.docking.org/parser.shtml Parser].
 
{{TOCright}}
 
* If your target is not in the PDB, or you edited a PDB file, use the [http://blaster.docking.org/start.shtml Preparer]. The steps are:
** 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 should be where you expect the ligand to go.
** Click "DOCK" and wait for the job to run (typically under 1 hour).
 
* 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 the DOCK Blaster paper (Irwin et al., J Med Chem, 2009, in press, please consult the [[DOCK Blaster:Sample_Data | sample data]].
 
= Preparation =
 
* [[DOCK Blaster:Preliminaries | Before you begin]]
 
* [[DOCK Blaster:Prepare Input | Prepare Input ]]
** [[DOCK Blaster:Prepare Receptor | Prepare Receptor]]
** [[DOCK Blaster:Prepare Ligand | Prepare Ligand]]
** [[DOCK Blaster:Other Input Options | Other Input Options]]
** [[DOCK Blaster:Input Troubleshooting | Input Troubleshooting]]
 
= Calculation =
* [[DOCK Blaster:Job Management | Job Management]]
* [[DOCK Blaster:Results | Results ]]
** [[DOCK Blaster:Initial Evaluation | Initial Evaluation]]
** [[DOCK Blaster:Results Browser | Results Browser]]
** [[DOCK Blaster:Large Database Docking | Large Database Docking]]
** [[DOCK Blaster:Custom Database | Custom Database]]
* [[DOCK Blaster:Technical Details | Technical Details]] of the calculation
 
= Interpretation =
* [[DOCK Blaster:Acquiring Compounds | Acquire Compounds]]
* [[DOCK Blaster:Test Compounds | Test Compounds]]
 
= Other topics =
* [[DOCK Blaster:Philosophy | Philosophy]]
* [[DOCK Blaster:Annotations | Annotations ]]
* [[DOCK Blaster:History | History ]]
* [[DOCK Blaster:Credits | Credits]]
 
To cite DOCK Blaster, please reference Irwin, Shoichet, Mysinger et al., "Automated docking screens: a feasibility study", J Med Chem (2009), in press.
 
= Help =
For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists
[http://blur.compbio.ucsf.edu/mailman/listinfo/blaster-fans blaster-fans at docking.org]. We welcome your feedback about DOCK Blaster. Please send bug reports
to support at docking.org. Please send opinions to comments at docking.org.
 
= Versions =
The current version is 1.0.1, released August 6, 2009.
 
Work on DOCK Blaster began in the fall of 2000.  The first web-based interface became available inside the lab in 2003. Selective pre-alpha testing started in 2006, alpha testing with external users in 2007, and wide-spread beta testing in 2008.  For more info, please see [[DOCK Blaster:History]].
 
[[Category:DOCK Blaster]]
[[Category:Portal]]

Revision as of 00:00, 11 March 2014

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