Category:DOCK Blaster - Revision history

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	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.		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. In 2022 we created a new version of DOCK Blaster, [[pydock3]].

	= What you need to start =		= What you need to start =

Frodo at 09:37, 13 March 2014

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	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:~~Portal~~]]		[[Category:Topic]]

Frodo at 00:19, 11 March 2014

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	~~[[Image:Dblogo.png\|thumb\|right\|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.		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.

Frodo at 00:00, 11 March 2014

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

Therese: Created page with "DOCK Blaster"

2012-10-08T22:21:06Z

Created page with "DOCK Blaster"

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