DOCK Blaster:Protocols - Revision history

Frodo at 03:51, 13 March 2014

2014-03-13T03:51:44Z

← Older revision		Revision as of 03:51, 13 March 2014
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	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:Manual]]		[[Category:Manual]]
	[[Category:~~Protocols~~]]		[[Category:Tutorials]]

Therese: 6 revisions

2012-10-08T20:02:11Z

6 revisions

← Older revision	Revision as of 20:02, 8 October 2012
(No difference)

Frodo at 01:06, 13 February 2009

2009-02-13T01:06:11Z

← Older revision		Revision as of 01:06, 13 February 2009
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	= Before docking =		= Before docking =

	== Protocol B1: ==		== Protocol B1: filtering molecules ==

	* x		* x
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	== Protocol B2: ~~Assemble a list of~~ decoys ==		== Protocol B2: making decoys ==

	* x		* x
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	* z		* z

	== Protocol B3: Prepare a ligand for docking ==		== Protocol B3: Prepare ligand for docking ==

	* x		* x
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	* z		* z

	== Protocol B4: ~~Prepare a list of~~ N random molecules ==		== Protocol B4: Get N random molecules ==

	* x		* x
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	* z		* z

	== Protocol B5: ~~Generate~~ 3D ~~representations of molecules from SMILES~~ ==		== Protocol B5: SMILES to 3D mol2/SDF ==

	* x		* x
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	== Protocol B6: ==		== Protocol B6: Autodock pdbqt format==

	* x		* x
	* y		* y
	* z		* z

			== Protocol B7: Clustering ligands ==
			* x
			* y
			* z

			== Protocol B8: protonate receptor ==

			* x
			* y
			* z

			== Protocol B9: search supplier catalogs (pre filtering) ==

			* x
			* y
			* z

			== Protocol B10: identify aggregators ==

			* x
			* y
			* z

			== Protocol B11: exhaustive search ==

			* x
			* y
			* z

			== Protocol B12: make a database subset ==

			* x
			* y
			* z

			== Protocol B13: xxx ==

			* x
			* y
			* z


	= Docking =		= Docking =

Frodo at 00:17, 13 February 2009

2009-02-13T00:17:48Z

← Older revision		Revision as of 00:17, 13 February 2009
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	= Before docking =		= Before docking =

	== Protocol B1:		== Protocol B1: ==

			* x
			* y
			* z


	== Protocol B2: Assemble a list of decoys ==		== Protocol B2: Assemble a list of decoys ==

			* x
			* y
			* z

	== Protocol B3: Prepare a ligand for docking ==		== Protocol B3: Prepare a ligand for docking ==

			* x
			* y
			* z

	== Protocol B4: Prepare a list of N random molecules ==		== Protocol B4: Prepare a list of N random molecules ==

			* x
			* y
			* z

	== Protocol B5: Generate 3D representations of molecules from SMILES ==		== Protocol B5: Generate 3D representations of molecules from SMILES ==

			* x
			* y
			* z


	== Protocol B6: ==		== Protocol B6: ==

			* x
			* y
			* z

	= Docking =		= Docking =

	== Protocol D1: Dock a single ligand to a single target ==		== Protocol D1: Dock a single ligand to a single target ==

			* x
			* y
			* z


	= After docking =		= After docking =

	== Protocol A1: Cluster molecules ==		== Protocol A1: Cluster molecules ==

			* x
			* y
			* z

	== Protocol A2: Purchase compounds ==		== Protocol A2: Purchase compounds ==

			* x
			* y
			* z


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	== Protocol U1: similarity searching ==		== Protocol U1: similarity searching ==

			* x
			* y
			* z


	== Protocol U2: generate 2D depiction from SMILES ==		== Protocol U2: generate 2D depiction from SMILES ==

			* x
			* y
			* z

	== Protocol U3: xxx ==		== Protocol U3: xxx ==

			* x
			* y
			* z

Frodo at 00:16, 13 February 2009

2009-02-13T00:16:54Z

← Older revision		Revision as of 00:16, 13 February 2009
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	Protocols are procedural lego bricks to carry out some manipulation or series of manipulations involved in or peripheral to ligand discovery. They are different from [[tutorials]], which are thematic and project-oriented, and typically may call upon one or more protocols.		Protocols are procedural lego bricks to carry out some manipulation or series of manipulations involved in or peripheral to ligand discovery. They are different from [[tutorials]], which are thematic and project-oriented, and typically may call upon one or more protocols.

			{{TOCright}}

	= Before docking =		= Before docking =

Frodo at 00:16, 13 February 2009

2009-02-13T00:16:39Z

← Older revision		Revision as of 00:16, 13 February 2009
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	~~== Protocol 1: Dock a single~~ ligand ~~to a single target ==~~		Protocols are procedural lego bricks to carry out some manipulation or series of manipulations involved in or peripheral to ligand discovery. They are different from [[tutorials]], which are thematic and project-oriented, and typically may call upon one or more protocols.



	=~~= Protocol 2: Dock a ligand with lists of experimental actives and inactives =~~=		= Before docking =

			== Protocol B1:
			== Protocol B2: Assemble a list of decoys ==

			== Protocol B3: Prepare a ligand for docking ==

	== Protocol 3: ~~Dock to~~ a ~~target containing a co-factor : DHFR~~ ==		== Protocol B4: Prepare a list of N random molecules ==

			== Protocol B5: Generate 3D representations of molecules from SMILES ==

			== Protocol B6: ==

			= Docking =

			== Protocol D1: Dock a single ligand to a single target ==

			= After docking =

			== Protocol A1: Cluster molecules ==

			== Protocol A2: Purchase compounds ==



			= Unrelated to docking =

			== Protocol U1: similarity searching ==


			== Protocol U2: generate 2D depiction from SMILES ==

			== Protocol U3: xxx ==

	~~== Protocol 4: Dock to a metalloenzyme : Carbonic Anhydrase ==~~

Frodo at 21:47, 8 November 2007

2007-11-08T21:47:26Z

← Older revision		Revision as of 21:47, 8 November 2007
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	== Protocol 4: Dock to a metalloenzyme : Carbonic Anhydrase ==		== Protocol 4: Dock to a metalloenzyme : Carbonic Anhydrase ==



			[[Category:DOCK Blaster]]
			[[Category:Manual]]
			[[Category:Protocols]]

JohnIrwin at 20:41, 18 December 2006

2006-12-18T20:41:45Z

New page

== Protocol 1: Dock a single ligand to a single target ==

== Protocol 2: Dock a ligand with lists of experimental actives and inactives ==

== Protocol 3: Dock to a target containing a co-factor : DHFR ==

== Protocol 4: Dock to a metalloenzyme : Carbonic Anhydrase ==