Getting started with DOCK 3.7 - Revision history

Khtang at 19:03, 10 January 2019

2019-01-10T19:03:23Z

← Older revision		Revision as of 19:03, 10 January 2019
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	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Tutorials]]		[[Category:Tutorials]]
			[[Category:NEED ATTENTION]]

Frodo at 15:04, 24 March 2014

2014-03-24T15:04:27Z

← Older revision		Revision as of 15:04, 24 March 2014
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	Here are steps to get started with [[DOCK 3.7]] . If you don't already have the necessary physical infrastructure, you'll need to [[So you want to set up a lab \|set it up]]. If you haven't already installed [[DOCK 3.7]], here are the [[Install DOCK 3.7 \| installation instructions]].		Here are steps to get started with [[DOCK 3.7]] . If you don't already have the necessary physical infrastructure, you'll need to [[So you want to set up a lab \|set it up]]. If you haven't already installed [[DOCK 3.7]], here are the [[Install DOCK 3.7 \| installation instructions]].

			{{TOCright}}

	So, now that you have [[DOCK 3.7]] running, and that basic ./all-test.sh script works, here is how to get started:		So, now that you have [[DOCK 3.7]] running, and that basic ./all-test.sh script works, here is how to get started:

Frodo at 08:22, 13 March 2014

2014-03-13T08:22:29Z

← Older revision		Revision as of 08:22, 13 March 2014
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	Here are steps to get [[DOCK 3.7]] installed ~~and running on your own system~~, ~~including~~ the ~~entire docking pipeline, analysis tools and database building~~.		Here are steps to get started with [[DOCK 3.7]] . If you don't already have the necessary physical infrastructure, you'll need to [[So you want to set up a lab \|set it up]]. If you haven't already installed [[DOCK 3.7]], here are the [[Install DOCK 3.7 \| installation instructions]].

			So, now that you have [[DOCK 3.7]] running, and that basic ./all-test.sh script works, here is how to get started:

			= Docking preparation from receptor and ligand alone =
	= ~~Test 2:~~ Docking preparation from receptor and ligand alone =
	Here we prepare the endogenous human metabolites for docking.		Here we prepare the endogenous human metabolites for docking.
	mkdir -p ~/docking/test1		mkdir -p ~/docking/test1
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	blastermaster -v		blastermaster -v

	= ~~Test 3.~~ Prepare library for docking =		= Prepare library for docking =
	Here we prepare the endogenous human metabolites.		Here we prepare the endogenous human metabolites.
	mkdir -p ~/database/testa		mkdir -p ~/database/testa
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	build_smiles_ligand hmdbendo_p0.smi		build_smiles_ligand hmdbendo_p0.smi

	= ~~Test 4.~~ Dock custom library =		= Dock custom library =
	Go to the directory where you can see working and dockfiles directories from Test 2 above.		Go to the directory where you can see working and dockfiles directories from Test 2 above.
	setup_db2_lots 1 jobname ~/database/testd # nb directory from Test 3 above.		setup_db2_lots 1 jobname ~/database/testd # nb directory from Test 3 above.
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	where <db_dir> is the directory containing the .db2.gz database files.		where <db_dir> is the directory containing the .db2.gz database files.

	= ~~Test 5.~~ Run DUD and DUDE benchmarks ==		= Run DUD and DUDE benchmarks ==
	*NB THIS SECTION IS STILL IN DEVELOPMENT *		*NB THIS SECTION IS STILL IN DEVELOPMENT *
	And generate statistics to assess how well docking is working.		And generate statistics to assess how well docking is working.
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	* [[Run analysis tools on DUDE]]		* [[Run analysis tools on DUDE]]

	= ~~Test 6.~~ Acquire public library and dock it =		= Acquire public library and dock it =
	Use [[ZINC Subset DB2 file locations]] to locate [[mol2db2 format]] libraries of popular subsets until they are available in [[ZINC]] (later in 2014).		Use [[ZINC Subset DB2 file locations]] to locate [[mol2db2 format]] libraries of popular subsets until they are available in [[ZINC]] (later in 2014).

	= ~~Test 7.~~ Dock starting from PDB code =		= Dock starting from PDB code =
	* [[Run be_blasti]]		* [[Run be_blasti]]
	* run blastermaster (see Test 2 above)		* run blastermaster (see Test 2 above)
	* run docking (see test 4 above)		* run docking (see test 4 above)

	= ~~Test 8.~~ Perform fine-tuned docking run =		= Perform fine-tuned docking run =
	== fine tune docking spheres (hot spots) ==		== fine tune docking spheres (hot spots) ==
	* step 1		* step 1

Frodo at 07:41, 13 March 2014

2014-03-13T07:41:09Z

← Older revision		Revision as of 07:41, 13 March 2014
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	Here are steps to get [[DOCK 3.7]] installed and running on your own system, including the entire docking pipeline, analysis tools and database building.		Here are steps to get [[DOCK 3.7]] installed and running on your own system, including the entire docking pipeline, analysis tools and database building.

	~~1. [[So you want to set up a lab]]~~

	~~2. [[Install DOCK 3.7]]~~
	~~{{TOCright}}~~

Frodo at 07:37, 13 March 2014

2014-03-13T07:37:24Z

@@ Line 4: / Line 4: @@
 . [[Install DOCK 3.7]]
 {{TOCright}}
 = Test 2: Docking preparation from receptor and ligand alone =

Frodo at 07:36, 13 March 2014

2014-03-13T07:36:47Z

← Older revision		Revision as of 07:36, 13 March 2014
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	Here are steps to get [[DOCK 3.7]] installed and running on your own system, including the entire docking pipeline, analysis tools and database building.		Here are steps to get [[DOCK 3.7]] installed and running on your own system, including the entire docking pipeline, analysis tools and database building.

			1. [[So you want to set up a lab]]

			2. [[Install DOCK 3.7]]

	= Timeline =		= Timeline =

Frodo: /* Middleware */

2014-03-13T02:28:18Z

Middleware

← Older revision		Revision as of 02:28, 13 March 2014
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	= Middleware =		= Middleware =
	[[Compbio middleware]]		[[Compbio middleware]] needed to support our software and a computational pharmacology lab.

	= Our software =		= Our software =

Frodo: /* Our software */

2014-03-12T16:47:48Z

Our software

← Older revision		Revision as of 16:47, 12 March 2014
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	= Our software =		= Our software =
	Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at [http://dock.compbio.ucsf.edu/~~Online_licensing~~/dock_license_application.html ~~http://~~dock.compbio.ucsf.edu/~~Online_licensing~~/dock_license_application.html].		Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at
			[http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html]

	mkdir -p ~/code/DOCK		mkdir -p ~/code/DOCK
	cd ~/code/DOCK		cd ~/code/DOCK

Frodo at 16:42, 12 March 2014

2014-03-12T16:42:03Z

← Older revision		Revision as of 16:42, 12 March 2014
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	{{TOCright}}		{{TOCright}}

	= ~~Acquire 3rd party software~~ =		= Hardware and Operating System =
			* O/S: We recommend [[Centos]].
			* Hardware: We recommend Intel or AMD. [[Supported platforms for DOCK 3.7]].

			= Middleware =
	[[Compbio middleware]]		[[Compbio middleware]]

	= ~~Acquire our~~ software =		= Our software =
	Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at [http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html].		Here we install a private copy under a user's account. It is easy to generalize this to a global location, e.g. /nfs/software . You can request a license and a copy (free to academics, a bargain for for-profits) at [http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html http://dock.compbio.ucsf.edu/Online_licensing/dock_license_application.html].
	mkdir -p ~/code/DOCK		mkdir -p ~/code/DOCK

Frodo: /* Acquire 3rd party software */

2014-03-12T16:37:07Z

Acquire 3rd party software

← Older revision		Revision as of 16:37, 12 March 2014
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	= Acquire 3rd party software =		= Acquire 3rd party software =
	~~== Essential ==~~		[[Compbio middleware]]
	* Computer and operating system. We recommend [[~~Centos~~]] ~~on either Intel or AMD. [[Supported platforms for DOCK 3.7]].~~
	* [[Python]] - 2.7 series
	* [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.
	* [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building.
	* 3D modeling - [[PyMol]] or [[Chimera]]
	* [[Matplotlib]] - currently only needed for analysis plots (enrichment)
	* [[MSMS]] - currently only needed by [[be_blasti]]
	~~== Recommended ==~~
	* [[rdkit]] - recommended and soon to be essential for the DOCK 3.7 pipeline.
	* [[OGS/GE]] - queuing system. OpenGridEngine is included in [[Centos]] and you do not need to install it separately.

	= Acquire our software =		= Acquire our software =