DOCKovalent 3.7 - Revision history

Kyle: Update dock licensing website

2025-07-15T20:09:54Z

Update dock licensing website

← Older revision		Revision as of 20:09, 15 July 2025
Line 8:		Line 8:

	* Apply for a DOCK3.7 license:		* Apply for a DOCK3.7 license:
	** go here: [[~~http~~://~~dock~~.~~compbio~~.~~ucsf.edu~~/~~Online_Licensing/dock_license_application.html~~ dock Academic License]]		** go here: [[https://license.docking.org/application dock Academic License]]
	** select version DOCK3.7		** select version DOCK3.7
	** fill in the required information		** fill in the required information

Dudenko: /* INDOCK parameters */

2019-07-29T14:36:03Z

INDOCK parameters

← Older revision		Revision as of 14:36, 29 July 2019
Line 88:		Line 88:
	'''bond_ang2''' - the 'ideal' bond angle for SG-Lig1-Lig2 (look at length explantation above for '''ang2_range''', and '''ang2_step''')		'''bond_ang2''' - the 'ideal' bond angle for SG-Lig1-Lig2 (look at length explantation above for '''ang2_range''', and '''ang2_step''')

	The default parameters for sampling (bond length and two bond ~~angels~~ are suitable for thioethers (e.g. when docking acrylamides to cysteines) these should be changed for different electrophile/nucleophile combinations.		The default parameters for sampling (bond length and two bond angles are suitable for thioethers (e.g. when docking acrylamides to cysteines) these should be changed for different electrophile/nucleophile combinations.
	Some parameters you might want to use are listed below, but more work is being done in this vein as you read these lines.		Some parameters you might want to use are listed below, but more work is being done in this vein as you read these lines.

Khtang: /* General setup */

2019-01-03T21:51:45Z

General setup

← Older revision		Revision as of 21:51, 3 January 2019
Line 19:		Line 19:
	The rest of the tutorial will assume DOCKBASE is set.		The rest of the tutorial will assume DOCKBASE is set.

	* you need an amsol binary, you can get amsol 7.1 <ref>[http://comp.chem.umn.edu/amsol/ Get amsol 7.1]</ref> and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if you are in the lab make a symbolic link to this amsol version:		* you need an amsol binary, you can get amsol 7.1<ref>[http://comp.chem.umn.edu/amsol/ Get amsol 7.1]</ref> and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if '''you are in the lab''' make a symbolic link to this amsol version:
	ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .		ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .

Khtang at 21:45, 3 January 2019

2019-01-03T21:45:29Z

← Older revision		Revision as of 21:45, 3 January 2019
Line 156:		Line 156:

	* Different electrophiles have different inherent reactivity. This is not taken into account in any way during the docking. The docked library should be matched to the application you are interested in. If you are looking for a non-toxic compound that may be active in cells you might consider unsubstituted acrylamides that are considered mild. If on the other hand you are looking for something that can label your protein in-vitro for crystallization studies Bromo-acetamide is very very reactive. Most of the covalent docking libraries were designed with fairly mild electrophiles but keep this consideration in mind when selecting which library to dock and which compounds to test.		* Different electrophiles have different inherent reactivity. This is not taken into account in any way during the docking. The docked library should be matched to the application you are interested in. If you are looking for a non-toxic compound that may be active in cells you might consider unsubstituted acrylamides that are considered mild. If on the other hand you are looking for something that can label your protein in-vitro for crystallization studies Bromo-acetamide is very very reactive. Most of the covalent docking libraries were designed with fairly mild electrophiles but keep this consideration in mind when selecting which library to dock and which compounds to test.
			==Notes==
			<references />

	Back to [[:Category:Covalent]]		Back to [[:Category:Covalent]]

	[[Category:Covalent]]		[[Category:Covalent]]

Khtang: /* General setup */

2019-01-03T21:44:49Z

General setup

← Older revision		Revision as of 21:44, 3 January 2019
Line 19:		Line 19:
	The rest of the tutorial will assume DOCKBASE is set.		The rest of the tutorial will assume DOCKBASE is set.

	* you need an amsol binary, you can get amsol 7.1 [http://comp.chem.umn.edu/amsol/] and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if you are in the lab make a symbolic link to this amsol version:		* you need an amsol binary, you can get amsol 7.1 <ref>[http://comp.chem.umn.edu/amsol/ Get amsol 7.1]</ref> and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if you are in the lab make a symbolic link to this amsol version:
	ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .		ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .

TBalius: /* Sending a run */

2015-05-12T22:36:10Z

Sending a run

@@ Line 98: / Line 98: @@
 * First setup the directory structure for docking:
-<code>$DOCKBASE/docking/setup/setup_db2.csh /path/to/ligand/lig_db2/ </code>
+  <code>$DOCKBASE/docking/setup/setup_db2.csh /path/to/ligand/lig_db2/ </code>
 tip: use FULL path to the db files (and not ../../etc)
-Foreach .db2.gz file this will create a separate running dir
+For each .db2.gz file this will create a separate running dir
-* Sumbit the docking job:
+* Setting up directory structure for docking of pre-computed ligand libraries (here we use alkylhalides as an example):
 - locally:
-- on cluster2:
+  cd lig
-[to be added]
+  <code>$DOCKBASE/docking/DOCK/bin/dock64 </code>
 == Analysis and interpretation of the results ==

TBalius: /* INDOCK parameters */

2015-05-12T21:17:05Z

INDOCK parameters

← Older revision		Revision as of 21:17, 12 May 2015
Line 93:		Line 93:
	* It is also (highly) recommended to allow bumping in a covalent run, especially of the rigid part.		* It is also (highly) recommended to allow bumping in a covalent run, especially of the rigid part.
	Set '''bump_rigid''' to 100.0 and '''bump_maximum''' to 100.0 - one can play around with these to balance speed and sampling.		Set '''bump_rigid''' to 100.0 and '''bump_maximum''' to 100.0 - one can play around with these to balance speed and sampling.
			* Change '''check_clashes''' to '''no'''.

	== Sending a run ==		== Sending a run ==

TBalius: /* Sending a run */

2015-05-12T19:22:24Z

Sending a run

← Older revision		Revision as of 19:22, 12 May 2015
Line 104:		Line 104:
	* Sumbit the docking job:		* Sumbit the docking job:
	- locally:		- locally:
	<code> cd lig; $DOCKBASE/docking/DOCK/~~src/i386~~/dock64~~</code>~~		<code> cd lig; $DOCKBASE/docking/DOCK/bin/dock64

	- on cluster2:		- on cluster2:

TBalius: /* General setup */

2015-05-12T18:45:17Z

General setup

← Older revision		Revision as of 18:45, 12 May 2015
Line 7:		Line 7:
	== General setup ==		== General setup ==

			* Apply for a DOCK3.7 license:
			** go here: [[http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html dock Academic License]]
			** select version DOCK3.7
			** fill in the required information
			** be patient because a real person approve the license and also get your e-mails.
			** Download the tar.gz file and copy it to your desired location on the cluster.
			** tar -zxvf [file name].tar.gz

	* You have checked out DOCK3.7.x and have it under /path/to/DOCK		* You have checked out DOCK3.7.x and have it under /path/to/DOCK
	* setenv DOCKBASE /path/to/DOCK		** setenv DOCKBASE /path/to/DOCK
	The rest of the tutorial will assume DOCKBASE is set.		The rest of the tutorial will assume DOCKBASE is set.

TBalius: /* General setup */

2015-05-12T18:34:14Z

General setup

← Older revision		Revision as of 18:34, 12 May 2015
Line 11:		Line 11:
	The rest of the tutorial will assume DOCKBASE is set.		The rest of the tutorial will assume DOCKBASE is set.

	* you need an amsol binary, you can get amsol 7.1 [http://comp.chem.umn.edu/amsol/] and apply a patch to make it comparable with our docking methods [amsol 7 patch].		* you need an amsol binary, you can get amsol 7.1 [http://comp.chem.umn.edu/amsol/] and apply a patch to make it comparable with our docking methods [[amsol 7 patch]]. Or if you are in the lab make a symbolic link to this amsol version:
			ln -s /nfs/home/londonir/code/git_trunk/DOCK/ligand/amsol/amsol7.1 .

	== Custom Ligand / Library Generation ==		== Custom Ligand / Library Generation ==