DOCK 3.7 - Revision history

Btingle: /* Tutorials */

2021-07-27T17:03:06Z

Tutorials

← Older revision		Revision as of 17:03, 27 July 2021
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	* [[DOCK 3.7 with GIST tutorials]]		* [[DOCK 3.7 with GIST tutorials]]
	* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]		* [[DOCK 3.7 tutorial based on Webinar 2017/06/28]]

			== DOCK 3.8 Tutorials ==

			* [[How to dock in DOCK3.8]]
			* [[Docking Analysis in DOCK3.8]]

	= Prepare Receptor =		= Prepare Receptor =

Jklyu at 17:29, 31 March 2021

2021-03-31T17:29:47Z

← Older revision		Revision as of 17:29, 31 March 2021
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	* [[Adding Static Waters to the Protein Structure]]		* [[Adding Static Waters to the Protein Structure]]
	* [[Flexible Docking]]		* [[Flexible Docking]]
			* [[Coloring and Subcluster Matching]]
	* [[Visualize docking grids]]		* [[Visualize docking grids]]
	* [[Minimize protein-ligand complex with AMBER]]		* [[Minimize protein-ligand complex with AMBER]]

Yingyang: /* FEP+ and AutoQSAR/DeepChem with Schrodinger Suites */

2021-02-26T18:58:01Z

FEP+ and AutoQSAR/DeepChem with Schrodinger Suites

← Older revision		Revision as of 18:58, 26 February 2021
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	* [[TC analog searching in ZINC]]		* [[TC analog searching in ZINC]]

	= FEP+ and ~~AutoQSAR/DeepChem~~ with Schrodinger Suites=		= FEP+ and ML with Schrodinger Suites=
	* [[FEP+ for GPCR]]		* [[FEP+ for GPCR]]
	* [[AutoQSAR/DeepChem for billions of molecules]]		* [[AutoQSAR/DeepChem for billions of molecules]]

Yingyang at 18:32, 26 February 2021

2021-02-26T18:32:46Z

← Older revision		Revision as of 18:32, 26 February 2021
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	* [[Substructure searching]]		* [[Substructure searching]]
	* [[TC analog searching in ZINC]]		* [[TC analog searching in ZINC]]

			= FEP+ and AutoQSAR/DeepChem with Schrodinger Suites=
			* [[FEP+ for GPCR]]
			* [[AutoQSAR/DeepChem for billions of molecules]]

	= Previous verisons and compatibility =		= Previous verisons and compatibility =

Bbender at 14:55, 23 September 2020

2020-09-23T14:55:46Z

← Older revision		Revision as of 14:55, 23 September 2020
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	= Running Docking =		= Running Docking =
	'''These scripts are also out of date. Where is setup_zinc15_file_number.py ~~and variations~~?'''		'''These scripts are also out of date. Where is setup_zinc15_file_number.py for LSD?'''
	* [[Running docking 3.7]] - JJI currently working on this.		* [[Running docking 3.7]] - JJI currently working on this.
	* [[Running DOCK 3.7]] - this seems to be slightly dated.		* [[Running DOCK 3.7]] - this seems to be slightly dated.
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	= Analysis =		= Analysis =
	* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)		* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)
			* [[How to process results from a large-scale docking]] : contains the blazing fast scripts for LSD processing
	* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)		* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)
	* [[Other Useful Stuff]]		* [[Other Useful Stuff]]

Bbender at 14:51, 23 September 2020

2020-09-23T14:51:59Z

← Older revision		Revision as of 14:51, 23 September 2020
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	= Analysis =		= Analysis =
	* [[Analyzing DOCK Results]]		* [[Analyzing DOCK Results]] - this is extract_all.py and getposes.py; not optimized for LSD (i.e. blazing_fast)
	* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)		* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)
	* [[Other Useful Stuff]]		* [[Other Useful Stuff]]

Bbender at 14:51, 23 September 2020

2020-09-23T14:51:00Z

← Older revision		Revision as of 14:51, 23 September 2020
Line 60:		Line 60:

	= Running Docking =		= Running Docking =
			'''These scripts are also out of date. Where is setup_zinc15_file_number.py and variations?'''
	* [[Running docking 3.7]] - JJI currently working on this.		* [[Running docking 3.7]] - JJI currently working on this.
	* [[Running DOCK 3.7]] - this seems to be slightly dated.		* [[Running DOCK 3.7]] - this seems to be slightly dated.

Bbender at 14:48, 23 September 2020

2020-09-23T14:48:47Z

← Older revision		Revision as of 14:48, 23 September 2020
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	= Tutorials =		= Tutorials =
	These are getting quite old, need updating		'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''
	* [[DOCK 3.7 2014/09/25 FXa Tutorial]]		* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
	* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded		* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded
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	= Prepare Receptor =		= Prepare Receptor =
			'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''
	* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands		* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
	* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster		* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
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	= Prepare Screening Library =		= Prepare Screening Library =
	For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building		'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''
	* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]		* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
	* [[ligand preparation 3.7]]		* [[ligand preparation 3.7]]

Bbender at 14:46, 23 September 2020

2020-09-23T14:46:40Z

@@ Line 14: / Line 14: @@
 * [[So you want to set up a lab]] - only if you don't already have hardware ready.
 * [[Install DOCK 3.7]]
 * [[Getting started with DOCK 3.7]]
 * [[Blastermaster]] - Prepare input for and then run [[DOCK 3.7]]. Mostly full option list for blastermaster
@@ Line 34: / Line 27: @@
 * [[DOCKovalent lysine inhibitor design tutorial]]
 * [[DOCKovalent cysteine inhibitor design tutorial]]
 = Prepare Receptor =
@@ Line 49: / Line 52: @@
 = Prepare Screening Library =
 * [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
 * [[ligand preparation 3.7]]

Bbender at 14:00, 23 September 2020

2020-09-23T14:00:58Z

← Older revision		Revision as of 14:00, 23 September 2020
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	* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands		* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
	* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster		* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
	* [[Using_thin_spheres_in_DOCK3.7]]		* [[Using_thin_spheres_in_DOCK3.7]] - how to add thin spheres directly during blastermaster run (single set of parameters)
	* [[How to do parameter scanning]]		* [[How to do parameter scanning]] - how to scan various combinations of low dielectric and ligand desolvation thin spheres without rerunning blastermaster
	*[[Matching Sphere Scan]]		*[[Matching Sphere Scan]] - how to randomly perturb the matching sphere
	*[[Removing Spheres (The Chase Method)]]		*[[Removing Spheres (The Chase Method)]] - removing thin spheres around a specific site in the binding pocket instead of having a continuous layer
	* [[Adding Static Waters to the Protein Structure]]		* [[Adding Static Waters to the Protein Structure]]
	* [[Flexible Docking]]		* [[Flexible Docking]]