DOCK Blaster:Tutorials - Revision history

Therese: 40 revisions

2012-10-08T20:02:14Z

40 revisions

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Revision as of 20:02, 8 October 2012

Frodo at 10:30, 1 September 2009

2009-09-01T10:30:32Z

← Older revision		Revision as of 10:30, 1 September 2009
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	'''Introduction'''		'''Introduction'''

			NOTE: these tutorials did not get finished before the paper appeared in J Med Chem. Please manage as best you can until we write them properly

	We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of [[DOCK Blaster]] as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.		We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of [[DOCK Blaster]] as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.

Frodo at 23:32, 14 July 2009

2009-07-14T23:32:49Z

← Older revision		Revision as of 23:32, 14 July 2009
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	'''Introduction'''		'''Introduction'''

	We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of ~~this service~~ as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.		We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of [[DOCK Blaster]] as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.

	{{TOCright}}		{{TOCright}}

Frodo at 23:26, 14 July 2009

2009-07-14T23:26:08Z

← Older revision		Revision as of 23:26, 14 July 2009
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	You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.		You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.

	= [[DOCK Blaster:Tutorial 1 \| Dock to human ~~estrogen receptor alpha, ER~~-~~alpha~~]] =		= [[DOCK Blaster:Tutorial 1 \| Dock to human thyroid hormone beta-1]] =
	* Target category: Nuclear receptor		* Target category: Nuclear receptor
	* Effort: Easy		* Effort: Easy
	* Problem type: Minimal information		* Problem type: Minimal information
	* PDB code: ~~1L2I~~		* PDB code: 1N46

	= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =		= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =

Frodo: /* Dock to human estrogen receptor alpha, ER-alpha */

2009-02-13T00:02:01Z

Dock to human estrogen receptor alpha, ER-alpha

← Older revision		Revision as of 00:02, 13 February 2009
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	* Problem type: Minimal information		* Problem type: Minimal information
	* PDB code: 1L2I		* PDB code: 1L2I

	~~Simply browse to the URL~~
	~~[http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I~~
	~~http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I]~~
	~~and click “DOCK” when prompted.~~

	= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =		= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =

Frodo at 23:58, 12 February 2009

2009-02-12T23:58:24Z

← Older revision		Revision as of 23:58, 12 February 2009
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	= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha]] =		= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha]] =
	Target category: Nuclear receptor		* Target category: Nuclear receptor
	Effort: Easy		* Effort: Easy
	Problem type: Minimal information		* Problem type: Minimal information
	PDB code: 1L2I		* PDB code: 1L2I

	Simply browse to the URL		Simply browse to the URL
Line 19:		Line 19:

	= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =		= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =
			* Target category: Nuclear receptor
	Target category: Nuclear receptor		* Effort: Medium
	Effort: Medium		* Problem type: Minimal information
	Problem type: Minimal information		* PDB code: XXXX
	PDB code: XXXX

	A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.		A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.

	= [[DOCK Blaster:Tutorial 3 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =		= [[DOCK Blaster:Tutorial 3 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =

			* Target category: Nuclear receptor
			* Effort: Medium
			* Problem type: Minimal information
			* PDB code: XXXX

	This is a classic case from the history of molecular docking, also from [[DUD]] with an extensive literature. It serves to illustrate the use of a co-factor bound to the target.		This is a classic case from the history of molecular docking, also from [[DUD]] with an extensive literature. It serves to illustrate the use of a co-factor bound to the target.


	= [[DOCK Blaster:Tutorial 4 \| Dock to angiotensin II converting enzyme (ACE)]] =		= [[DOCK Blaster:Tutorial 4 \| Dock to angiotensin II converting enzyme (ACE)]] =

			* Target category: Nuclear receptor
			* Effort: Medium
			* Problem type: Minimal information
			* PDB code: XXXX

	This case, also from [[DUD]], illustrates the use of DOCK Blaster on zinc metalloenzymes.		This case, also from [[DUD]], illustrates the use of DOCK Blaster on zinc metalloenzymes.

	= [[DOCK Blaster:Tutorial 5 \| Only apo structure available]] =		= [[DOCK Blaster:Tutorial 5 \| Only apo structure available]] =

			* Target category: Nuclear receptor
			* Effort: Medium
			* Problem type: Minimal information
			* PDB code: XXXX

	DOCK to cruzain, a cystein protease target for Chagas' Disease, for which only an apo structure is available.		DOCK to cruzain, a cystein protease target for Chagas' Disease, for which only an apo structure is available.
	Describes both modeling a ligand in, and using protein residues in the binding site to indicate the binding site. Lack of diagnostics because of no available ligand.		Describes both modeling a ligand in, and using protein residues in the binding site to indicate the binding site. Lack of diagnostics because of no available ligand.

	= [[DOCK Blaster:Tutorial 6 \| No crystal structure available]] =		= [[DOCK Blaster:Tutorial 6 \| No crystal structure available]] =

			* Target category: Nuclear receptor
			* Effort: Medium
			* Problem type: Minimal information
			* PDB code: XXXX


	DOCK to a target for which no crystal structure is available.		DOCK to a target for which no crystal structure is available.
	Describes the use of Blast/Modbase to obtain and evaluate a structure.		Describes the use of Blast/Modbase to obtain and evaluate a structure.
Line 43:		Line 68:

	= [[DOCK Blaster:Tutorial 7 \| Multiple crystal structures available]] =		= [[DOCK Blaster:Tutorial 7 \| Multiple crystal structures available]] =

			* Target category: Nuclear receptor
			* Effort: Medium
			* Problem type: Minimal information
			* PDB code: XXXX


	Multiple crystal structures available.		Multiple crystal structures available.
	Multiple actives and inactives available.		Multiple actives and inactives available.

Frodo at 23:56, 12 February 2009

2009-02-12T23:56:15Z

← Older revision		Revision as of 23:56, 12 February 2009
Line 2:		Line 2:

	We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.		We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.

			{{TOCright}}

	You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.		You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.

	~~{{TOCright}}~~

	= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha]] =		= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha]] =

Frodo at 23:56, 12 February 2009

2009-02-12T23:56:01Z

← Older revision		Revision as of 23:56, 12 February 2009
Line 1:		Line 1:
	'''Introduction'''		'''Introduction'''

	~~{{TOCright}}~~

	We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.		We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.
Line 7:		Line 5:
	You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.		You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.

	= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha =		{{TOCright}}

			= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha]] =
	Target category: Nuclear receptor		Target category: Nuclear receptor
	Effort: Easy		Effort: Easy

Frodo at 23:55, 12 February 2009

2009-02-12T23:55:19Z

← Older revision		Revision as of 23:55, 12 February 2009
Line 1:		Line 1:
	'''Introduction'''		'''Introduction'''

	{{TOCright}}		{{TOCright}}
	Tutorials are a pragmatic way to get started. We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate by example how we imagine this service should be used.

	You do not need to run a tutorial before you use DOCK Blaster, but it ~~doesn't hurt, won't~~ take long~~, and is recommended~~. ~~Try~~ to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article. The categories of targets we will consider are:		We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate how we imagine this service should be used.

			You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.

			= [[DOCK Blaster:Tutorial 1 \| Dock to human estrogen receptor alpha, ER-alpha =
			Target category: Nuclear receptor
			Effort: Easy
			Problem type: Minimal information
			PDB code: 1L2I

			Simply browse to the URL
			[http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I
			http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I]
			and click “DOCK” when prompted.

			= [[DOCK Blaster:Tutorial 2 \| Dock to minearalocorticoid receptor (MR)]] =

	* nuclear receptor		Target category: Nuclear receptor
	* enzyme		Effort: Medium
	* metalloenzyme		Problem type: Minimal information
	* kinase		PDB code: XXXX
	* GPCR
	* homology model

	~~= [[DOCK Blaster:Tutorial 1 \| Dock to minearalocorticoid receptor (MR)]] =~~
	A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.		A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.

	= [[DOCK Blaster:Tutorial 2 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =		= [[DOCK Blaster:Tutorial 3 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =
	This is a classic case from the history of molecular docking, also from [[DUD]] with an extensive literature. It serves to illustrate the use of a co-factor bound to the target.		This is a classic case from the history of molecular docking, also from [[DUD]] with an extensive literature. It serves to illustrate the use of a co-factor bound to the target.

	= [[DOCK Blaster:Tutorial 3 \| Dock to angiotensin II converting enzyme (ACE)]] =		= [[DOCK Blaster:Tutorial 4 \| Dock to angiotensin II converting enzyme (ACE)]] =
	This case, also from [[DUD]], illustrates the use of DOCK Blaster on zinc metalloenzymes.		This case, also from [[DUD]], illustrates the use of DOCK Blaster on zinc metalloenzymes.

	= [[DOCK Blaster:Tutorial 4 \| Only apo structure available]] =		= [[DOCK Blaster:Tutorial 5 \| Only apo structure available]] =
	DOCK to cruzain, a cystein protease target for Chagas' Disease, for which only an apo structure is available.		DOCK to cruzain, a cystein protease target for Chagas' Disease, for which only an apo structure is available.
	Describes both modeling a ligand in, and using protein residues in the binding site to indicate the binding site. Lack of diagnostics because of no available ligand.		Describes both modeling a ligand in, and using protein residues in the binding site to indicate the binding site. Lack of diagnostics because of no available ligand.

	= [[DOCK Blaster:Tutorial 5 \| No crystal structure available]] =		= [[DOCK Blaster:Tutorial 6 \| No crystal structure available]] =
	DOCK to a target for which no crystal structure is available.		DOCK to a target for which no crystal structure is available.
	Describes the use of Blast/Modbase to obtain and evaluate a structure.		Describes the use of Blast/Modbase to obtain and evaluate a structure.
	Describes checking the model of the target for suitability for docking.		Describes checking the model of the target for suitability for docking.

	= [[DOCK Blaster:Tutorial 6 \| Multiple crystal structures available]] =		= [[DOCK Blaster:Tutorial 7 \| Multiple crystal structures available]] =
	Multiple crystal structures available.		Multiple crystal structures available.
	Multiple actives and inactives available.		Multiple actives and inactives available.

Frodo at 01:21, 22 October 2008

2008-10-22T01:21:29Z

← Older revision		Revision as of 01:21, 22 October 2008
Line 1:		Line 1:
	'''Introduction'''		'''Introduction'''
	{{TOCright}}		{{TOCright}}
	~~These tutorials~~ are ~~designed to illustrate the use of DOCK Blaster using real world examples, with data drawn from and referenced back~~ to ~~the chemical and biological literature~~. We ~~recommend you complete at least one tutorial before trying with your own data. If you~~ have to ~~pick only one~~, ~~we suggest you choose~~ the ~~tutorial that most closely resembles your own research situation. Each~~ of ~~these tutorials should provide a useful first time experience for a beginner. Each is targeted at a particular kind of docking scenario~~, ~~some of which are further discussed~~ in ~~the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article~~.		Tutorials are a pragmatic way to get started. We have tried to identify projects that are representative of common projects, illustrative of the features and weaknesses of this service as it currently stands, and didactic, in as much as they illustrate by example how we imagine this service should be used.

	~~Tutorials are organized like~~ a ~~grant~~, ~~which we hope you find helpful~~. ~~(If not~~, ~~let us know!)~~.		You do not need to run a tutorial before you use DOCK Blaster, but it doesn't hurt, won't take long, and is recommended. Try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the [[DOCK Blaster:Preliminaries \| preliminary considerations]] article. The categories of targets we will consider are:

			* nuclear receptor
			* enzyme
			* metalloenzyme
			* kinase
			* GPCR
			* homology model

	= [[DOCK Blaster:Tutorial 1 \| Dock to minearalocorticoid receptor (MR)]] =		= [[DOCK Blaster:Tutorial 1 \| Dock to minearalocorticoid receptor (MR)]] =
	A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.		A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.

	= [[DOCK Blaster:Tutorial 2 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =		= [[DOCK Blaster:Tutorial 2 \| Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =