DOCK Blaster:Tutorial 1 - Revision history

Khtang at 02:22, 11 January 2019

2019-01-11T02:22:31Z

← Older revision		Revision as of 02:22, 11 January 2019
Line 1:		Line 1:
	'''DOCK Blaster Tutorial 1. Dock to Human Thyroid Hormone Receptor Beta-1 (TR beta)''' ~~A[[DOCK Blaster:Tutorials \| DOCK Blaster Tutorial]].~~		'''DOCK Blaster Tutorial 1. Dock to Human Thyroid Hormone Receptor Beta-1 (TR beta)'''
	~~{{TOCright}}~~

			A[[DOCK Blaster:Tutorials \| DOCK Blaster Tutorial]].


			==Step 1==
			a. Browse to the DOCK Blaster main page:
			http://blaster.docking.org/
			and select '''Start with a PDB code''' from the '''DOCK''' pull down menu:
			http://blaster.docking.org/parser.shtml
			b. In the PDB code field, enter 1N46, the PDB code for TR beta.
			http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocashort?id=1N46
			Click on '''DOCK''' to start.

	~~Step 1. Browse to the DOCK Blaster main page:~~
	~~[http://blaster.docking.org/ ] and select~~
	~~"Start with a PDB code" from the "DOCK" pull down menu:~~
	~~[http://blaster.docking.org/parser.shtml]~~
	~~In the PDB code field, enter 1N46, the PDB code for TR beta.~~
	~~[http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocashort?id=1N46]~~
	~~Click on “DOCK” to start.~~

	If you are really impatient you can do all of the above		If you are really impatient you can do all of the above
	by simply clicking here:		by simply clicking here:
	[http://blaster.docking.org/cgi-bin/parser.pl?code=1N46]		http://blaster.docking.org/cgi-bin/parser.pl?code=1N46

	Step 2. You will get a confirmation page showing that the target has been looked up correctly at the PDB. To proceed, click on "DOCK". Write down the DOCK Blaster Job ID number. You will need it. The docking process is now queued, and may have started if the system is not overloaded.		==Step 2==
			You will get a confirmation page showing that the target has been looked up correctly at the PDB. To proceed, click on "DOCK". Write down the DOCK Blaster Job ID number. You will need it. The docking process is now queued, and may have started if the system is not overloaded.
			[[File:DOCK_Blaster_step1a.png\|300px\|center]]

	Step 3. Click on the link to browse progress at the bottom of the page		==Step 3==
			Click on the link to browse progress at the bottom of the page
	http://blaster.docking.org/cgi-bin/jobwatch.pl?job_id=35605&pin=		http://blaster.docking.org/cgi-bin/jobwatch.pl?job_id=35605&pin=
	(replace the job number with your actual job number. This one will not work)		(replace the job number with your actual job number. This one will not work)

Frodo at 00:11, 11 March 2014

2014-03-11T00:11:41Z

← Older revision		Revision as of 00:11, 11 March 2014
Line 37:		Line 37:
	= Literature Cited =		= Literature Cited =
	We refer you to our publications pages for theory and practice of docking and virtual screening.		We refer you to our publications pages for theory and practice of docking and virtual screening.
	* [[Publications:DOCK]]
	* [[Publications:ZINC]]
	* [[Publications:DUD]]
	* [[Publications:Reviews_and_opinion]]
	* [[Publications:Targets]]

	Document status: working tutorial. Please correct any errors you may find.		Document status: working tutorial. Please correct any errors you may find.

	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:Tutorials]]		[[Category:Tutorials]]

Therese: 20 revisions

2012-10-08T20:02:12Z

20 revisions

← Older revision

Revision as of 20:02, 8 October 2012

Frodo at 10:31, 1 September 2009

2009-09-01T10:31:31Z

← Older revision		Revision as of 10:31, 1 September 2009
Line 13:		Line 13:
	If you are really impatient you can do all of the above		If you are really impatient you can do all of the above
	by simply clicking here:		by simply clicking here:
	[http://blaster.docking.or/cgi-bin/parser.pl?code=1N46]		[http://blaster.docking.org/cgi-bin/parser.pl?code=1N46]

	Step 2. You will get a confirmation page showing that the target has been looked up correctly at the PDB. To proceed, click on "DOCK". Write down the DOCK Blaster Job ID number. You will need it. The docking process is now queued, and may have started if the system is not overloaded.		Step 2. You will get a confirmation page showing that the target has been looked up correctly at the PDB. To proceed, click on "DOCK". Write down the DOCK Blaster Job ID number. You will need it. The docking process is now queued, and may have started if the system is not overloaded.

Frodo at 00:19, 15 July 2009

2009-07-15T00:19:28Z

@@ Line 1: / Line 1: @@
-'''DOCK Blaster Tutorial 1. Dock to Mineralocorticoid receptor''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]].
+'''DOCK Blaster Tutorial 1. Dock to Human Thyroid Hormone Receptor Beta-1 (TR beta)''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]].
 {{TOCright}}
-Simply browse to the URL
+Step 1. Browse to the DOCK Blaster main page:
-[http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I
+[http://blaster.docking.org/ ] and select
-http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I]
+"Start with a PDB code" from the "DOCK" pull down menu:
- and click “DOCK” when prompted.
+[http://blaster.docking.org/parser.shtml]
-= Specific Aims =
+Step 4. When the job has finished, you will be in the "Calibration Done" state as shown in the progress bar with the yellow paint near the top of the page.  You will see a report that reports how well docking worked.
-* 1. Can DOCK Blaster re-dock the native ligand close to its crystallographically observed position, with a competitive score?
+Step 5. Interpreting the calibration summary table
-= Background and Significance =
+Step 7. Launching a docking job
 = Literature Cited =

Frodo at 00:02, 13 February 2009

2009-02-13T00:02:15Z

@@ Line 1: / Line 1: @@
 '''DOCK Blaster Tutorial 1. Dock to Mineralocorticoid receptor''' A[[DOCK Blaster:Tutorials | DOCK Blaster Tutorial]].
 {{TOCright}}
 [[Image:2aa2.jpg|thumb|right|Mineralocorticoid receptor, PDB 2aa2]]

JohnIrwin at 05:37, 29 November 2007

2007-11-29T05:37:28Z

← Older revision		Revision as of 05:37, 29 November 2007
Line 23:		Line 23:
	We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare the data yourself. See [[DOCK Blaster:Input Preparation \| Input Preparation]] for details.		We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare the data yourself. See [[DOCK Blaster:Input Preparation \| Input Preparation]] for details.

	== Protocol P1 - Prepare input files ==		== Protocol 1 - Prepare input files ==
	* P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selecting the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files. On windows, you do this by right mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation \| Input Preparation]]).		* P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selecting the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files. On windows, you do this by right mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation \| Input Preparation]]).

	[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]		[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]

	== Protocol P2 - Submit job and review results ==		== Protocol 2 - Submit job and review results ==
	* P2.1. Go to the [http://blaster.docking.org \| DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1). Fill in the form as in the figure, as follows.		* P2.1. Go to the [http://blaster.docking.org \| DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1). Fill in the form as in the figure, as follows.
	** a. In the "Target" field, select the receptor, rec.pdb.		** a. In the "Target" field, select the receptor, rec.pdb.
Line 58:		Line 58:
	Preliminary results above show that docking is able to enrich known actives from among a database of decoys. This suggests that prospective docking for discovery of novel ligands is reasonable and can be expected to suggest interesting compounds to test.		Preliminary results above show that docking is able to enrich known actives from among a database of decoys. This suggests that prospective docking for discovery of novel ligands is reasonable and can be expected to suggest interesting compounds to test.

	== Protocol P3. Dock purchasable fragments ==		== Protocol 3. Dock purchasable fragments ==

	== Protocol P4. Review and interpret docking ==		== Protocol 4. Review and interpret docking ==

	== Protocol P5. Prioritize for testing ==		== Protocol 5. Prioritize for testing ==

	== Protocol P6. Suggested variations ==		== Protocol 6. Suggested variations ==

	== Possible problems & other approaches ==		== Possible problems & other approaches ==

Frodo at 00:59, 28 November 2007

2007-11-28T00:59:51Z

← Older revision		Revision as of 00:59, 28 November 2007
Line 1:		Line 1:
	'''DOCK Blaster Tutorial 1. Dock to Mineralocorticoid receptor''' A[[DOCK Blaster:Tutorials \| DOCK Blaster Tutorial]].		'''DOCK Blaster Tutorial 1. Dock to Mineralocorticoid receptor''' A[[DOCK Blaster:Tutorials \| DOCK Blaster Tutorial]].
			{{TOCright}}
	[[Image:2aa2.jpg\|thumb\|right\|Mineralocorticoid receptor, PDB 2aa2]]		[[Image:2aa2.jpg\|thumb\|right\|Mineralocorticoid receptor, PDB 2aa2]]

Line 13:		Line 13:
	[[Image:Aldosterone.png\|thumb\|right\|Aldostereone, the crystallographically observed ligand of MR in PDB 2aa2]]		[[Image:Aldosterone.png\|thumb\|right\|Aldostereone, the crystallographically observed ligand of MR in PDB 2aa2]]

	~~{{TOCright}}~~

	= Background and Significance =		= Background and Significance =
Line 39:		Line 39:

	If you have followed the steps above, your screen should now look something like Figure Tut1-1 (right).		If you have followed the steps above, your screen should now look something like Figure Tut1-1 (right).
	[[Image:DBtut1_2f.jpg\|thumb\|right\|Figure T1.2 - Scrutinizer - data are uploaded, checked, and the job is started].		[[Image:DBtut1_2f.jpg\|thumb\|right\|Figure T1.2 - Scrutinizer - data are uploaded, checked, and the job is started]].

	* P2.2. Depending on available system resources, your job is now either running, or queued to run when a slot becomes available. If your screen does not look like Figure T1.2, check the input and try again. If the job is still failing after the third attempt, please write to support at docking.org for assistance.		* P2.2. Depending on available system resources, your job is now either running, or queued to run when a slot becomes available. If your screen does not look like Figure T1.2, check the input and try again. If the job is still failing after the third attempt, please write to support at docking.org for assistance.
Line 45:		Line 45:
	* P2.3. Read what is reported by the Scrutinizer (Figure T1.2), and proceed to the Job Watcher by clicking on the link at the bottom of the page when you are ready.		* P2.3. Read what is reported by the Scrutinizer (Figure T1.2), and proceed to the Job Watcher by clicking on the link at the bottom of the page when you are ready.

	* P2.4. You should now be in the Job Watcher (Figure T1.3). Depending on how much time has elapsed, and how busy our cluster is, you will see a progress report of the current status of your job. As time passes, the yellow status indicator should progress from left to right indicating the progress of your job through Target Preparation and Calibration. ~~[[Image:DBtut1_3f.jpg\|thumb\|right\|Figure T1.3]]~~		* P2.4. You should now be in the Job Watcher (Figure T1.3). Depending on how much time has elapsed, and how busy our cluster is, you will see a progress report of the current status of your job. As time passes, the yellow status indicator should progress from left to right indicating the progress of your job through Target Preparation and Calibration.

	* P2.5. If all goes as usual, your job will have completed within an hour. You may reload the Job Watcher at any time to get an updated status report of your job. When calibration is complete, you may review the preliminary results and decide on the next course of action.		* P2.5. If all goes as usual, your job will have completed within an hour. You may reload the Job Watcher at any time to get an updated status report of your job. When calibration is complete, you may review the preliminary results and decide on the next course of action.

	* P2.6 Review Calibration results. blah blah blah.		* P2.6 Review Calibration results. blah blah blah.
			[[Image:DBtut1_3f.jpg\|thumb\|right\|Figure T1.3]]


	~~[[Image:DBtut1_4f.jpg\|thumb\|right\|Figure T1.4]]~~


Line 66:		Line 67:

	== Possible problems & other approaches ==		== Possible problems & other approaches ==

			[[Image:DBtut1_4f.jpg\|thumb\|right\|Figure T1.4]]

	= Literature Cited =		= Literature Cited =

Frodo at 18:59, 27 November 2007

2007-11-27T18:59:58Z

← Older revision		Revision as of 18:59, 27 November 2007
Line 23:		Line 23:
	We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare the data yourself. See [[DOCK Blaster:Input Preparation \| Input Preparation]] for details.		We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare the data yourself. See [[DOCK Blaster:Input Preparation \| Input Preparation]] for details.

	== Protocol P1 - ~~Acquire target structure and prepare~~ input files ==		== Protocol P1 - Prepare input files ==
	* P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selecting the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files. On windows, you do this by right mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation \| Input Preparation]]).		* P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selecting the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files. On windows, you do this by right mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation \| Input Preparation]]).

	[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]		[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]

	== Protocol P2 - Submit job and review ~~preliminary~~ results ==		== Protocol P2 - Submit job and review results ==
	* P2.1. Go to the [http://blaster.docking.org \| DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1). Fill in the form as in the figure, as follows.		* P2.1. Go to the [http://blaster.docking.org \| DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1). Fill in the form as in the figure, as follows.
	** a. In the "Target" field, select the receptor, rec.pdb.		** a. In the "Target" field, select the receptor, rec.pdb.
Line 57:		Line 57:
	Preliminary results above show that docking is able to enrich known actives from among a database of decoys. This suggests that prospective docking for discovery of novel ligands is reasonable and can be expected to suggest interesting compounds to test.		Preliminary results above show that docking is able to enrich known actives from among a database of decoys. This suggests that prospective docking for discovery of novel ligands is reasonable and can be expected to suggest interesting compounds to test.

	== Protocol P3. Dock ~~the "fragment-like"~~ purchasable ~~compounds from ZINC~~ ==		== Protocol P3. Dock purchasable fragments ==

	== Protocol P4. Review and interpret ~~fragment~~ docking ~~results~~ ==		== Protocol P4. Review and interpret docking ==

	== Protocol P5. ~~Follow up calculations and variations~~ ==		== Protocol P5. Prioritize for testing ==

	== Possible problems ~~and alternative~~ approaches ==		== Protocol P6. Suggested variations ==

			== Possible problems & other approaches ==

	= Literature Cited =		= Literature Cited =

Frodo at 18:56, 27 November 2007

2007-11-27T18:56:57Z

← Older revision		Revision as of 18:56, 27 November 2007
Line 19:		Line 19:

	Hippocampal mineralocorticoid receptors play a major role in the control of the hypothalamus-pituitary-adrena (HPA) axis, and thus MR is a target for drug discovery.		Hippocampal mineralocorticoid receptors play a major role in the control of the hypothalamus-pituitary-adrena (HPA) axis, and thus MR is a target for drug discovery.



	= Preliminary Results =		= Preliminary Results =
	We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare data ~~to conform with~~ [[DOCK Blaster:Input Preparation \| ~~DOCK Blaster's~~]] ~~basic requirements. To do this tutorial, please carefully follow the steps below. This tutorial usually takes about two hours, but most of the time is simply waiting~~ for ~~the computers to do the work on our servers~~.		We will attempt to use DOCK Blaster to answer these questions, using data that has been prepared in advance. If you wish to use DOCK Blaster on your own project, you must prepare the data yourself. See [[DOCK Blaster:Input Preparation \| Input Preparation]] for details.

	== Protocol 1 - ~~aquire~~ target structure and prepare input files ==		== Protocol P1 - Acquire target structure and prepare input files ==
			* P1.1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and browse the DUD40 set, selecting the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files. On windows, you do this by right mouse clicking and selecting "save link as". If you are using your own target, you must prepare the files yourself (see [[DOCK Blaster:Input Preparation \| Input Preparation]]).
	* 1. Go to the benchmarking data page [http://data.docking.org/ data.docking.org] and ~~select~~ the DUD40 set, ~~and then~~ the [http://data.docking.org/dud40/mr/ MR set]. Download each of these five files ~~(e.g~~. by right mouse clicking ~~on them if~~ you are ~~in windows~~).

	[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]		[[Image:DBtut1_1f.jpg\|thumb\|right\|Figure T1.1 - Prepare input and launch job]]

	* 2. Go to the [http://blaster.docking.org \| DOCK Blaster page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1).		== Protocol P2 - Submit job and review preliminary results ==
			* P2.1. Go to the [http://blaster.docking.org \| DOCK Blaster main page] and select [http://blaster.docking.org/start.shtml \| Queue A Job] from the DOCK! pull down menu (Figure T1.1). Fill in the form as in the figure, as follows.
	* 3. Fill in the form as follows.		** a. In the "Target" field, select the receptor, rec.pdb.
	** 5. In the next field "~~docked~~ ligand" select the xtal-lig.mol2 ~~file~~.		** b. In the next field, select "Docked ligand" and select the ligand, xtal-lig.mol2.
	** 6. ~~Optionally~~, ~~you may~~ select the actives.smi ~~and~~ inactives.smi ~~from the next two lines~~.		** c. In the "Actives" field, select the actives.smi file.
	** 7. ~~Enter~~ your email address ~~if you wish to receive progress reports by email~~.		** d. In the "Inactives" field, select the inactives.smi file.
	** 8. ~~Enter~~ a ~~brief comment~~ about ~~the calculation~~.		** e. In "Email for reports", enter your email address (optional).
	** 9. ~~(optional: enter cofactor~~.~~par below)~~		** f. In the "Aim of this experiment" field, write a short memo about what you are doing.
			** g. Check your input, and click "DOCK!" when you are ready.

	If you have followed the steps above, your screen should now look something like Figure Tut1-1 (right).		If you have followed the steps above, your screen should now look something like Figure Tut1-1 (right).
			[[Image:DBtut1_2f.jpg\|thumb\|right\|Figure T1.2 - Scrutinizer - data are uploaded, checked, and the job is started].

			* P2.2. Depending on available system resources, your job is now either running, or queued to run when a slot becomes available. If your screen does not look like Figure T1.2, check the input and try again. If the job is still failing after the third attempt, please write to support at docking.org for assistance.

	** 10. ~~Click on "DOCK" to upload the files and begin docking~~. ~~You will be taken to~~ the ~~"Submission~~ Scrutinizer~~", as depicted in~~ Figure ~~Tut1-~~2.		* P2.3. Read what is reported by the Scrutinizer (Figure T1.2), and proceed to the Job Watcher by clicking on the link at the bottom of the page when you are ready.

			* P2.4. You should now be in the Job Watcher (Figure T1.3). Depending on how much time has elapsed, and how busy our cluster is, you will see a progress report of the current status of your job. As time passes, the yellow status indicator should progress from left to right indicating the progress of your job through Target Preparation and Calibration. [[Image:DBtut1_3f.jpg\|thumb\|right\|Figure T1.3]]

	** 11. ~~Your~~ job ~~should now be running~~. ~~If it~~ is ~~not~~, ~~there is either some part~~ of ~~the above instructions you did not follow, or we are currently experiencing problems with our systems~~.		* P2.5. If all goes as usual, your job will have completed within an hour. You may reload the Job Watcher at any time to get an updated status report of your job. When calibration is complete, you may review the preliminary results and decide on the next course of action.

	** 12. ~~Read through the submission scrutinizer, and go to the Job Watcher by clicking on the link at the bottom of the page~~..~~. http://blaster.docking.org/cgi-bin/jobmon.pl~~		* P2.6 Review Calibration results. blah blah blah.

	** 13. You should now be in the Job Watcher. Depending on how much time has elapsed, and how busy our cluster is, you will see a progress report of your job. It might look something like Figure Tut1-3. [[Image:~~DBtut1_3f~~.jpg\|thumb\|right\|Figure T1.3]]		[[Image:DBtut1_4f.jpg\|thumb\|right\|Figure T1.4]]

	** 14. If all goes well, the job will complete in about an hour. You may reload the page at anytime to get updated status of the job progress.

	** 15. Preliminary docking normally begins after the site preparation is complete, often about 15 minutes after you first submitted the job. Once preliminary docking results are available, new links appear in the job watcher to allow you to start to see docked ligands. Caution: until the preliminary docking is complete, it can be misleading to rely upon incomplete preliminary docking results to reach any conclusions about the docking results.

	~~[[Image:DBtut1_4f.jpg\|thumb\|right\|Figure T1.4]]~~

	== ~~Examining the Results ==~~		= Proposed Research =
			Preliminary results above show that docking is able to enrich known actives from among a database of decoys. This suggests that prospective docking for discovery of novel ligands is reasonable and can be expected to suggest interesting compounds to test.

	== ~~Docking a Database~~ ==		== Protocol P3. Dock the "fragment-like" purchasable compounds from ZINC ==

	== ~~Browsing~~ and ~~interpreting the~~ results ==		== Protocol P4. Review and interpret fragment docking results ==

	== Follow up and variations ==		== Protocol P5. Follow up calculations and variations ==

	== Possible problems and alternative approaches ==		== Possible problems and alternative approaches ==




	~~= Research Plan =~~




	= Literature Cited =		= Literature Cited =
			We refer you to our publications pages for theory and practice of docking and virtual screening.
			* [[Publications:DOCK]]
			* [[Publications:ZINC]]
			* [[Publications:DUD]]
			* [[Publications:Reviews_and_opinion]]
			* [[Publications:Targets]]

			Document status: working tutorial. Please correct any errors you may find.





	[[Category:DOCK Blaster]]		[[Category:DOCK Blaster]]
	[[Category:Tutorials]]		[[Category:Tutorials]]