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DOCK Blaster Tutorials
'''Introduction'''


== 1. DOCK MTX to DHFR (example of cofactor) ==
*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*
** 1. Go to DOCK Blaster web page [http://blaster.docking.org blaster.docking.org]. Please note that during pre-alpha testing this page is different. Contact [[John Irwin]] for details. [[Image:Tut1-1.jpg|thumb|right|Figure Tut1-1]]
** 2. Click on "Start docking!" to go to the input preparation page.
** 3. Click on "HELP" to open up the documentation for input preparation in a separate window.  
*** 3.1. In the documentation window, click on "Sample Data" at the end of the first paragraph.
*** 3.2 In the sample data window, click on the link to data.docking.org
*** 3.3. Click on DUD40.
*** 3.4. Click on CDK2.
*** 3.5. Right mouse to save all five files in this directory on your disk.
*** 3.6. Close the documentation window, returning to the DOCK Blaster input form.
** 4. Click on the first "Browse" button (to the right of Target) and select the rec.pdb file you just downloaded.
** 5. In the next field "docked ligand" select the xtal-lig.mol2 file.
** 6. Optionally, you may select the actives.smi and inactives.smi from the next two lines. [[Image:Tut1-2.jpg|thumb|right|Figure Tut1-2]]
** 7. Enter your email address if you wish to receive progress reports by email.
** 8. Enter a brief comment about the calculation.
** 9. (optional: enter cofactor.par below)


If you have followed the steps above, your screen should now look something like Figure Tut1-1 (right).
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.


** 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.
{{TOCright}}


** 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.
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.  


** 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/jobwatch.pl?job_id=32&pin=
= [[DOCK Blaster:Tutorial 1 | Dock to human thyroid hormone beta-1]] =
* Target category: Nuclear receptor
* Effort: Easy
* Problem type: Minimal information
* PDB code: 1N46


** 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:Tut1-3.jpg|thumb|right|Figure Tut1-3]]
= [[DOCK Blaster:Tutorial 2 | Dock to minearalocorticoid receptor (MR)]] =
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX


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


** 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.
= [[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.




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


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


== 2. DOCK X to carbonic anhydrase (example of metalloenzyme) ==
This case, also from [[DUD]], illustrates the use of DOCK Blaster on zinc metalloenzymes.


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


== 3. DOCK to target X, but no ligand available ==
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX


== 4. DOCK to Y, many controls 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.


== 5. ==
= [[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.
Describes the use of Blast/Modbase to obtain and evaluate a structure.
Describes checking the model of the target for suitability for docking.
 
= [[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 actives and inactives available.
How to optimise the use of DOCK Blaster for this case.
 
You are welcome to write new tutorials - this IS a wiki! You are also welcome to suggest new tutorials, to support at docking.org.
 
[[Category:DOCK Blaster]]
[[Category:Tutorials]]

Latest revision as of 20:02, 8 October 2012

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.

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 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 to human thyroid hormone beta-1

  • Target category: Nuclear receptor
  • Effort: Easy
  • Problem type: Minimal information
  • PDB code: 1N46

Dock to minearalocorticoid receptor (MR)

  • Target category: Nuclear receptor
  • Effort: Medium
  • Problem type: Minimal information
  • 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.

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.


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.

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. 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.

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. Describes the use of Blast/Modbase to obtain and evaluate a structure. Describes checking the model of the target for suitability for docking.

Multiple crystal structures available

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


Multiple crystal structures available. Multiple actives and inactives available. How to optimise the use of DOCK Blaster for this case.

You are welcome to write new tutorials - this IS a wiki! You are also welcome to suggest new tutorials, to support at docking.org.

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