DOCK Blaster:Tutorials: Difference between revisions

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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.


{{TOCright}}
{{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.


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
 
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)]] =
 
* 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 65:


= [[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.

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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