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'''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.
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{{TOCright}}
'''Introduction to Tutorials'''


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. They are scripted in a way that you might actually use in your research. We also offer [[DOCK Blaster:Protocols | protocols]], which differ from tutorials by being more abstract, more modular and more focused on the desired end result. Tutorials are thus more illustrative of how to use [[DOCK Blaster]] for those who have never used it before. Any one of these tutorials should provide a useful first time experience for beginners. Each one is targeted at a particular kind of docking scenario, some of which are further discussed in the [[DOCK Blaster:Preliminaries | preliminary considerations]] article.
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.  


Each tutorial contains:
= [[DOCK Blaster:Tutorial 1 | Dock to human thyroid hormone beta-1]] =
* a conceptual summary
* Target category: Nuclear receptor
* literature references
* Effort: Easy
* a consideration of the practical details in adapting theory to calculation
* Problem type: Minimal information
* pointers to available data
* PDB code: 1N46
* step by step instructions including with screenshots
* a guide to how to interpret and use the results
* suggestions of follow up experiments and variations
* a consideration of possible problems and alternative approaches


== [[DOCK Blaster:Tutorial 1 | Dock to COX-2]] ==
= [[DOCK Blaster:Tutorial 2 | Dock to minearalocorticoid receptor (MR)]] =
The simplest illustration of the use of DOCK Blaster.
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX


Special feature: none.
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 2 | Dock MTX to DHFR]] ==
* Target category: Nuclear receptor
DOCK Methotrexate (MTX) to Dihydrofolate reductase (DHFR).
* Effort: Medium
This is one of the oldest examples used in molecular docking, for which there is an extensive literature (refs, reviews). It illustrates the use of a single crystal structure of an enzyme target with a ligand bound. It illustrates the handling of a co-factor in docking.
* Problem type: Minimal information
* PDB code: XXXX


Special feature: uses a cofactor (NADPH).
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 | A Zn Metalloenzyme]] ==
= [[DOCK Blaster:Tutorial 4 | Dock to angiotensin II converting enzyme (ACE)]] =
DOCK and arylsulfonamide to carbonic anhydrase and suggest compounds to purchase.


Special feature: the use of special ZINC subsets containing relevantly deprotonated ligands.
* 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.


== [[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's 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.


Special feature: lack of diagnostics because of no available ligand.
* 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.
 
= [[DOCK Blaster:Tutorial 6 | No crystal structure available]] =
 
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX




== [[DOCK Blaster:Tutorial 5 | 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 7 | Multiple crystal structures available]] =
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX




== [[DOCK Blaster:Tutorial 6 | Multiple crystal structures available]] ==
Multiple crystal structures available.  
Multiple crystal structures available.  
Multiple actives and inactives available.
Multiple actives and inactives available.
How to optimise the use of DOCK Blaster for this case.
How to optimise the use of DOCK Blaster for this case.


Special feature: use of multiple crystal structures.
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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