Difference between revisions of "DOCK Blaster:Tutorials"

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'''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.
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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!).
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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:
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* nuclear receptor
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* enzyme
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* metalloenzyme
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* kinase
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* GPCR
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* 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.  
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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)]] =

Revision as of 01:21, 22 October 2008

Introduction

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 preliminary considerations article. The categories of targets we will consider are:

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

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.

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.

Dock to angiotensin II converting enzyme (ACE)

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

Only apo structure 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.

No crystal structure 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 checking the model of the target for suitability for docking.

Multiple crystal structures available

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.