DOCK Blaster:Tutorials: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
m (40 revisions)
 
(26 intermediate revisions by 2 users not shown)
Line 1: Line 1:
{{Wiktionary}}
'''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}}
'''Introduction to Tutorials'''
DOCK Blaster 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 we imagine you might actually use DOCK Blaster for research. We also offer [[DOCK Blaster:Protocols | protocols]], which are designed to illustrate in a more abstract form many more of the tasks that can be performed using [[DOCK Blaster]].


Each tutorial contains:
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.
* a conceptual summary of the scientific questions being investigated
* pointers to relevant literature
* a consideration of the practical details in adapting theory to calculation
* pointers to available data to use
* step by step instructions, with screenshots, describing how to proceed
* a guide to how to evaluate and use the results
* suggestions of follow up experiments, variations
* a consideration of problems that may occur and what to do about them


== [[DOCK Blaster:Tutorial 1]] ==
= [[DOCK Blaster:Tutorial 1 | Dock to human thyroid hormone beta-1]] =
DOCK Methotrexate (MTX) to Dihydrofolate reductase (DHFR) ==
* Target category: Nuclear receptor
This is one of the oldest examples used in molecular docking.
* Effort: Easy
It illustrates the use of a single crystal structure with a ligand bound.
* Problem type: Minimal information
It illustrates the use of special co factor parameter.
* PDB code: 1N46


= [[DOCK Blaster:Tutorial 2 | Dock to minearalocorticoid receptor (MR)]] =
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX


== [[DOCK Blaster:Tutorial 2]] ==
A [[nuclear hormone receptor]], drawn from [[DUD]], that illustrates the use of DOCK Blaster when both actives and inactive controls are available.
DOCK arylsulfonamide to carbonic anhydrase.
This is an example of docking to Zn metalloenzymes.
Also describes the use of special ZINC subsets containing relevantly deprotonated ligands.


== [[DOCK Blaster:Tutorial 3]] ==
= [[DOCK Blaster:Tutorial 3 | Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] =
DOCK to target X, 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.
An additional difficulty is the lack of diagnostics because of no ligand.


* 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 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.


, many controls available ==
= [[DOCK Blaster:Tutorial 4 | Dock to angiotensin II converting enzyme (ACE)]] =
=== Conceptual Overview ===
* question 1.
* question 2.
=== Literature References ===


=== From Theory to Action ===
* 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.


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


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


=== Launch Preliminary Calculation ===
DOCK to cruzain, a cystein protease target for Chagas' Disease, for which only an apo structure is available.
** step 1
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.
** step 2
** step 3
** step 4
** step 5


=== Examining the Results ===
= [[DOCK Blaster:Tutorial 6 | No crystal structure available]] =


=== Docking a Database ===
* Target category: Nuclear receptor
* Effort: Medium
* Problem type: Minimal information
* PDB code: XXXX


=== Follow up, variations ===


=== Possible problems and alterative strategies ===
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




== [[DOCK Blaster:Tutorial 5]] ==
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.


=== Conceptual Overview ===
You are welcome to write new tutorials - this IS a wiki! You are also welcome to suggest new tutorials, to support at docking.org.
* question 1.
* question 2.
=== Literature References ===
 
 
=== From Theory to Action ===
 
 
=== Launch Preliminary Calculation ===
** step 1
** step 2
** step 3
** step 4
** step 5
 
=== Examining the Results ===
 
=== Docking a Database ===
 
=== Follow up, variations ===


=== Possible problems and alterative strategies ===
[[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.

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_Blaster:Tutorials&oldid=1098"