DOCK Blaster:Tutorials: Difference between revisions
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'''Introduction to Tutorials''' | '''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. | 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. If you have to pick one, we suggest you choose a tutorial that most closely resembles your own research situation. 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. | ||
{{TOCright}} | {{TOCright}} | ||
Tutorials are organized like a grant, which we hope you find helpful. (Let us know!). | |||
= [[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. | |||
= [[DOCK Blaster:Tutorial 2 | Dock methotrexate (MTX) to dihydrofolate reductase (DHFR)]] = | |||
This is a classic case from the history of molecular docking, with an extensive literature, and serves to illustrate the use of a co-factor bound to the target. | |||
= [[DOCK Blaster:Tutorial 3 | Dock to angiotensin II converting enzyme (ACE), a zinc Metalloenzyme]] = | |||
This case, also from DUD, illustrates the use of DOCK Blaster on zinc metalloenzymes. | |||
= [[DOCK Blaster:Tutorial 4 | Only apo structure available]] = | |||
DOCK to cruzain, a cystein protease target for Chagas's Disease, for which only an apo structure is 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. | 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 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 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. | ||
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:DOCK Blaster]] | ||
[[Category:Tutorials]] | [[Category:Tutorials]] | ||
Revision as of 01:44, 28 November 2007
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. If you have to pick one, we suggest you choose a tutorial that most closely resembles your own research situation. 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 preliminary considerations article.
Tutorials are organized like a grant, which we hope you find helpful. (Let us know!).
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, with an extensive literature, and serves to illustrate the use of a co-factor bound to the target.
Dock to angiotensin II converting enzyme (ACE), a zinc Metalloenzyme
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'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. 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.