DOCK Blaster:Tutorials: Difference between revisions
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An additional difficulty is the lack of diagnostics because of no ligand. | An additional difficulty is the lack of diagnostics because of no ligand. | ||
== [[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 == | |||
=== Conceptual Overview === | === Conceptual Overview === | ||
* question 1. | * question 1. | ||
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== | == [[DOCK Blaster:Tutorial 5]] == | ||
Multiple crystal structures available. | |||
Multiple actives and inactives available. | |||
How to optimise the use of DOCK Blaster for this case. | |||
=== Conceptual Overview === | === Conceptual Overview === | ||
* question 1. | * question 1. | ||
Revision as of 15:01, 21 December 2006
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 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:
- 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 Methotrexate (MTX) to Dihydrofolate reductase (DHFR) == This is one of the oldest examples used in molecular docking. It illustrates the use of a single crystal structure with a ligand bound. It illustrates the use of special co factor parameter.
DOCK Blaster:Tutorial 2
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 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.
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 ==
Conceptual Overview
- question 1.
- question 2.
Literature References
From Theory to Action
Acquire Sample Data
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
DOCK Blaster:Tutorial 5
Multiple crystal structures available. Multiple actives and inactives available. How to optimise the use of DOCK Blaster for this case.
Conceptual Overview
- question 1.
- question 2.
Literature References
From Theory to Action
Launch Preliminary Calculation
- step 1
- step 2
- step 3
- step 4
- step 5