DOCK Blaster:Tutorials: Difference between revisions

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== Introduction to Tutorials ==
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'''Introduction to Tutorials'''
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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]].
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]].



Revision as of 17:45, 21 December 2006

Introduction to Tutorials

__DISAMBIG__

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

Examining the Results

Docking a Database

Follow up, variations

Possible problems and alterative strategies