DOCK Blaster:Tutorials: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
No edit summary
Line 12: Line 12:
* a consideration of problems that may occur and what to do about them
* a consideration of problems that may occur and what to do about them


== [[DOCK Blaster:Tutorial 1]]: DOCK Methotrexate (MTX) to Dihydrofolate reductase (DHFR) ==
== [[DOCK Blaster:Tutorial 1]] ==
DOCK Methotrexate (MTX) to Dihydrofolate reductase (DHFR) ==
This is one of the oldest examples used in molecular docking.
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 a single crystal structure with a ligand bound.
Line 18: Line 19:




== DOCK X to carbonic anhydrase (example of metalloenzyme) ==
== [[DOCK Blaster:Tutorial 2]] ==
DOCK arylsulfonamide to carbonic anhydrase.
This is an example of docking to Zn metalloenzymes.
 
 
=== Conceptual Overview ===
=== Conceptual Overview ===
* question 1.
* question 1.

Revision as of 14:55, 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.


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 to target X, but no ligand available

Conceptual Overview

  • question 1.
  • question 2.

From Theory to Action

Acquire Sample Data

Launch Preliminary Calculation

Examining the Results

Docking a Database

Follow up, variations

Possible problems and alterative strategies

DOCK to Y, 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

No title yet

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