DOCK Blaster:Tutorials

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 X to carbonic anhydrase (example of metalloenzyme)

Conceptual Overview

• question 1.
• question 2.

Launch Preliminary Calculation

• • step 1
  • step 2
  • step 3
  • step 4
  • step 5

DOCK to target X, but no ligand available

Conceptual Overview

• question 1.
• question 2.

DOCK to Y, many controls available

Conceptual Overview

• question 1.
• question 2.

Launch Preliminary Calculation

• • step 1
  • step 2
  • step 3
  • step 4
  • step 5

No title yet

Conceptual Overview

• question 1.
• question 2.

Launch Preliminary Calculation

• • step 1
  • step 2
  • step 3
  • step 4
  • step 5