DOCK Blaster:Tutorials

Introduction

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. We recommend you complete at least one tutorial before trying with your own data. If you have to pick only one, we suggest you choose the tutorial that most closely resembles your own research situation. Each of these tutorials should provide a useful first time experience for a beginner. Each 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. (If not, 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, also from DUD with an extensive literature. It serves to illustrate the use of a co-factor bound to the target.

Dock to angiotensin II converting enzyme (ACE)

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' 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.