DOCK Blaster:Tutorials

Introduction to Tutorials

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. They are scripted in a way that you might actually use in your research. We also offer protocols, which differ from tutorials by being more abstract, more modular and more focused on the desired end result. Tutorials are thus more illustrative of how to use DOCK Blaster for those who have never used it before. Any one of these tutorials should provide a useful first time experience for beginners. Each one is targeted at a particular kind of docking scenario, some of which are further discussed in the preliminary considerations article.

Each tutorial contains:

• a conceptual summary
• literature references
• a consideration of the practical details in adapting theory to calculation
• pointers to available data
• step by step instructions including with screenshots
• a guide to how to interpret and use the results
• suggestions of follow up experiments and variations
• a consideration of possible problems and alternative approaches

Dock to COX-2

The simplest illustration of the use of DOCK Blaster.

Special feature: none.

Dock MTX to DHFR

DOCK Methotrexate (MTX) to Dihydrofolate reductase (DHFR). This is one of the oldest examples used in molecular docking, for which there is an extensive literature (refs, reviews). It illustrates the use of a single crystal structure of an enzyme target with a ligand bound. It illustrates the handling of a co-factor in docking.

Special feature: uses a cofactor (NADPH).

A Zn Metalloenzyme

DOCK and arylsulfonamide to carbonic anhydrase and suggest compounds to purchase.

Special feature: the use of special ZINC subsets containing relevantly deprotonated ligands.

Only apo structure available

DOCK to cruzain, a cystein protease target for Chagas's 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.

Special feature: 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.

Special feature: use of multiple crystal structures.