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 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 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.

A Zn Metalloenzyme

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.

Only apo structure available

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.

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.