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 Blaster:Tutorial 2

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.

DOCK Blaster:Tutorial 3

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.

DOCK Blaster:Tutorial 4

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.

DOCK Blaster:Tutorial 5

Multiple crystal structures available. Multiple actives and inactives available. How to optimise the use of DOCK Blaster for this case.