We have tried to identify projects that are *representative* of common projects, *illustrative* of the features and weaknesses of this service as it currently stands, and *didactic*, in as much as they illustrate how we imagine this service should be used.
You do not need to run a tutorial before you use DOCK Blaster, but we recommend it and it will not take long. Scan the list and try to pick an example that resembles your current project, in terms of available information and perhaps target class, ligand chemistry, or binding site situation. Please see also the preliminary considerations article for the "big picture". The categories of targets we will consider are: nuclear receptor, enzyme, metallo-enzyme, kinase, GPCR. The types of problems we consider are : good information, minimal information, insufficient information, and excessive information. The level of effort for the tutorial is either easy, moderate, or hard.
Target category: Nuclear receptor Effort: Easy Problem type: Minimal information PDB code: 1L2I
Simply browse to the URL [http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I http://blaster.docking.or/cgi-bin/parser.pl?code=1L2I]
and click “DOCK” when prompted.
Target category: Nuclear receptor Effort: Medium Problem type: Minimal information PDB code: XXXX
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.
This case, also from DUD, illustrates the use of DOCK Blaster on zinc metalloenzymes.
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.
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 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.