Example of Disorder
Here is an example of how to treat disorder manually. It is also and example of how to proceed with DOCK Blaster fails to identify a ligand automatically.
1. 3DJL. fails to work automatically in DOCK Blaster.
2. Download the PDB file.
3. Extract all ATOM cards, including CA and FAD and call it "rec.pdb"
4. Look at the receptor in the graphics.
5. color the disordered side chains (gln48, trp424, gln93, leu132, arg375, lys387, gln488, etc). Which ones impinge on the binding site? Answer 424.
5. Pick disorder model to use: B version of trp424. The rest can be left.
6. Where is the binding site (assuming FAD stays put)? Answer: resiudes 191, 184, 424, 437, 137 circle the binding site. copy these residues into a "binding site definition file"
7. submit to DOCK Blaster, using the start with a structure page.
8. watch the job progress.