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 PDB file.

3. Extract all ATOM cards and call it "rec.pdb"

4. Extract FAD ligand and call it "fad.pdb"

5. Extract all disordered side chains. These are Gln48, Trp424, Gln93, Leu132, Arg375. Put them in separate files, and create gln48a.pdb, gln48b.pdb and so on for each disorder model.

6. In the graphics, load rec.pdb, fad.pdb, and each of the "a" versions of the disordered residues.

7. For each residue, consider the implications of the b form. It may be easier to do this with the rec.pdb not displayed.

8. pick the best form of each disordered side chain based on their impact on the presumed binding site.

9. re-incorporate into the protein model.

10. define the binding site by extracting key residues from rec.pdb

11. run dock blaster manually by supplying the files.