Example of Disorder: Difference between revisions

From DISI
Jump to navigation Jump to search
mNo edit summary
 
mNo edit summary
Line 4: Line 4:
1. 3DJL.  fails to work automatically in DOCK Blaster.
1. 3DJL.  fails to work automatically in DOCK Blaster.


2. Download PDB file.  
2. Download the PDB file.  


3. Extract all ATOM cards and call it "rec.pdb"
3. Extract all ATOM cards, including CA and FAD and call it "rec.pdb"


4. Extract FAD ligand and call it "fad.pdb"
4. Look at the receptor in the graphics.


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.
5. color the disordered side chains (gln48, trp424, gln93, leu132, arg375, lys387, gln488, etc). Which ones impinge on the binding site?  Answer 424.


6. In the graphics, load rec.pdb, fad.pdb, and each of the "a" versions of the disordered residues.  
5. Pick disorder model to use: B version of trp424. The rest can be left.


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


8. pick the best form of each disordered side chain based on their impact on the presumed binding site.  
7. submit to DOCK Blaster, using the
[http://blaster.docking.org/start.shtml start with a structure] page.  


9. re-incorporate into the protein model.
8. watch the job progress.
 
10. define the binding site by extracting key residues from rec.pdb
 
11. run dock blaster manually by supplying the files.

Revision as of 19:07, 10 August 2009

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.

Retrieved from "http://wiki.docking.org/index.php?title=Example_of_Disorder&oldid=2769"