Example of Disorder - Revision history

Frodo at 16:12, 14 February 2014

2014-02-14T16:12:32Z

← Older revision		Revision as of 16:12, 14 February 2014
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	8. watch the job progress.		8. watch the job progress.

	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]
	[[Category:Docking]]		[[Category:Docking]]

Frodo at 03:34, 14 February 2014

2014-02-14T03:34:58Z

← Older revision		Revision as of 03:34, 14 February 2014
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	8. watch the job progress.		8. watch the job progress.

			[[Category:Tutorial]]
			[[Category:Docking]]

Therese: 2 revisions

2012-10-08T20:24:11Z

2 revisions

← Older revision

Revision as of 20:24, 8 October 2012

Frodo at 19:07, 10 August 2009

2009-08-10T19:07:16Z

← Older revision		Revision as of 19:07, 10 August 2009
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	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~~.

Frodo at 18:11, 10 August 2009

2009-08-10T18:11:46Z

New page

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.