[Dock-fans] Duplicates definition

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 9 13:37:42 PDT 2009


Hi,

On Thu, Jun 04, 2009 at 03:36:38PM +0200, Yogesh Aher wrote:
> 
> I couldn't find in the documentation, How the DOCK algorithm defines the
> duplicate poses? Whether it considers interactions or the RSMD or
> surrounding residues!
> Also, whether they are deleted or kept as such in the final output of
> flexible as well as rigid docking methods.

One could say that there are no duplicate poses due to the nature of
pose generation.  But note that there can be scoring, minimizing,
and rmsd clustering involved in the process.

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OrientingtheLigand
Matches are formed best first, with respect to the difference
in the ligand and site point internal distances. 

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AnchorandGrow
The anchor orientations are evaluated and optimized using the scoring ...

As far as output details, see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput

Scott



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