[Dock-fans] Duplicates definition

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 30 11:33:30 PDT 2009


Hi,

On Mon, Jun 15, 2009 at 11:45:51AM +0200, Yogesh Aher wrote:
> Dear Scott,
> 
> Thank you for your reply. I have another query:
> 
> I am using DOCK 6.02 for docking some of my ligands in the protein. With
> anchor_and_grow algorithm used in flexible docking, I get lot of clashes and
> un-acceptable conformations of the ligands, which I think are not valid.
> Will you please let me know how to deal with this kind of problem.

use_internal_energy
use_clash_overlap
bump_filter

are relevant input parameters; see manual for details.

Scott

> On Tue, Jun 9, 2009 at 10:37 PM, Scott Brozell <sbrozell at rci.rutgers.edu>wrote:
> 
> > 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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