[Dock-fans] orientations and conformations

Ravinder Abrol abrol at wag.caltech.edu
Wed Jul 1 08:58:00 PDT 2009


Hi Scott,
Thanks for your reply. Can you clarify a bit the definitions of 
pruning_max_orients and pruning_clustering_cutoff in terms of the 
methodology? It is not clear from the definitions provided by you, whether 
these play any role in the sampling of the flexible part of the ligand.
Ravi

--------------------------------------------------------------------
On Tuesday 30 June 2009 17:41, Scott Brozell wrote:
> Hi,
>
> On Mon, Jun 22, 2009 at 04:17:32AM -0700, Ravinder Abrol wrote:
> > I am running Dock 6.2 using a flexible ligand for generating many poses
> > to use with our own scoring functions and I want to control the number of
> > conformations that are generated at the end. I am only using bumps and
> > clash_overlap to eliminate poses. I understand the anchor and grow
> > approach but how I can control it with the available input options
> > available is not clear to me. I am providing below results of two runs
> > along with partial input used to generate them. If you can help me make
> > sense of the numbers, that will greatly help.
> >
> > >Run1
> >
> > Input1:
> > max_orientations  1000
> > pruning_use_clustering  yes
> > pruning_max_orients  100
> > pruning_clustering_cutoff  1000
> > Output1:
> >  Anchors: 1
> >  Orientations:  492
> >  Conformations:  975
> >
> > >Run2
> >
> > Input2:
> > max_orientations  1000
> > pruning_use_clustering  yes
> > pruning_max_orients  1000
> > pruning_clustering_cutoff  1000
> > Output2:
> >  Anchors:  1
> >  Orientations:  492
> >  Conformations:  1023
> >
> > Does 492 mean that it found 492 possible placements of the anchor?
>
> Yes, where a placement means
> rigidly oriented in the active site (orientation) by matching its
> heavy atoms centers to the receptor sphere centers
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AnchorandGrow
> i.e., the anchor was docked 492 ways.
>
> > If yes, then how is pruning_max_orients and pruning_clustering_cutoff
> > used? I don't understand that in Run2 I specified 1000 for
> > pruning_clustering_cutoff, but at the end I got 1023 conformations.
>
> The above anchor orientations are then ranked according to their score,
> spatially clustered by heavy atom root mean squared deviation (RMSD), and
> pruned
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#PruningtheConformation
>SearchTree Note that the definitions of pruning_max_orients and
> pruning_clustering_cutoff are swapped in the manual; they should be
>
>     (if pruning_use_clustering = yes)
>
>     * pruning_max_orients [100] (int):
>       #The maximum number of anchor orientations carried forward in the
> anchor & grow #search (previously named num_anchor_orients_for_growth)
>     * pruning_clustering_cutoff [100] (int):
>       #The pruning value cutoff for anchor orientations promoted to the
>       #conformational search (previously named
> number_confs_for_next_growth) #Note that this is the N_c in the Pruning the
> Conformation Search Tree #equation.
>
> Thus in run2 pruning_max_orients is greater and more Conformations are
> ultimately obtained after growth.
>
> > In other words, is there a way to control the final number of
> > conformations that are generated?
>
> Yes for normal DOCKing calculations; see e.g., num_scored_conformers
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
> The controls are not designed for preempted running that merely
> generates structures.
>
> Scott

-- 
________________________________________________

 Ravinder Abrol
 139-74, Beckman Institute
 Division of Chemistry and Chemical Engineering
 Caltech, Pasadena, CA 91125
 Phone: 1.626.395.8143
   Fax: 1.626.585.0917
 Email: abrol at wag.caltech.edu
________________________________________________


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