[Dock-fans] orientations and conformations

Scott Brozell sbrozell at rci.rutgers.edu
Wed Jul 1 18:17:51 PDT 2009


Hi,

They both play a role in that they characterize the anchor orientations
used in the ligand growth stage.
pruning_clustering_cutoff is number_confs_for_next_growth 
which is N_c in the equation in
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#PruningtheConformationSearchTree
pruning_max_orients is the maximum number of anchor orientations
before growth.
For more details on the methodology, this might be the best place
to start:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#EwingetalJCAMD2001

Scott

On Wed, Jul 01, 2009 at 08:58:00AM -0700, Ravinder Abrol wrote:
> 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.


More information about the Dock-fans mailing list