[Dock-fans] orientations and conformations

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 30 17:41:24 PDT 2009


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
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
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

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
The controls are not designed for preempted running that merely
generates structures.


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