[Dock-fans] Sphere Generation

Scott Brozell sbrozell at scripps.edu
Fri Apr 4 14:52:01 PDT 2008


Hi,

On Fri, 4 Apr 2008, Imtiaz M. wrote:

> I am following the DOCk tutorial for my Docking Experiment.
> 
> For sphere generation I have found the following in the tutorial
> 
> OPTION 1.
> To convert the first and largest cluster in the sphere file to pdb format,
> use the command "showsphere < sphgen_cluster.in"
> http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/sphgen_cluster.in>".
> Below is a picture of the largest cluster, where the protein is shown in
> purple and the spheres are shown in yellow
> (sphgen_cluster.pdb<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/sphgen_cluster.pdb>
> 
> I do not know the active site in my receptor file  now how I can
> create "sphgen_cluster.sph"
> so that I can use this instead of selected _sphere.sph  or other wise  how i
> can creat my selected _sphere.sph if active site is not known to me.

The tutorial also contains:
The largest cluster is typically the ligand binding site of the receptor.

Another option is to use all the clusters; this is only tractable if the
number of spheres is not too big.  If it is too big then use divide and conquer
to create several smaller managable targets by going back to step 1.

On the other hand there are usually clues to the likely active site(s):
visualize the receptor; examine the literature.

Scott





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