[Dock-fans] similarity clustering

Scott Brozell sbrozell at rci.rutgers.edu
Tue Apr 20 19:11:36 PDT 2010


Hi,

On Mon, Apr 19, 2010 at 04:41:12PM -0400, Ben Keshet wrote:
> I have a question that is a little beyond DOCK / ZINC but some users 
> will likely know the answer:
> I want to cluster molecules of a large library based on some simple 
> structure features. Does anyone know any academic-free software that can 
> do that?
> 
> For example, I docked ~360,000 molecules. Some of the molecules in the 
> top 200 are actually very similar structurally, so I want to cluster 
> them into one group. This meant to allow an in-vitro testing of a 
> diverse population. I am sure that this is a pretty common task, however 
> for some reason I am having hard time finding suitable applications.

I haven't done that, but:
http://ligand.info/
might be useful.
Chimera can only do clustering of a
conformational ensemble (where each member contains the same atoms)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html

Try searching the CCL archives.

Scott



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