[Dock-fans] similarity clustering

Ben Keshet keshet1 at umbc.edu
Mon Apr 19 13:41:12 PDT 2010

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.

Many thanks,

Ben Keshet
PhD Student
Chemical&  Biochemical Engineering
UMBC (Univ. of Maryland, Baltimore County)

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