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enzyme/small-molecule docking? Vague How_to?

Darren P Nickerson dnicker at black.ox.ac.uk
Tue Jul 5 18:23:50 EST 1994


	This was posted to bionet.molec-model without a reply.  Thought I'd try
for a larger forum before abandoning this:

If anyone could provide suggestions as to the best way to proceed with the
following modelling problem I would be most grateful.  Since entering the
realm of modelling on SGI's my experience has been limited. . .

Using the .pdb coordinates for a given protein, I would like to be able to
probe the interaction of a small molecule with this large enzyme.  We have a
good idea that there exists a "channel" into which a 10-carbon fatty acid
inserts itself, but would like to be able to actually model the complex.

Ideally I would like to be able to do this in InsightII, and Quanta if I have
to.  Basically, I would appreciate a very rough guide as to what must be done,
which modules to use etc.  Can I build the fatty acid in BioPolymer for
instance.  Insertion of this FA into the channel followed by some sort of
energy minimization routing, or interaction energies would be most helpful,
but is this realistic?                    

Thanks in advance for any replies.

-Darren

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