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PostPosted: Thu Jan 14, 2016 3:31 pm 
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Joined: Tue Jan 12, 2016 4:44 pm
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Good morning,

We are about to synthesize a potential inactivator that is intended to bind covalently to an active site cysteine. Several structures of this enzyme have been published. Naturally we are interested in making an inhibitor that interacts favorably with side-chains at the active site via electrostatics, H-bonding, etc. Suppose we assume that a covalent bond forms. Is Autodock a good program for us to use in answering this question? As I see it, we would be trying to see what conformation the inhibitor takes when covalently linked to the enzyme. I just don't know enough about molecular modeling to answer this question.


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