Dear Sir/Madam,
Experimentally (x-ray structures for drug-bound and unbound structures are compared), it is known that a protein has a conformation change upon drug binding.
I model the protein-drug complex with AMBER, for 10 ns. I studied the correlation motion of each residues for this complex. I found the residues next to the drug binding sites has -1 correlation coefficients with a specific protein domain.
Should I interpret the result as follows:
The correlative motion between the drug binding site and the protein domain may have implication to the conformation change upon drug binding revealed in x-ray structures (bound vs unbound) structures.
If I want to further examine how the correlated motion are mediated from the drug binding site to the protein domain, what analysis should i do?
Best regards,
Catherine
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Received on Thu May 12 2011 - 08:00:04 PDT
