Re: [AMBER] NMR-based restraints

From: David A Case via AMBER <amber.ambermd.org>
Date: Tue, 13 Dec 2022 11:36:34 -0500

On Mon, Dec 12, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>
>>From NMR experiments of a protein-protein interaction, I know which
>>residues have the greatest change in chemical shifts for one of the
>>partners upon complexation. Is there a restraint I can use to maximize
>>these contacts starting from, perhaps, representative docking poses?

You could "make up" distance restraints between the residues that should be in
contact. You will probably need to experiment some. Be aware that you will
want to get out more than you put in: if you bias the system to produce
certain contacts, think about what you will learn from such a simulation.

....dac


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Received on Tue Dec 13 2022 - 09:00:02 PST
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