SMD Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Wed Jan 12 2022 - 22:13:20 CST

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I have a peptide binding in a pocket of a larger protein and I would like to get a rough and quick estimate of their interaction. Would a constant velocity steered MD be good enough to for this?

Would I select all of the atoms on the peptide and pull it out of the larger protein while the larger protein is anchored?

What if part of the peptide just unfolds instead of leaving the binding site?

 Kelly L. McGuire

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