[AMBER] Several alpha-helices stitched together - how would you stress-test it with MD?

From: Homeo Morphism <homeo.morphizm.gmail.com>
Date: Tue, 28 Jan 2020 13:48:35 +0300

We are trying to assemble a long alpha-helix by stitching together known
but shorter alpha-helices.

We've gone through the appropriate literature on the subject before
committing to individual fragments and the secondary structure prediction
tools are saying there's a chance our final structure will end up folding
as a long alpha-helix indeed.

Is there any way we can also buttress these results with MD simulations? I
can think of two obvious things:

1) just waiting for it to unfold from an already folded state;

2) watching how it will be folding from a completely unfolded state or a
random coil.

Any other suggestions?

Thank you.
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Received on Tue Jan 28 2020 - 03:00:02 PST
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