AMBER Archive (2006)

Subject: Re: AMBER: RMSD: is it related to flexibility?

From: David A. Case (
Date: Wed Oct 04 2006 - 10:08:32 CDT

On Wed, Oct 04, 2006, a a wrote:
> I got two protein structures with different performance on the loop
> mobilitiy, one of them move very fast, another one is about 10 time less
> flexible, based on our experimental data.

The answer probably depends on what kind of experimental data one is talking
about here; that will effectively determine what is being measured and
represented as "flexibility". And that, in turn, will help decide what sorts
of calculations might be relevant.


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