I think it partially originates not just from MD, but from NMR. When
solving a protein structure by NMR, one generally gets a number of
structures that fit the constraints, and if you look at the RMSD between
those different but equally likely models, the RMSD can be in the range of
~0.5-2 angstroms, depending on how compact the structure is (i.e. more
loops will lead to higher RMSD values).
I'm not sure of a particular reference, but if I was trying to validate it,
I'd look for older NMR structural references, rather than MD ones.
~Aron
On Thu, Jan 24, 2013 at 6:05 PM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Dear all,
>
> the RMSD value of protein backbone movements is an often-used measure
> for the similarity to the initial structure. A value of ca. 2 Angstroem
> is thereby generally thought to indicate a stable simulation, as this
> value is obtained for simulations of globular proteins.
>
> My question now is: Is anybody aware of published work, where the
> foundation of this (or a similar) value has been obtained by some
> analysis or theoretical consideration? Or is this (globular protein =
> 2.0 A) just common knowledge/experience?
>
> Thanks in advance!
>
> Anselm
>
>
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Jan 24 2013 - 16:30:02 PST
