Hey Anselm,
I usually give thought to the same problem and there is at least two references I can recommend:
1. Maiorov, V. N. & Crippen, G. M. Size-independent comparison of protein three-dimensional structures. Proteins 22, 273–283 (1995).1. Maiorov, V. N. & Crippen, G. M. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. J Mol Biol 235, 625–634 (1994).
They are "old" but will be very informative about RMSDs
Best regards.
> Message: 2
> Date: Thu, 24 Jan 2013 19:02:32 -0500
> From: Aron Broom <broomsday.gmail.com>
> Subject: Re: [AMBER] RMSD of globular proteins
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALLoAac30BCu1CsPyPDsJnmwXe-arVVoECXjP-CnXpvrvBODHQ.mail.gmail.com>
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>
> 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 Fri Jan 25 2013 - 13:00:02 PST
