Dear Julio and Aron,
thank you for your answers, which were very helpful.
Best regards,
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).
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Received on Wed Jan 30 2013 - 01:00:02 PST
