In article <3odceg$dah at nexus.uiowa.edu> kpmurphy at blue.weeg.uiowa.edu (murphy kenneth p) writes:
>> This brings up a question I've always had regarding structure prediction. How
> close do you have to be to the crystal structure to say you predicted it? When
> you say 1.0 A, do you mean for all atoms or just backbone? What's the rmsd for
> NMR and xtal structures of the same protein if you include all atoms and not
> just backbone?
I would be happy with anything that could help me understand the biological
function of the protein, even if it is 10 A away.
For the first RMSD is not a very good measure but I do not know anything better.
Let me think loudly (or recall from memory):
1) Differences between different BPTI forms (3-9pti excluding 8pti) is less than
1 A for backbone and prrobably between 1 and 1.5 A
2) Root mean square fluctuations (tempfactors) are less than 1 A.
3) Best MD simulations are close to 1A rmsd for all atoms.
4) IL-4 (?) differences between NMR and X-ray are close to 1 A (slightly more a guess)
So this would mean that I would be satisfied to get 1-2 A accuracy.
But I think we are a long way from there.
arne
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From: Arne Elofsson
Email: arne at hodgkin.mbi.ucla.edu
WWW: http://www.doe-mbi.ucla.edu/arne/main.html
