I would suggest to look at the papers of Thomas Schneider that deal
with that subject.
http://www.ncbi.nlm.nih.gov/pubmed/10818348?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Objective comparison of protein structures: error-scaled difference
distance matrices.
... there are also other publications on the subject by the same author.
Since this work is published you could also suggest to the referee to
read it.
Tassos
On Apr 11, 2008, at 15:08, Van Den Berg, Bert wrote:
We had a similar issue recently where we tried to draw conclusions
about a domain having the same conformation in wildtype and mutant
proteins. One reviewer got back saying the resolution of the
structures was too low (3-3.5 A) to say anything meaningful. Of
course everything will depend not only on resolution, but also on
how small the changes are that you want to draw conclusions about.
So how does the uncertainty of atom positons depend on the
resolution? Can one just take the Luzatti coordinate error or is it
more complicated than that?
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115
Worcester MA 01605
Phone: 508 856 1201 (office); 508 856 1211 (lab)
e-mail: [EMAIL PROTECTED]
http://www.umassmed.edu/pmm/faculty/vandenberg.cfm
From: CCP4 bulletin board on behalf of Jim Naismith
Sent: Fri 4/11/2008 6:04 AM
To: [email protected]
Subject: [ccp4bb] Low resol structure
Dear All,
I have an interesting problem, we have a 3.45A
structure of
a membrane protein. We have just been told that the structure is
"too low
resolution to be considered as the uncertainty is too high". We use
the
structure to identify helices which have moved.
Is there a blanket ban on low res structure operating at the moment?
The structure was refined extremely tightly, MolPROB 98th centile.
(I will
happily send the data and structure to anyone who wishes to
validate.) The
editors simply ignored everything but the res limit (I/sI in the
last shell
was 1.8 with a redundancy of 4)
Of course we will begin the usual journal shopping. However, does
anyone
know how to convince editors and non-xtallographers that 3.45A is
valid?
Best
Jim
James H. Naismith FRSE |Research mailto:[EMAIL PROTECTED]
and.ac.uk
Professor of Chemical Biology |Teaching mailto:[EMAIL PROTECTED]
Centre for Biomolecular Sciences |Office: 1334-463792
The North Haugh |Fax : 1334-467229
The University |Lab : 1334-467245
St. Andrews |In UK add 0 to start of number
Fife Scotland, U.K., KY16 9ST |http://www.st-and.ac.uk/~strucbio
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