Gert,
There is nothing wrong with suggesting 45 softwares, as one of those may
do exactly what a person needs and save loads of time.
Besides, comparing protein structures locally need not involve any
superposition method. I would say comparing torsion angles/distances
between atoms is a more common solution to this problem. There are still
cutoffs and weights to consider of course. Approaches vary on how to
handle those (e.g. theoretical or through validation), but I seriously
doubt your response constitutes 'case closed'.
Kind regards,
Dmytro.
On 10/04/17 12:06, Gert Vriend wrote:
Rather then now start mentioning yet 45 other 3D superposition
softwares, I think a pointer to the Wikipedia should suffice:
https://en.wikipedia.org/wiki/Structural_alignment
The Russian Doll effect (if you align more residues the comparison stats
get worse) is best explained (my opinion) by the CATH people (Orengo
group), and Arthur Lest is the only one (still, I think) who has been
thinking extensively about the cutoff question.
Greetings
Gert
From: Reza Khayat
Sent: Sunday, April 9, 2017 6:07 PM
To: CCP4 bulletin board
Subject: Structure comparison
Hi,
I have refined several structures of a protein from different space
groups and would like to compare them to one another. Is there a
program/software suite that would provide an objective comparison
of the structures and identify regions where the structures are
sufficiently different from one another to warrant a closer look? I
think the most important aspect of the analysis would be defining a
threshold (possibly based on resolution and structure statistics)
that would identify sufficient difference between structures. Thanks.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
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handelsregister onder nummer 41055629.
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