On 12/20/10 05:49, <Liu Zhao > wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as green,is homologous .But the structure of my protein
can't be obtained by using molecular replacement. And both structures
have much different, especially in B chain. If my structure is a new
one? thank you for help.
The structure appears to consist of 3 distinct domains, a central beta
barrel and two mostly alpha helical domains.
RE the failure of molecular replacement - you don't say how hard you
tried. Given a starting structure like that, I would have tried
searching separately with models for the various domains. I also cannot
tell from two images how similar the helical domains are; is it just a
simple rotation, or is the arrangement of helices substantially different?
There are algorithms for comparing protein folds.
This article addresses your need, but is a bit old:
http://www.ncbi.nlm.nih.gov/pubmed/14696188
"Evaluation of protein fold comparison servers."
Novotny M
<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Novotny%20M%22%5BAuthor%5D>,
Madsen D
<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Madsen%20D%22%5BAuthor%5D>,
Kleywegt GJ
<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Kleywegt%20GJ%22%5BAuthor%5D>.
Proteins. 2004 Feb 1;54(2):260-70.
PMID: 14696188 [PubMed - indexed for MEDLINE]
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
