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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