Hi Obayed,
If I understood your question well,
you are looking for something called "secondary structure prediction".
I googled these keywords and found this server:
http://bioinf.cs.ucl.ac.uk/psipred/
You may find other interesting servers on the web and
some literature comparing them.
I think such methods need only the sequence of your
protein to predict its secondary structures.
Hope this helps,
Francois.
On 07/19/2011 02:14 PM, Eric Larson wrote:
Hi Obayed,
you could give in situ protolysis a try. This is where you add a bit of
protease along with you target protein to the crystallization drop. It
has been quite successful for the folks at the SGC. Here are the
relevant references:
Dong A, et al. In situ proteolysis for protein crystallization and
structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID:
17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461)
Wernimont A, Edwards A. In situ proteolysis to generate crystals for
structure determination: an update. PLoS One. 2009;4(4):e5094. PMID:
19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432)
good luck,
Eric
================================
Eric T. Larson, PhD
Biomolecular Structure Center
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
email: larso...@u.washington.edu
================================
On Mon, 18 Jul 2011, Obayed Ullah wrote:
Hi all
I wrote last time but got only one feedback. I know some of you guys
must have this experience that how to delete loops from the
protein. Please help me with suggestions.
I am working with a human protein which have around 20% sequence
identity with the other proteins of the same family. Structure
of some of the proteins from this family have been solved. All the
solved structures have around 20% identity with my protein. I
am trying to crystallize the protein but it looks like very hard to
get crystal. I have tried different N and C terminally
truncated constructs for crystallization but no crystal. My feeling is
that probably there is some flexible loops with in the
protein which limiting the crystallization.
So I want to delete the loops with in the protein (not to truncate in
the terminal, I already have done this). I am not asking
suggestion about how to delete the loop rather how to decide where the
loop is. I am not sure how much it will be helpful to get a
homology model of such a protein having low sequence identity. Is
there any strategy to decide where the loop could be? Does
anybody know any established/ rational method to do that.
Waiting for your suggestions
Obayed Ullah
