I've found that predator is one of the best services of this sort:
Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997)
Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator
The server is slow but the service is good.
James
On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote:
> 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: [log in to unmask]
>> ================================
>>
>> 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
>>>
>>>
>>>
>>>
>>>
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