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: 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 >>> >>> >>> >>> >>>
