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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 >> >> >> >> >>