Homer is one of the best services for homology modeling: http://protein.cribi.unipd.it/Homer/
James On Jul 19, 2011, at 2:06 PM, Paul Kraft wrote: > Hi Obayed, > even though there is 20% sequence identity you may be able to get a very good > homology model, especially if there is more than one protein structure in the > PDB with 20% homology. Then you can overlap the pdbs and find out what > structurally needs to be preserved as opposed to what is in total homology > preserved. Typically it is the position of turns residues G, D, S, P, N etc. > You won't know until you thread your protein through both pdbs and compare > them all. Swiss Pro's Expasy has an easy program that will take an alignment > with a pdb and generate a homology model with loops spliced in and energy > minimized. There are many other more or less complicated programs, but it's a > good one to start with. > Paul > > Dr. Paul Kraft > Structural Biologist > cell 586-596-2770 > email: [email protected] > email: [email protected] > > > This communication and any attachments contain information which is > confidential and may also be privileged. It is for the exclusive use of the > intended recipient(s). If you are not the intended recipient(s) please note > that any form of disclosure, distribution, copying or use of this > communication or the information in it or in any attachments is strictly > prohibited and may be unlawful. If you have received this communication in > error, please notify the sender and delete the email and destroy any copies > of it. > > E-mail communications cannot be guaranteed to be secure or error free, as > information could be intercepted, corrupted, amended, lost, destroyed, arrive > late or incomplete, or contain viruses. We do not accept liability for any > such matters or their consequences. Anyone who communicates with us by e-mail > is taken to accept the risks in doing so. > > --- On Tue, 7/19/11, James Stroud <[email protected]> wrote: > > From: James Stroud <[email protected]> > Subject: Re: [ccp4bb] Off Topic: How to delete loops from a protein > To: [email protected] > Date: Tuesday, July 19, 2011, 2:37 AM > > 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: [email protected] > >> ================================ > >> > >> 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 > >>> > >>> > >>> > >>> > >>>
