On 3/1/11 6:31 AM, Marco Sette wrote: > I have a protein consisting of a C-terminal and N-terminal region. > While for the C-terminal one I have a good template either Modeller > or Blast don't suggest templates for the N-terminal one. I have some > suggestion using Modweb (which search performs Modweb?) but not very > good. Could ou suggest me a website to search for a template? I > looked at the mailing list (very long...) but seems this question has > not been posed. Many thanks,
Since Modeller is a package for comparative modeling, if you don't have a template, you cannot model that region of your model.
I don't know what you mean by "Modeller ... doesn't suggest templates" since Modeller doesn't suggest templates for you. Perhaps you mean you are doing a sequence-sequence search to look for templates (step 1 of the basic tutorial) and you didn't find any? BLAST does essentially the same thing - except that it's using an approximation rather than "real" dynamic programming, so it runs faster - so is also unlikely to find a template if this search doesn't work.
ModWeb supplements this basic sequence-sequence search with more sensitive profile-based searches (it also tries PSI-BLAST, which is a similar method). But there are many other methods available to search for templates - e.g. HMM-based. One thing you could do is look at the best performers for the last CASP contest and see how they detect templates - some of those are available as web servers.
Ben Webb, Modeller Caretaker