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.