> > > field and i'm having trouble finding resources to obtain computer
> > > programs/software for homology-based secondary structure modelling.
> > > can you give me some advice on where i can obtain
> > > such software? in specific, i'm hoping to be able to find a program
> > > that can model a rpotein
> > > whose primary structure is unknown.
MODELLER is certainly the right tool for what you are looking for.
However, before you can use it, you need a good structural template to start
with, which may be difficult to find if your target protein has only low
sequence homology to structures that are available in the PDB
I found the following two servers helpful for this task, and they may also
give you already an answer in what concerns your protein's secondary
structure:
The Fugue search against the Homstrad database is quite useful and
informative:
http://www-cryst.bioc.cam.ac.uk/~fugue/prfsearch.html
Then there is the more general meta-server at BIOINFO.PL which queries a
large number of threading servers (including Fugue):
http://bioinfo.pl/meta/
But the output is much more extensive and thus more difficult to explore.
I hope this helps, kind regards,
Karsten Suhre, IGS-CNRS, Marseille, France.