> > > 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.