[BioPython] Homology Modeling question

[Peter (BioPython)]

Omid Khalouei wrote:
> Hello,
> 
> My question is not specifically related to Biopython, I wanted to know 
> if homology modeling can be used reliably to see the effects of single 
> amino acid substitutions. I mean is homoloy modeling useful for 
> predicting the structure of those sequences for which there is no know 
> structure or can it also be used for a more "fine tuning" analysis such 
> as changing one amino acid on a PDB structure and then performing 
> homology modeling using that same PDB structure as template?

I was under the impression that for homology modelling you provide an 
alignment of your sequence with several other sequences with associated 
known structures.  Have you looked at the Sali Lab's program MODELLER:

http://salilab.org/modeller/

For the simple case of "fine tuning" analysis with a single amino acid 
substitute, homology modelling might be overkill.  A simple substitution 
using the same backbone positions and initial direction for the side 
chain, followed by a molecular dynamics energy minimization of the side 
chain may be enough.  This particular question has cropped before on the 
MMTK mailing lists - MMTK is a python molecular dynamics library:

http://starship.python.net/crew/hinsen/MMTK/index.html
http://starship.python.net/pipermail/mmtk/

> Also is there any uptodate forum for homology modeling? I looked it up 
> on Google but postings were for back in 1990's.

I don't know.

Peter