[BioPython] Creating fusion protein like constructs with BioPython

[Peter]

Mitchell Stanton-Cook wrote:
> Hello all.
> 
> I am trying to create fusion protein-like model from two separate pdb files.
> I introduce a CYS mutant in the target protein, and then wish to form a
> disulphide bound between it and a small peptide.
> 
> This is pure computational work.
> 
> ...
> 
> 1) Can I use Bio.PDB to do this above task or do I need to look at something
> else?

My gut instinct is that yes, you probably can - but you will have to do 
a lot of the work with your own code.  Its not something I have ever 
tried though.

> 2) Does anyone have any ideas on how to complete this goal?

You might want to have a look at MMTK, which on the face of it would be 
better suited.  Assuming MMTK will read both PDB files you might have 
better luck - this proviso is because I have found MMTK will choke on 
"odd" PDB files, and its support for non-standard residues could be better.

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

Peter