I have a question about the most effective way of modelling a protein
that is in a different conformation to the structure? I am hoping to
make a homology model, then rotate a helix about its center and allow
modeller to remake the model (allow energy minimisation etc) to
determine the effects on the whole protein. Is there a way to do this?
You can certainly build homology models (of course), and Modeller
includes several methods for rotating, translating or otherwise
transforming a set of atoms: see
http://salilab.org/modeller/9v7/manual/node233.html for an example. The
only problem you will run into is the minimization, since you will have
to change the energy function somehow. The default energy function tries
to make the model look like the template, and this is obviously not
going to work if you want to build the model in a different
conformation. You may be able to use a conventional dynamics package
such as CHARMM or GROMACS though to relax the structure.