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Re: [modeller_usage] helix model

Jairo Rocha wrote:
> I have some sequences from real bacteria that correspond to one protein
> in the pdb, 1SIG.
> Of course, they have lots of mutations. I would like  to know which
> changes the structure would have, due to these mutations.
> I used Modeller to answer that question, for the first time. The
> predicted structures are very very similar to the given structure.
> I am surprised that some helices are not broken or bended just a bit.
> As far as I know, to get a helix requires several energy states to
> coincide, so it is difficult that by change I get the helix.
> So it seems to me the program just copies the structure.

Modeller is a package for comparative modeling, so by construction your
target model is going to look like the template(s). It doesn't exactly
"copy" the structure, but certain structural features (e.g. dihedral
angles, CA-CA distances, etc.) in aligned templates will be preserved in
the model. So if you have a template aligned that has helical structure,
it is practically certain that the model will generate will also be
helical, regardless of the actual sequence. (Of course, something like
poly-P probably wouldn't be helical, but then that's probably a failure
of your alignment method if you've aligned poly-P with a helical
sequence anyway.)

You probably don't want homology information if you're investigating
mutations with structural changes. You can certainly use Modeller for
this though - just don't use the homology information (see the mutate
model script in the Modeller wiki for an example).

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage