Subhendu wrote:
Hi everyone,
I am currently in the process of solving some antigen-antibody
complex structures. I was wondering if people here have used
Modeller and Rosetta for homology modeling and have any
recommendations.I would like to build the model of the
antigen/antibody to the known structure of the antibody/antigen ( to
get a model of the complex while my crystallization/structure
solving process continues).I have experience in Modller but I have
not tried Rosetta or the newer PyRosetta (which looks interesting).
In the event of docking a protein to another are there any great
programs that people here have used/recommend?
Because Modeller is a general purpose tool while RosettaAntibody has
some specialized knowledge of antibodies you might want to consider
giving Rosetta a try. A couple reasons:
(1) Modeller operates at the local level of structure. It isn't
written to specifically optimize relative domain orientations, such
as between VL and VH. RosettaAb includes a specific step for
optimizing domain orientation, which could improve your chances with
MR if you intend to use the homology model for that purpose.
(2) For identifying templates, if you use the sort of global sequence
alignment tools in Modeller to choose a template, you may end up with
a template that has high identity in the framework region but the CDR
loop lengths are not the same. Rosetta takes a more sensible
piecemeal approach where it will identify a template for the
framework, and other templates for the CDRs based on the loop length.
Of course, you can do this manually if you want to use Modeller since
Modeller supports multiple templates, but it's more work.
-Eric
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