Thank you, guys. Subhendu On Wed, Dec 16, 2009 at 5:21 AM, Eric Bennett <er...@pobox.com> wrote:
> 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 > > -- >
