Re: [ccp4bb] Rosetta vs Modeller
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 --
Re: [ccp4bb] Rosetta vs Modeller
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 --
[ccp4bb] Rosetta vs Modeller
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? I would really appreciate your suggestions/insights. Subhendu UCSF
Re: [ccp4bb] Rosetta vs Modeller
Subhendu I wonder if you approached this issue by molecular replacement using the antigen-binding fragment (Fab) of any antibody (e.g. 1FVD). You can separate the Fab into the two domains; Variable and Constant, delete the loops from each, and use them as models in Molecular replacement. Please let me know if you need more details using this approach Akram Alian UCSF From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of subhendu chakraborti Sent: Tuesday, December 15, 2009 7:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rosetta vs Modeller 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? I would really appreciate your suggestions/insights. Subhendu UCSF
