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September 22, 2014 at 3:09 pm #1997Anonymous
I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.
I searched a while for usage examples of snugdock..but couldn’t fine anything. In past i used rosettadock..but it was not about antibodies..and now since the antibody structures are missing, i really think that incorporating information of ensemble models can give a more robust docking solution.
Question: did anyone use snugdock+ensembledock or even apart??
Thanks so much!!!
October 20, 2014 at 8:42 pm #10464Anonymous
You should be able to use the snugdock app like most of the Rosetta apps. Pass in -l for a PDBLIST or -s for a single PDB.
Additional options for your antibody modeling:
By default, chainbreaks are checked in the CDR regions. This is so that you know if you have a messed up CDR that is probably unfixable by most of the antibody applications (and may in fact get worse). To override this, pass
The next set of options correspond to the Numbering scheme and CDR definition you use. Previously, only Chothia numbering scheme was understood by RosettaAntibody. All used the Aroop CDR definition. Now, Rosetta understands many more and these should all be compatable with the antibody apps. This is not yet documented anywhere, but will be soon.
Control these with the -numbering_scheme and -cdr_definition options. North CDR definitions are used by the recent North/Dunbrack CDR clustering paper. If your antibody is output by the Rosetta Antibody server, it will be in the Chothia numbering scheme and it used the Aroop CDR definitions to do the H3 and post-graft modeling. Arbitrary Antibodies from the PDB can be renumbered to the AHO_Scheme here: http://dunbrack2.fccc.edu/PyIgClassify/
Understood numbering schemes:
Understood CDR Definitions:
Hope this gets you started! Sorry for the late reply!
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