(This application is unreleased)
Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) PI: Roland Dunbrack
Last Doc Update: 2/15/2014
This application aims to relax cdrs using circular harmonic constraints for each identified cluster. CDR definitions are North/Dunbrack.
Antibodies must be renumbered in some numbering scheme. See below for acceptable options. To renumber to AHO, as used in the original paper, please use this site: http://dunbrack2.fccc.edu/PyIgClassify/
The application will first identify each CDR of your antibody to one of the canonical North/Dunbrack CDR clusters. Dihedral constraints based on a recent high-resolution dataset of PDB antibodies are then added to the CDRs and all CDRs are relaxed. THis will be expanded for greater flexibility.
Follows typical Rosetta options including relax and minimization-based options. Be sure to pass -numbering_scheme if using something other than Chothia. Options are: Chothia_Scheme, Enhanced_Chothia_Scheme, AHO_Scheme, IMGT_Scheme. Kabat_Scheme is also accepted, but not fully supported due to H1 numbering conventions. Use Kabat_Scheme with caution.