Overview:

This application aims to relax cdrs using circular harmonic constraints for each identified cluster. CDR definitions are North/Dunbrack.

Requirements:

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/

Algorithm:

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.

App: relax_cdrs

Options:

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.