Overview:

This application matches each CDR of an antibody to North/Dunbrack CDR clusters (See North, B., A. Lehmann, et al. (2011). JMB 406(2): 228-256.) based on the lowest dihedral distance to each 'center' member of the cluster. Identifications with distances will be echoed in the output PDB file and printed to the screen.

Setup

Antibodies need to be numbered in any numbering scheme accepted by Rosetta. These include: 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.

Antibodies can be renumbered to the AHO_Scheme at http://dunbrack2.fccc.edu/PyIgClassify/

Run

App: identify_cdr_clusters

Options:

Typical Rosetta options are followed. Use -no_output to not have pdb files echoed. Make sure to pass -numbering_scheme with your antibody's numbering scheme if it is not renumbered in Chothia.