sabr-kit 0.1.0

Structure-based Antibody Renumbering

Structure-based Antibody Renumbering

SAbR (Structure-based Antibody Renumbering) renumbers antibody PDB files using the 3D coordinate of backbone atoms. It uses custom forked versions of SoftAlign and ANARCI to align structures to SAbDaB-derived consensus embeddings and renumber to various antibody schemes, respectively.

To install:

git clone --recursive https://github.com/delalamo/SAbR.git
cd SAbR/
pip install -e .

Running SAbR:

usage: sabr [-h] -i INPUT_PDB -c INPUT_CHAIN -o OUTPUT_PDB [-n NUMBERING_SCHEME] [-t] [--overwrite] [-v]

Structure-based Antibody Renumbering (SAbR) renumbers antibody PDB files using the 3D coordinate of backbone atoms.

options:
  -h, --help            show this help message and exit
  -i INPUT_PDB, --input_pdb INPUT_PDB
                        Input pdb file
  -c INPUT_CHAIN, --input_chain INPUT_CHAIN
                        Input chain
  -o OUTPUT_PDB, --output_pdb OUTPUT_PDB
                        Output pdb file
  -n NUMBERING_SCHEME, --numbering_scheme NUMBERING_SCHEME
                        Numbering scheme, default is IMGT. Supports IMGT, Chothia, Kabat, Martin, AHo, and Wolfguy.
  -t, --trim            Remove regions outside aligned V-region
  --overwrite           Overwrite PDB
  -v, --verbose         Verbose output