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Here we provide the code to run the antibody protocol ofHADDOCK by using the residues belonging to thehypervariable (HV) loops.We useANARCI[Dunbar, J. et al (2016). Nucleic Acids Res. 44. W474-W478] to renumber the antibody according to the Chothia numbering scheme and to identify the HV loops.

Install it usingConda.

git clone https://github.com/haddocking/HADDOCK-antibody-antigen.gitcd HADDOCK-antibody-antigen# Create conda environment from environment.yaml file:conda env create -f environment.yamlconda activate haddock-antibody

If you are still using Python 2, please, consider usingolder version

conda activate haddock-antibody# Renumber antibody with the Chothia schemepython ImmunoPDB.py -i 4G6K.pdb -o 4G6K_ch.pdb --scheme c --fvonly --rename --splitscfv# Format the antibody in order to fit the HADDOCK format requirements# and extract the HV loop residues and save them into a filepython ab_haddock_format.py 4G6K_ch.pdb 4G6K-HADDOCK.pdb A> active.txt# Add END and TER statements to the .pdb filepdb_tidy 4G6K-HADDOCK.pdb> oo; mv oo 4G6K-HADDOCK.pdb

For the convenience all three commands can be run as one command with:

conda activate haddock-antibodypython run.py --pdb 4G6K.pdb

It is also possible to process a whole folder with pdb files as well as subfolders with only one command:

conda activate haddock-antibodypython run.py --pdb folder_with_pdbs

The version ofImmunoPDB.py script that we are re-distributing as part of this protocol has some limitations and cannot handle all naming schemes, please se the list below:

• martin ✅
• chotia ✅
• imgt ❌
• kabat ✅
• aho ❌
• wolguy ❌

Issues with this script are out of the scope of this repository, please raise an issue at theANARCI repository if you have any problems with it.