Here we provide the code to run the antibody protocol of HADDOCK by using the residues belonging to the hypervariable (HV) loops. We use ANARCI [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 using Conda.

git clone https://github.com/haddocking/HADDOCK-antibody-antigen.git
cd HADDOCK-antibody-antigen

# Create conda environment from environment.yaml file:
conda env create -f environment.yaml
conda activate haddock-antibody

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

conda activate haddock-antibody

# Renumber antibody with the Chothia scheme
python 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 file
python ab_haddock_format.py 4G6K_ch.pdb 4G6K-HADDOCK.pdb A > active.txt

# Add END and TER statements to the .pdb file
pdb_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-antibody

python 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-antibody

python run.py --pdb folder_with_pdbs

The version of ImmunoPDB.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 the ANARCI repository if you have any problems with it.