This repo accompanies the preprint "Efficient sampling of PROTAC-induced ternary complexes".

Create a new conda environment and install rdkit: conda create -c conda-forge -n <your-env-name> rdkit

Activate your environment and install the rest of the requirements: conda activate <your-env-name> pip install -r requirements.txt

chmod +x src/ternify.py

cd data/6hr2

../../src/ternify.py

Analyze the results

python ../../scripts/rmsd.py

or

cd data/wdr5/7q2j

../../../src/ternify.py -p ../input/tcs_wdr5.inp

Analyze the results

python ../../../scripts/rmsd_m.py poi_7q2j_aligned_on_5nvx_l_by_VHL.pdb

The box shall cover the entire PPIs interface of interest and extend at least 5 angstrom away from the surface of the anchroing protein.

Check the parameter file (default: tcs.inp) in a data directory for preparation of input files and parameters