Identifying peptide-receptor interactions using AlphaFold-Multimer.
af_scripts/run_alphafold_msaonly.py
into the root directory of alphafold (that contains run_alphafold.py
). This script only runs the data generation pipeline and omits the neural network execution.af_scripts/precompute_msas.py
to make all MSAs. The working directory needs to be the alphafold root dir. To change the data or run parameters, modify the variables on lines 14 to 21.af_scripts/predict_from_precomputed.py
to predict all pairwise complexes. Modify the variables on lines 18 to 26 if you changed the data or msa directories. The script is meant to be executed on a GPU node and spawns multiple AlphaFold processes in parallel. Modify GPU_AVAILABLE
starting from line 34 to match your GPU setup (default assumes 8 GPUs available)qc_metrics.py
. In benchmark.ipynb
, we apply this function to all results, aggregate the metrics and rank the receptors. The notebook produces the results presented in the manuscript.