GRASE

GNN-based Recommendation of Active and Stable Enzymes

Prerequisites

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
pip3 install -r requirements.txt

Pocket Prediction

Change the input_pdb = "aes72_af3.pdb" in inference.py to the desired PDB file and run the following command:

cd pythia-pocket
python inference.py

residue-level embedding

Change the ../aes72/blast_top100_pdb/*.pdb in extract.py to the desired PDB files and run the following command:

cd pythia-pocket
python extract.py

Search

Change these information in search.py:

pt_dic = "../aes72/blast_top100_pdb/" # Directory containing the embedding files
reference_pt = "aes72.pdb.pt" # Reference embedding file of the query
position = 147 # Position of the residue of query to search for
ouput_file = "../aes72/blast_top100_pdb/147.csv" # Output file to save the search results

Run:

cd pythia-pocket
python search.py

Protein Stability Score

Change the fpath_pdb = "../examples/1pga.pdb" in score.py to the desired PDB file and run the following command:

cd pythia
python score.py