conda create -n naepro python=3.8 -y 
conda activate naepro 
conda install pytorch=1.10.2 cudatoolkit=11.3 -c pytorch -y 
bash setup.sh 

We provide the checkpoints used in the paper in Google Drive

Please download the checkpoints and put them in the models folder.

If you want to train your own model, please follow the training guidance below

bash train.sh

bash design.sh

There are five items in the output directory:

1. protein.txt refers to the designed protein sequence
2. src.seq.txt refers to the ground truth sequences
3. pdb.txt refers to the target PDB ID and the corresponding chains
4. pred_pdbs refers to the directory of designed pdbs
5. tgt_pdbs refers to the directory of target pdbs