CS492(B) Project Team 4

Third-party libraries

• Install omegafold
• Install FoldX and place executable inside the working directory

Environment

• Install PyTorch version 1.12.0 compatible with your CUDA version
• Other dependencies can be found in requirements.txt

Data and Pretrained checkpoints

The dataset and pretrained omegafold checkpoint will be automatically downloaded when you run the code.

Code

• baselines.py: test random mutation and genetic algorithm baseline
• train.py: train function predictor GNN
• optimize.py: optimize proteins using our definition of state and action
• optimize_onehot.py: optimize proteins given one-hot encoded sequence as state (ablation)