This folder contains code for demonstration of protein design using a language model. The code was used to perform the two design tasks specified at the paper Language models generalize beyond natural proteins .
Refer to the two notebooks at this folder to run the fixed backbone and free generation design tasks.
To run the two design tasks from shell, do the following:
- First, install additional requirements:
pip install -r additional_requirements.txt - Running Fixed backbone design:
python -m lm_design task=fixedbb pdb_fn=$PWD/2N2U.pdb - Running Free generation design:
python -m lm_design task=free_generation
Notes:
Use the seed=<number> flag to generate different designs, e.g:
python -m lm_design task=free_generation seed=42
Control generated length in free generation using free_generation_length=<number>, e.g:
python -m lm_design task=free_generation free_generation_length=68
Other, more advanced configurations can be observed at config.yaml
The data from the preprint is available under paper-data/. This includes designed sequences, their predicted structures, experimental validation results, linear projection for pairwise distance prediction, and details on dataset construction for model training.