esm/source/examples/lm-design/README.md

LM design examples

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 .

Notebook examples

Refer to the two notebooks at this folder to run the fixed backbone and free generation design tasks.

Shell examples

To run the two design tasks from shell, do the following:

1. First, install additional requirements: pip install -r additional_requirements.txt
2. Running Fixed backbone design: python -m lm_design task=fixedbb pdb_fn=$PWD/2N2U.pdb
3. 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

Paper data

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.