esm/source/examples/protein-programming-language/README.md

Protein programming language

This repository contains an implementation of the programming language described in the paper A high-level programming language for generative protein design.

Tutorial

We have provided a tutorial notebook describing the basics of writing programs and running optimization loops. The notebook can be run in Colab:

Design programs

We have also provided some example programs as described in our original paper.

Design task	Figure in paper	Program file
Free hallucination	Figure 2A	free_hallucination.py
Fixed backbone design	Figure 2D	fixed_backbone.py
Secondary structure design	Figure 2G	secondary_structure.py
Functional site scaffolding	Figure 2H	functional_site_scaffolding.py
Symmetric monomer design	Figure 3A	symmetric_monomer.py
Two-level symmetric homo-oligomer design	Figure 4A	symmetric_two_level_multimer.py
Symmetric binding site scaffolding	Figure 5A	symmetric_binding.py