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| # 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](https://www.biorxiv.org/content/10.1101/2022.12.21.521526v1). | |
| ## Tutorial | |
| We have provided a [tutorial notebook](tutorial.ipynb) describing the basics of writing programs and running optimization loops. | |
| The notebook can be run in Colab: | |
| [<img src="https://colab.research.google.com/assets/colab-badge.svg">](https://colab.research.google.com/github/facebookresearch/esm/blob/main/examples/protein-programming-language/tutorial.ipynb) | |
| ## 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](programs/free_hallucination.py) | | |
| | Fixed backbone design | Figure 2D | [fixed_backbone.py](programs/fixed_backbone.py) | | |
| | Secondary structure design | Figure 2G | [secondary_structure.py](programs/secondary_structure.py) | | |
| | Functional site scaffolding | Figure 2H | [functional_site_scaffolding.py](programs/functional_site_scaffolding.py) | | |
| | Symmetric monomer design | Figure 3A | [symmetric_monomer.py](programs/symmetric_monomer.py) | | |
| | Two-level symmetric<br>homo-oligomer design | Figure 4A | [symmetric_two_level_multimer.py](programs/symmetric_two_level_multimer.py) | | |
| | Symmetric binding site<br>scaffolding | Figure 5A | [symmetric_binding.py](programs/symmetric_binding.py) | | |