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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.

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