google-deepmind/alphaprotein-novo

AlphaProtein Novo (AP Novo) is a generative diffusion pipeline for de novo enzyme design via structural motif scaffolding. This package includes a diffusion model which co-generates protein structures and sequences conditioned on a catalytic motif and ligand context. This is run using rungenerator.py. To form an end-to-end pipeline, the diffusion model is combined with optional sequence redesign using LigandMPNN (runligandmpnn.py), structure prediction using AlphaFold 3 (runalphafold.py), and evaluation metrics (evaluatedesign.py). The runpipeline.py script runs all stages in sequence. See the Quickstart section for a basic launch command and Example Design Campaigns for more detailed examples. Any publication that discloses findings arising from using this source code, the model parameters, or outputs produced by those should cite the Designing enzymes for new-to-nature chemistry and non-natural substrates with AlphaProtein Novo paper. :ledger: Note: Pretrained model weights are not part of this package and must be downloaded from Google Cloud Storage (see Model…