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AlphaProtein Novo (AP Novo) is a generative diffusion pipeline for de novo enzyme design via structural motif scaffolding. Its diffusion model co-generates protein structures and sequences, conditioned on a catalytic motif and ligand context.
The repository provides an end-to-end pipeline. It combines the generator with optional sequence redesign using LigandMPNN, structure prediction with AlphaFold 3 (including a leaving-atom fine-tuned variant for covalent intermediates), and evaluation metrics. A single run_pipeline.py script runs all stages from a manifest file, and example campaigns such as a Kemp eliminase benchmark are included. A bioRxiv preprint describes the method; creator coverage reports lab-tested enzymes (e.g. for piperidine production and DEHP breakdown) that are not yet peer-reviewed.
Code is released under Apache-2.0. Pretrained weights are not in the repository and are downloaded from Google Cloud Storage under separate terms of use, as are the AlphaFold 3 weights. It requires a Python 3.12 environment with JAX (GPU recommended), and is aimed at computational protein and enzyme design researchers.
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AI that designs new enzymes from scratch, both structure and sequence, validated with AlphaFold 3. Lab-tested enzymes produce piperidine and break down DEHP; not yet peer-reviewed.
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