| --- |
| language: en |
| license: mit |
| tags: |
| - protein-design |
| - sequence-design |
| - jax |
| - equinox |
| - protein-mpnn |
| - ligand-mpnn |
| library_name: aminx |
| --- |
| |
| # aminx weights — v0.1.0a1 |
|
|
| JAX/Equinox reimplementation of [ProteinMPNN](https://github.com/dauparas/ProteinMPNN) and [LigandMPNN](https://github.com/dauparas/LigandMPNN). |
|
|
| Weights are converted from the original PyTorch checkpoints and verified to ≥0.999 Pearson correlation with the reference implementation (atol/rtol 1e-4 for all families; side-chain packer: atol 1e-4/rtol 1e-3). |
|
|
| ## Usage |
|
|
| ```bash |
| pip install aminx # huggingface-hub is a required dep; weights download on first use |
| ``` |
|
|
| ```python |
| from aminx.io.weights import load_model |
| |
| model = load_model("proteinmpnn_v_48_020") |
| model = load_model("ligandmpnn_v_32_020_25") |
| model = load_model("solublempnn_v_48_020") |
| model = load_model("per_residue_label_membrane_mpnn_v_48_020") |
| model = load_model("ligandmpnn_sc_v_32_002_16") |
| ``` |
|
|
| Weights are cached to `~/.cache/huggingface/hub/` after first download. |
|
|
| ## Checkpoint topology |
|
|
| All families share: node/edge/hidden features = 128, encoder layers = 3, decoder layers = 3, vocab size = 21. The suffix digits in checkpoint names encode training noise level (e.g. `_020` = 0.20 Å backbone noise, per upstream convention) and atom context count (e.g. `_25`, `_16`). |
|
|
| | Family | Checkpoints | k_neighbors | num_positional_embeddings | Notes | |
| |---|---|---|---|---| |
| | ProteinMPNN | `proteinmpnn_v_48_{002,010,020,030}` | 48 | 32 | Original backbone | |
| | SolubleMPNN | `solublempnn_v_48_{002,010,020,030}` | 48 | 32 | Solubility-biased variant | |
| | LigandMPNN | `ligandmpnn_v_32_{005,010,020,030}_25` | 32 | 32 | 2 ligand-context layers; atom_context_num=25 | |
| | Membrane | `{global,per_residue}_label_membrane_mpnn_v_48_020` | 48 | 32 | physics_feature_dim=3 | |
| | Side-chain packer | `ligandmpnn_sc_v_32_002_16` | 32 | 16 | atom_context_num=16 | |
|
|
| ## Deprecation notice |
|
|
| The previous `maraxen/prxteinmpnn` repository is archived. Use this repo going forward. |
|
|
| ## Citation |
|
|
| If you use these weights, please cite the original works: |
|
|
| ```bibtex |
| @article{dauparas2022robust, |
| title={Robust deep learning-based protein sequence design using ProteinMPNN}, |
| author={Dauparas, Justas and others}, |
| journal={Science}, |
| year={2022} |
| } |
| |
| @article{dauparas2025atomic, |
| title={Atomic context-conditioned protein sequence design using LigandMPNN}, |
| author={Dauparas, Justas and others}, |
| journal={Nature Methods}, |
| volume={22}, |
| number={4}, |
| pages={717--723}, |
| year={2025} |
| } |
| ``` |
|
|
