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README.md

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+---
+license: apache-2.0
+library_name: jax
+tags:
+  - protein-structure-prediction
+  - alphafold3
+  - jax
+  - equinox
+  - biology
+---
+
+# Protenij — JAX/Equinox weights for Protenix
+
+This repository hosts JAX/Equinox-converted model weights (and a mirror of the
+original PyTorch `protenix-v2` checkpoint) for use with
+[protenij](https://github.com/escalante-bio/protenij), a JAX/Equinox translation
+of [Protenix](https://github.com/bytedance/Protenix), ByteDance's implementation
+of the AlphaFold 3 architecture.
+
+The JAX/Equinox weights are format conversions of the original PyTorch
+checkpoints released by ByteDance — the underlying model parameters are
+numerically identical, only the serialization format has changed (PyTorch `.pt`
+→ Equinox `.eqx` + pickled skeleton).
+
+## Files
+
+| File | Format | Size | Source |
+| --- | --- | --- | --- |
+| `protenix-v2.eqx` / `protenix-v2.skeleton.pkl` | Equinox | 1.86 GB | Converted from `protenix-v2.pt` |
+| `protenix-v2.pt` | PyTorch | 1.86 GB | Mirror of upstream ByteDance release |
+| `protenix_base_default_v1.0.0.eqx` / `.skeleton.pkl` | Equinox | — | Converted from upstream |
+| `protenix_base_20250630_v1.0.0.eqx` / `.skeleton.pkl` | Equinox | — | Converted from upstream |
+| `protenix_mini_default_v0.5.0.eqx` / `.skeleton.pkl` | Equinox | — | Converted from upstream |
+| `protenix_tiny_default_v0.5.0.eqx` / `.skeleton.pkl` | Equinox | — | Converted from upstream |
+| `components.v20240608.cif` | Data | — | CCD chemical components (upstream) |
+| `components.v20240608.cif.rdkit_mol.pkl` | Data | — | CCD rdkit mol cache (upstream) |
+| `clusters-by-entity-40.txt` | Data | — | PDB entity-40 clusters (upstream) |
+
+## Usage
+
+```python
+from protenix.backend import load_model
+model = load_model("protenix-v2")  # auto-downloads from this repo
+```
+
+## License and attribution
+
+Released under the **Apache License 2.0**, matching the upstream
+[bytedance/Protenix](https://github.com/bytedance/Protenix) project.
+
+The upstream Protenix README explicitly states:
+
+> "The Protenix project including both code and model parameters is released
+> under the Apache 2.0 License. It is free for both academic research and
+> commercial use."
+
+### Modification notice (Apache 2.0 §4(b))
+
+The `.eqx` and `.skeleton.pkl` files in this repository are **format
+conversions** of the original PyTorch checkpoints released by ByteDance. The
+PyTorch state dicts were loaded and the tensors re-serialized in Equinox format
+using
+[`protenix/backend.py`](https://github.com/escalante-bio/protenij/blob/main/protenix/backend.py)
+and
+[`translate_models.py`](https://github.com/escalante-bio/protenij/blob/main/translate_models.py).
+No weights were retrained, fine-tuned, or otherwise numerically modified.
+
+The `protenix-v2.pt` file in this repository is a bit-for-bit mirror of the
+original PyTorch checkpoint hosted at
+`https://protenix.tos-cn-beijing.volces.com/checkpoint/protenix-v2.pt` (mirrored
+here after the upstream URL became unreachable).
+
+### Copyright notice (Apache 2.0 §4(c))
+
+Copyright 2024 ByteDance and/or its affiliates. The original Protenix code and
+model parameters were released under Apache License 2.0. See the `LICENSE` file
+in this repository for the full license text.
+
+### Citations
+
+If you use these weights, please cite the original Protenix work:
+
+- Protenix repository: https://github.com/bytedance/Protenix
+- Protenix technical reports in `docs/` of the upstream repository
+
+## Disclaimer
+
+These files are provided as-is. The weights are format conversions only — for
+the authoritative source and for training code, model cards, and technical
+reports, refer to the [upstream ByteDance Protenix
+repository](https://github.com/bytedance/Protenix).