Publish OFoldX pipeline artifacts

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library_name: ofoldx
tags:
  - biology
  - biomolecular-design
  - protein
  - rna
  - dna
  - pipeline
  - alphafold3
  - structure-prediction
  - protein-structure
artifact_kind: pipeline
repo_id: oteam/protenix-base
license: apache-2.0
pipeline_tag: other
task: structure_prediction
model-index:
  - name: protenix-base
    results: []
widget:
  - pipeline_tag: other
    task: structure_prediction
    example_title: Single-chain protein
    text: |-
      >A
      MKTAYIAKQRQISFVKSHFSRQDILD
    input_format: fasta
  - pipeline_tag: other
    task: structure_prediction
    example_title: Protein complex
    text: |-
      >A
      MKTAYIAKQRQISFVKSHFSRQDILD
      >B
      GSHMRYFVTAVSRPGRGEPRFI
    input_format: fasta

protenix-base

OFoldX pipeline artifact for biomolecular structure prediction, using the alphafold3 architecture.

Disclaimer

This model card was generated by the OFoldX team for an OFoldX pipeline artifact. The upstream model authors did not write this card unless explicitly stated otherwise.

OFoldX is pre-alpha research software. Check the source checkpoint, upstream release, and local validation before using the artifact for scientific or operational decisions.

Model Details

AlphaFold 3-shaped structure-prediction model converted for the OFoldX runtime.

Converted Protenix v0.5.0 structure-prediction weights in an AlphaFold 3-shaped OFoldX implementation.

Model Provenance

Upstream Project: Protenix
Source Checkpoint: protenix_base_default_v0.5.0.pt
Source Release: https://github.com/bytedance/Protenix/blob/main/docs/supported_models.md
Primary Paper: Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction
Upstream License: Apache-2.0 for upstream Protenix code and model parameters

Model Specification

Field	Value
Repository	`oteam/protenix-base`
Artifact Kind	`pipeline`
Task	`structure_prediction`
Architecture	`alphafold3`
Entrypoint	`ofoldx.pipelines.structure_prediction.StructurePredictionPipeline`
Source Checkpoint	`protenix_base_default_v0.5.0.pt`

Source checkpoint: protenix_base_default_v0.5.0.pt; v0.5.0 is the upstream Protenix checkpoint release version, not part of the public repo id.

Usage

The artifact depends on the ofoldx library. Install it with pip:

pip install ofoldx

Pipeline Usage

Load the artifact from oteam/protenix-base with the OFoldX task pipeline. Use AutoModel or AutoProcessor only when you need lower-level control:

from ofoldx.pipelines import Pipeline

pipeline = Pipeline.from_pretrained("oteam/protenix-base")

When a matching processor is available, load it with AutoProcessor.from_pretrained(...) and pass the processed batch to the model.

Interface

Task: structure_prediction
Artifact kind: pipeline
Architecture: alphafold3
Runtime files: manifest.json, config.json, and model.safetensors when present

Training Details

OFoldX did not train these weights. This repository contains a converted checkpoint and OFoldX runtime metadata for loading it.

Training Data

The upstream Protenix v0.5.0 release reports a 2021-09-30 training-data cutoff. The Protenix training-data pipeline covers released wwPDB/mmCIF bioassemblies, MSAs, CCD cache data, and RCSB sequence clusters. OFoldX does not redistribute the training corpus.

Training Procedure

The upstream protenix_base_default_v0.5.0 model is an AF3-shaped all-atom structure-prediction checkpoint. OFoldX converts protenix_base_default_v0.5.0.pt to the OFoldX artifact format; it does not retrain the model.

Evaluation

OFoldX conversion reports and contract tests validate artifact structure and checkpoint loading. Task-level scientific evaluation should be checked against the corresponding upstream model release or paper.

Limitations

This artifact is distributed for research use.
Inputs must match the model-specific processor and expected biomolecular representation.
OFoldX is pre-alpha, so APIs and artifact metadata may still change before a stable release.

Citation

Please cite the upstream Protenix work for the source checkpoint. If OFoldX supports your work, please also cite or link the OFoldX project repository.

@article{protenix2025advancing,
  author = {ByteDance AML AI4Science Team and Chen, Xinshi and Zhang, Yuxuan and Lu, Chan and Ma, Wenzhi and Guan, Jiaqi and Gong, Chengyue and Yang, Jincai and Zhang, Hanyu and Zhang, Ke and others},
  title = {Protenix - Advancing Structure Prediction Through a Comprehensive AlphaFold3 Reproduction},
  year = {2025},
  doi = {10.1101/2025.01.08.631967},
  journal = {bioRxiv}
}

Contact

Please use OFoldX GitHub issues for questions or comments about this model card.

License

The Hub license metadata, when present, reflects the source checkpoint or upstream project license. The OFoldX project license is not yet finalized. The source checkpoint is associated with the upstream license noted above: Apache-2.0 for upstream Protenix code and model parameters. Review both OFoldX and upstream terms before redistribution or production use.

oteam
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protenix-base