StrucTrace: A Universal Fourier Watermark for Traceable Biomolecular Structures

Authors: Xu Wang^†, Chi Wang^†, Tin-Yeh Huang, Yiquan Wang, Siyuan Jiang, Yafei Yuan^*
†These authors contributed equally to this work.
^*Corresponding authors.

StrucTrace is a reference-guided Fourier-domain watermarking framework for traceable biomolecular structures. It embeds provenance payloads into flexible C-alpha coordinate regions as a post-processing step, preserving atomic-scale structural fidelity while enabling public provenance verification, hardware-bound access control and auditable digital-rights management.

Key Results

• Universal post-processing watermarking for deposited PDB files, cryo-EM structures and AI-designed proteins.
• 100% bit recovery in fidelity benchmarks, with side-chain RMSD no greater than 0.0015 Angstrom.
• High-capacity embedding of a 6,584-bit abstract into the human gamma-secretase cryo-EM structure.
• Defined recovery boundaries under rigid-body transformations, coordinate rounding, all-atom noise and local C-alpha perturbation.
• Three-tier safeguard model: public provenance, hardware-bound access and digital-rights management.

Figures

Figure 1. Universal Fourier-domain watermarking workflow. StrucTrace selects flexible C-alpha atoms, embeds payload bits by mid-frequency FFT amplitude modulation and reconstructs watermarked coordinates with minimal geometric perturbation.

Figure 2. Structural fidelity and universality. Large-scale RMSD and Rosetta-energy analyses show negligible perturbation, and 50 ns MD simulations preserve dynamic behaviour across natural, Rosetta-designed and RFdiffusion-generated proteins.

Figure 3. High-capacity embedding. A 6,584-bit abstract was embedded into the human gamma-secretase tetramer while retaining coordinate-level agreement with the original cryo-EM structure.

Figure 4. Robustness and tamper boundary. Reference-guided decoding is invariant to rigid-body transformations and standard PDB precision, while all-atom noise, local distortion and selected C-alpha perturbation define the recovery boundary.

Figure 5. Three-tier safeguards. Tier 1 provides public provenance verification, Tier 2 provides hardware-bound encrypted access, and Tier 3 provides auditable digital-rights management.

Install

After PyPI publication, install StrucTrace with:

pip install structrace

For local development, clone and install the package in editable mode:

git clone https://github.com/JLU-WangXu/Structrace.git
cd Structrace
pip install -e .

The command-line interface is then available as:

python -m structrace --help

If your Python scripts directory is on PATH, you can also use:

structrace --help

External software used for manuscript validation includes DSSP, GROMACS 2024.6, Rosetta and Foldseek.

Publishing

Build and validate the package locally:

python -m pip install --upgrade build twine
python -m build
python -m twine check dist/*

Upload to TestPyPI first:

python -m twine upload --repository testpypi dist/*

If the TestPyPI package installs and imports correctly, upload the same version to PyPI:

python -m twine upload dist/*

Quick Start

CLI

Embed a text watermark into a structure:

python -m structrace embed Robustness/00_baseline_cases/6MRR/6MRR_original.pdb \
  --text "npj SB" \
  -o tmp/6MRR_watermarked.pdb

Decode the watermark from the original and watermarked structures:

python -m structrace decode Robustness/00_baseline_cases/6MRR/6MRR_original.pdb \
  tmp/6MRR_watermarked.pdb \
  --bits 56

The --bits option can be set explicitly. If it is omitted, the CLI decodes 4 bits by default.

Python API

from structrace.watermark import decode_text, embed_text

master = "Robustness/00_baseline_cases/6MRR/6MRR_original.pdb"
query = "tmp/6MRR_watermarked.pdb"

embed_result = embed_text(master, "npj SB", query)
decode_result = decode_text(master, query)

print(embed_result.global_ca_rmsd)
print(decode_result.decoded_text)

Package Functions

Watermarking

• embed_text(input_pdb, text, output_pdb): encode UTF-8 text as bits and embed it.
• decode_text(master_pdb, query_pdb): recover the embedded UTF-8 text watermark from the original and watermarked structures.

Repository Map

• src/structrace/: installable Python package.
• Robustness/: robustness and preliminary watermark-validation examples.
• Security_Safeguards/: Tier 1, Tier 2 and Tier 3 safeguard demonstrations.
• High-density_embedding_stress_test/: gamma-secretase high-capacity embedding case.
• Molecular_Dynamics_Validation/: MD inputs, structures and analysis outputs.
• Bit_RMSD/ and Bit_Rosetta_energy/: large-scale fidelity benchmark tables.
• Figs/Figs/: revised manuscript figures.
• docs/: package implementation log and extended API examples.

Citation

@article{Wang2026StrucTrace,
  title  = {StrucTrace: A Universal Fourier Watermark for Traceable Biomolecular Structures},
  author = {Wang, Xu and Wang, Chi and Huang, Tin-Yeh and Wang, Yiquan and Jiang, Siyuan and Yuan, Yafei},
  journal = {npj structural biology},
  year   = {2026},
  note   = {Accepted}
}