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Protenix base v1.0.0 ​

Protenix predicts the 3D structure of proteins and molecular complexes from their sequences. It is an independent model from Boltz-2, built by a different team, so it is useful as a second opinion on a structure. Liatir runs it entirely on your computer.

What it does ​

From one or more protein, DNA or RNA sequences and optional small molecules, Protenix predicts where every atom sits, with a confidence score for each part of the structure.

Liatir runs it from five different random seeds, draws five structures from each, and returns the one Protenix itself ranks highest. On ubiquitin, a single seed produced the wrong fold in 6 of 11 tries; competing seeds recovered the right one each time.

Current status in Liatir ​

Protenix base v1.0.0 is published as a signed Runtime Box for Linux x86_64 with an NVIDIA GPU (CUDA 12.6). Windows computers with an NVIDIA GPU run the same box through WSL2. There is no macOS version.

Before publication, the exact box you download was checked against known science: from the sequence of ubiquitin alone, it reproduced the experimentally solved structure (PDB 1UBQ) to within 2.15 Å, and two runs from the same seed gave the same structure.

What to keep in mind ​

  • Predictions run without a multiple sequence alignment, because Liatir works offline. This is markedly less accurate for many proteins, and each result says so.
  • On ubiquitin, Protenix was slightly less accurate and about four times slower than Boltz-2. Its value is that it is independent: when both models agree, the structure is more trustworthy.
  • Protenix predicts structures only. For binding strength, use Boltz-2.

Expected inputs ​

Sequences of the chains in the complex, and optionally small molecules as SMILES.

Expected outputs ​

  • The best-ranked predicted structure as mmCIF, which opens in the 3D Structure Viewer, plus every structure drawn.
  • Confidence scores (pLDDT, pTM).
  • Jobs, Results and Runtime Box provenance, like every Liatir run.

Hardware and installation ​

You need an NVIDIA GPU. On the computer the box was validated on, a GeForce RTX 4060 Ti with 8 GB of memory, a 76-residue protein took about four minutes, using up to 3.4 GB of GPU memory and 4.3 GB of RAM. Before a larger run, Liatir tells you that it goes beyond what was measured and asks you to confirm.

Everything Protenix needs lives inside the Runtime Box and is never added to your system.

Official source ​