Liatir

Appearance

Boltz-2 ​

Boltz-2 predicts the 3D structure of proteins and molecular complexes from their sequences, and estimates how strongly a small molecule binds a protein. Liatir runs it entirely on your computer.

What it does ​

  • Structure Prediction: from one or more protein, DNA or RNA sequences and optional small molecules, Boltz-2 predicts where every atom sits, with a confidence score for each part of the structure.
  • Protein–Ligand Affinity: for one protein and one small molecule written as SMILES, it predicts the probability that the molecule binds, and an estimate of binding strength as log10(IC50) in micromolar. Lower values mean stronger binding.

Current status in Liatir ​

Boltz-2 2.2.1 is published as a signed Runtime Box for Linux x86_64 with an NVIDIA GPU (CUDA 12.9). 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 1.99 Å.
  • For human carbonic anhydrase II it called acetazolamide a binder with probability 0.99 and ranked it stronger than sulfanilamide, matching laboratory measurements.

What to keep in mind ​

  • Affinity values are estimates, not measurements. Boltz-2 predicts IC50, which is not the same quantity as a measured Ki, and on the molecules above its values were weaker than the laboratory ones. Use them to compare and rank candidates, not as exact numbers.
  • Telling a real binder from a molecule that does not bind was not part of the checks above.
  • Predictions run without a multiple sequence alignment, because Liatir works offline. Proteins with few known relatives may be predicted less accurately.

Expected inputs ​

  • Structure Prediction: sequences of the chains in the complex, and optionally small molecules as SMILES.
  • Protein–Ligand Affinity: one protein sequence and one small molecule as SMILES. Following Boltz-2's own limits, Liatir warns above 56 heavy atoms and refuses above 128.

Expected outputs ​

  • The predicted structure as mmCIF, which opens in the 3D Structure Viewer.
  • Confidence scores, and for affinity the binding probability and log10(IC50).
  • 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 one minute, and a 260-residue protein with a small molecule took about two minutes, using up to 3.6 GB of GPU memory and under 10 GB of RAM. Before a larger run, Liatir tells you that it goes beyond what was measured and asks you to confirm.

The download is about 12.7 GB and needs about 20 GB of disk once installed. Everything Boltz-2 needs lives inside the Runtime Box and is never added to your system.

Official source ​