AlphaFold 3 vs Boltz-2 vs ColabFold: Which Structure Predictor?

By BioDockify Computational Research Team · September 19, 2026 · Comparison

AlphaFold 3 vs Boltz-2 vs ColabFold compared: accuracy benchmarks (AUC 0.59 vs 0.53), licenses, ligand support, cost and the right tool for each project.

Read the complete article with tables, code and references on BioDockify.

Key References

• Abramson, J. et al. AlphaFold 3. Nature 630, 493–500 (2024). DOI: 10.1038/s41586-024-07487-w
• Wohlwend, J. et al. Boltz-2: binding affinity prediction. bioRxiv (2025). https://github.com/jwohlwend/boltz
• Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nature Methods 19, 679–682 (2022). DOI: 10.1038/s41592-022-01488-1
• Independent benchmark of biomolecular interaction predictors. Nature (2025).
• Isomorphic Labs. AlphaFold 3 announcement. https://isomorphiclabs.com

Scope & Limitations

Benchmark scores reflect test-set performance; individual targets vary ColabFold sessions are capped by Colab GPU quotas (typically a few hours/day) AF3 server terms prohibit commercial use of outputs