Boltz: Open-Source Generative Protein Structure Prediction and Design with Boltz-1, Boltz-2, and Boltz Lab
While single-chain protein structure prediction had seen dramatic progress, modeling complex molecular interactions—protein-ligand, protein-protein—and enabling generative protein design remained open challenges critical to drug discovery and biology.
How it works
Common implementation structure
How this type of workflow is generally built, generalized across documented cases — not tied to any one vendor's stack. Click any stage to read what happens there. Specific products that implement these stages appear in “Tools commonly seen” below.
Stage 1 · User submits design spec
Users feed the model blank tokens and a high-level spec such as an antibody framework.
Tools used
Boltz-1Boltz-2BoltzGenBoltz LabProtein Data Bank
Outcome
Boltz released open-source Boltz-1 and Boltz-2 models approaching AlphaFold 3 performance, and launched Boltz Lab—a platform running 10x faster than open-source versions—that achieved nanomolar binders for two-thirds of 9 novel validation targets with zero prior PDB interactions.
What failed first
Prior regression-based structure prediction models produced averaged outputs when the ground truth was ambiguous between multiple valid conformational states, rather than sampling the full posterior distribution of possible structures.