Boltz-2 (open AlphaFold3-style co-folding)

Overview

Boltz-2 (Passaro, Wohlwend et al. 2025; jwohlwend/boltz) is an open, commercially usable biomolecular structure model in the AlphaFold3 family: it co-folds proteins together with small-molecule ligands, nucleic acids, and multiple chains in a single prediction, and can predict binding affinity — capabilities AlphaFold2/ColabFold does not have. Use it when the biology is a complex with a ligand or other molecule types, not a bare protein.

When to Use This Skill

Use this skill when the user wants to:

• Co-fold a protein with a small-molecule ligand (SMILES or CCD code) into a holo complex.
• Predict a binding affinity alongside a co-folded pose.
• Fold protein–nucleic-acid or multi-entity assemblies in one pass.
• Get an open AlphaFold3-style prediction without proprietary access.

Does NOT Trigger