alterlab-boltz

# 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 | Scenario | Use instead | |----------|-------------| | Protein-only or protein–protein folding, no ligand | `alterlab-alphafold` | | Antibody–antigen / general one-FASTA multi-entity complex | `alterlab-chai` | | Dock a ligand into an **existing, fixed** receptor structure | `alterlab-diffdock` | | Retrieve an experimentally determined structure | `alterlab-pdb` | | Design a binding-pocket sequence around a ligand | `alterlab-ligandmpnn` | ## Core Capabilities ### 1. Protein + ligand co-folding Describe the complex in a YAML spec (chains + ligand by SMILES or CCD), then predict: ...