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boltzgen

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All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz.

When to use

• side-chain aware design
• designing around small molecules or ligands
• all-atom diffusion
• precise binding geometries
• YAML-based configuration
• protein binder design
• peptide design
• nanobody and antibody CDR design

When not to use

• backbone-only generation
• sequence-only design
• structure validation

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