Generation method
Design protein or antibody sequences for a structured complex
Choose ProteinMPNN, SolubleMPNN, LigandMPNN, or the antibody-specific AbMPNN model; generate sequence candidates for a full backbone or atomic-context complex, preserve chosen positions, and compare recovery, mutations, and model confidence.
Method details
Input checks
- Complete full-backbone PDB coordinates
- Standard method: one or more designable protein chains
- LigandMPNN: non-water atomic context for a ligand, nucleic acid, metal, cofactor, or other molecule
- AbMPNN: one heavy chain and an optional distinct light chain
- Up to 2 structures and 2,000 total residues per analysis
Expected results
- Ranked sequence designs — Compare model score or confidence, atomic-context confidence where applicable, and sequence recovery.
- Chain-resolved sequences and roles — Review designed chains without losing fixed context; AbMPNN results retain explicit heavy/light roles.
- Exact mutation list — Inspect residue changes using both sequence and PDB residue positions.
Example results
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