Design
Generate novel protein binders optimized for binding to a target structure. Binder specifications can be provided directly, uploaded as structure templates, or selected from Boltz-managed curated nanobody and antibody defaults. Results are scored by binding confidence (likelihood of protein-protein interaction) and structure confidence.
Start a protein de novo design run
List protein design runs
Get protein design run status
Get generated protein designs
Stop a running protein design run
Delete protein design run data
Estimate cost for a protein design run
ModelsExpand Collapse
class DesignStartResponse: …A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: InputBinderSpecificationBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
class InputBinderSpecificationStructureTemplateBinderSpecResponse: …Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: Dict[str, InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: Optional[List[InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
0-indexed position after which to insert. Use -1 to insert before the first residue.
rules: Optional[InputBinderSpecificationStructureTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationNoTemplateBinderSpecResponse: …Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: List[InputBinderSpecificationNoTemplateBinderSpecResponseEntity]Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseBond]]Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
rules: Optional[InputBinderSpecificationNoTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationBoltzCuratedBinderSpecResponse: …Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: Literal["boltz_nanobody", "boltz_antibody"]Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: Optional[InputBinderSpecificationBoltzCuratedBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: InputTargetTarget specification (structure template or template-free)
Target specification (structure template or template-free)
class InputTargetStructureTemplateTargetResponse: …Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: Dict[str, InputTargetStructureTemplateTargetResponseChainSelection]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
class InputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec: …Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
class InputTargetNoTemplateTargetResponse: …Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: List[InputTargetNoTemplateTargetResponseEntity]Entities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
class InputTargetNoTemplateTargetResponseEntityProteinEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponse: …
bonds: Optional[List[InputTargetNoTemplateTargetResponseBond]]Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputTargetNoTemplateTargetResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse: …Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponse: …Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
class DesignListResponse: …Summary of a protein design pipeline run (excludes input)
Summary of a protein design pipeline run (excludes input)
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
class DesignRetrieveResponse: …A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: InputBinderSpecificationBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
class InputBinderSpecificationStructureTemplateBinderSpecResponse: …Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: Dict[str, InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: Optional[List[InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
0-indexed position after which to insert. Use -1 to insert before the first residue.
rules: Optional[InputBinderSpecificationStructureTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationNoTemplateBinderSpecResponse: …Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: List[InputBinderSpecificationNoTemplateBinderSpecResponseEntity]Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseBond]]Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
rules: Optional[InputBinderSpecificationNoTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationBoltzCuratedBinderSpecResponse: …Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: Literal["boltz_nanobody", "boltz_antibody"]Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: Optional[InputBinderSpecificationBoltzCuratedBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: InputTargetTarget specification (structure template or template-free)
Target specification (structure template or template-free)
class InputTargetStructureTemplateTargetResponse: …Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: Dict[str, InputTargetStructureTemplateTargetResponseChainSelection]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
class InputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec: …Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
class InputTargetNoTemplateTargetResponse: …Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: List[InputTargetNoTemplateTargetResponseEntity]Entities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
class InputTargetNoTemplateTargetResponseEntityProteinEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponse: …
bonds: Optional[List[InputTargetNoTemplateTargetResponseBond]]Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputTargetNoTemplateTargetResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse: …Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponse: …Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
class DesignListResultsResponse: …A single generated protein design
A single generated protein design
entities: List[Entity]Entities of the designed binder complex. Includes both designed entities and fixed entities from the input.
Entities of the designed binder complex. Includes both designed entities and fixed entities from the input.
class EntityProteinEntity: …
class EntityRnaEntity: …
class EntityDnaEntity: …
metrics: MetricsStructural and binding quality metrics for a designed protein binder
Structural and binding quality metrics for a designed protein binder
class DesignStopResponse: …A protein design pipeline run that generates novel protein binders
A protein design pipeline run that generates novel protein binders
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: InputBinderSpecificationBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
class InputBinderSpecificationStructureTemplateBinderSpecResponse: …Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.
chain_selection: Dict[str, InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …Per-chain crop and design specification for a polymer chain in structure_template mode.
Per-chain crop and design specification for a polymer chain in structure_template mode.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.
design_motifs: Optional[List[InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
Replace a contiguous region of the sequence with a designed segment. Residues from start_index to end_index (inclusive) are replaced with a new sequence of the specified length.
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …Insert a designed segment at a specific position in the sequence.
Insert a designed segment at a specific position in the sequence.
0-indexed position after which to insert. Use -1 to insert before the first residue.
rules: Optional[InputBinderSpecificationStructureTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationNoTemplateBinderSpecResponse: …Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.
entities: List[InputBinderSpecificationNoTemplateBinderSpecResponseEntity]Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
Binder entities composing the design. At least one must be a designed_protein entity. Additional fixed entities (RNA, DNA, ligands) can be included as part of the complex.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Binder sequence specification. Fixed amino acids are written as literal single-letter codes. Designed regions are written as a length (fixed) or a length range (min..max). Example: “MKTAYI5..10VKSHFSRQ” means fixed MKTAYI, then 5-10 designed residues, then fixed VKSHFSRQ. “20” means 20 fully designed residues. “ACDE8GHI” means fixed ACDE, then 8 designed residues, then fixed GHI.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseBond]]Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein “1..3C1..2”, “C” is residue 1 (0-indexed) of the designed protein.
atom1: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
rules: Optional[InputBinderSpecificationNoTemplateBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
class InputBinderSpecificationBoltzCuratedBinderSpecResponse: …Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
Boltz-managed curated binder specification. Choose a curated nanobody or antibody family and Boltz will select from maintained template lists during design. The curated lists are managed by Boltz and may be updated over time to improve quality and coverage.
binder: Literal["boltz_nanobody", "boltz_antibody"]Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.
rules: Optional[InputBinderSpecificationBoltzCuratedBinderSpecResponseRules]Constraints applied during sequence design
Constraints applied during sequence design
Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)
Number of protein designs to generate. Must be between 10 and 1,000,000.
target: InputTargetTarget specification (structure template or template-free)
Target specification (structure template or template-free)
class InputTargetStructureTemplateTargetResponse: …Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.
chain_selection: Dict[str, InputTargetStructureTemplateTargetResponseChainSelection]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.
class InputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec: …Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.
crop_residues: Union[List[int], Literal["all"]]0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.
class InputTargetNoTemplateTargetResponse: …Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: List[InputTargetNoTemplateTargetResponseEntity]Entities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
class InputTargetNoTemplateTargetResponseEntityProteinEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponse: …
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponse: …
bonds: Optional[List[InputTargetNoTemplateTargetResponseBond]]Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: InputTargetNoTemplateTargetResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse: …Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Binding pocket residues keyed by chain ID. Each key is a chain ID (e.g. “A”) and the value is an array of 0-indexed residue indices that define the pocket on that chain.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponse: …Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
class DesignEstimateCostResponse: …Estimate response with monetary values encoded as decimal strings to preserve precision.
Estimate response with monetary values encoded as decimal strings to preserve precision.
breakdown: BreakdownCost breakdown for the billed application.
Cost breakdown for the billed application.
application: Literal["structure_and_binding", "small_molecule_design", "small_molecule_library_screen", 4 more]
Run
client.protein.design.run(*, binder_specification: protein_design_start_params.BinderSpecification, num_proteins: int, target: protein_design_start_params.Target, root_dir: str | PathLike[str], name: str | None, workspace_id: str | Omit, download_mode: DownloadMode | str | None, quiet: bool, poll_interval_seconds: float) -> Path