List curated protein design specifications
List binder-side protein design specifications from Boltz-managed curated nanobody or antibody libraries.
ParametersExpand Collapse
ReturnsExpand Collapse
class DesignListCuratedSpecificationsResponse: …
data: List[Data]
binder_specification: DataBinderSpecificationBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.
class DataBinderSpecificationStructureTemplateBinderSpec: …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, DataBinderSpecificationStructureTemplateBinderSpecChainSelection]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 DataBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec: …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[DataBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 DataBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 DataBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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.
structure: DataBinderSpecificationStructureTemplateBinderSpecStructureHow to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
rules: Optional[DataBinderSpecificationStructureTemplateBinderSpecRules]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 DataBinderSpecificationNoTemplateBinderSpec: …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[DataBinderSpecificationNoTemplateBinderSpecEntity]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 DataBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntity: …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 DataBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntity: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class DataBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntity: …
class DataBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntity: …
bonds: Optional[List[DataBinderSpecificationNoTemplateBinderSpecBond]]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: DataBinderSpecificationNoTemplateBinderSpecBondAtom1Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
class DataBinderSpecificationNoTemplateBinderSpecBondAtom1LigandAtom: …Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: DataBinderSpecificationNoTemplateBinderSpecBondAtom2Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
class DataBinderSpecificationNoTemplateBinderSpecBondAtom2LigandAtom: …Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: Optional[DataBinderSpecificationNoTemplateBinderSpecRules]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 DataBinderSpecificationBoltzCuratedBinderSpec: …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[DataBinderSpecificationBoltzCuratedBinderSpecRules]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 DataBinderSpecificationUniformlySampledBinderSpec: …A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.
binder_specifications: List[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecification]Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.
class DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpec: …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, DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecChainSelection]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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec: …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[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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.
structure: DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecStructureHow to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.
rules: Optional[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationStructureTemplateBinderSpecRules]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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpec: …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[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecEntity]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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntity: …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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntity: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntity: …
class DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntity: …
bonds: Optional[List[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecBond]]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: DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecBondAtom1Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
class DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecBondAtom1LigandAtom: …Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
atom2: DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecBondAtom2Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
class DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecBondAtom2LigandAtom: …Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.
rules: Optional[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationNoTemplateBinderSpecRules]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 DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationBoltzCuratedBinderSpec: …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[DataBinderSpecificationUniformlySampledBinderSpecBinderSpecificationBoltzCuratedBinderSpecRules]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)
List curated protein design specifications
import os
from boltz_api import Boltz
client = Boltz(
api_key=os.environ.get("BOLTZ_API_KEY"), # This is the default and can be omitted
)
response = client.protein.design.list_curated_specifications(
type="nanobody",
)
print(response.data){
"data": [
{
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"type": "url",
"url": "https://example.com"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"name": "name"
}
]
}Returns Examples
{
"data": [
{
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"type": "url",
"url": "https://example.com"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"name": "name"
}
]
}