Protein
Design novel protein binders, redesign selected residues in fixed structures, and screen protein libraries against targets.
ProteinDesign
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
List curated protein design specifications
Get protein design run status
Get generated protein designs
Stop a running protein design run
Resume a stopped 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, 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 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 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[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)
class InputBinderSpecificationUniformlySampledBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecification]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponse: …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, InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseStructure
rules: Optional[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntity]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBond]]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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponseRules]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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
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 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)
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, 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 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 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[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)
class InputBinderSpecificationUniformlySampledBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecification]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponse: …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, InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseStructure
rules: Optional[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntity]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBond]]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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponseRules]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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
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 in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
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, 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 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 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[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)
class InputBinderSpecificationUniformlySampledBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecification]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponse: …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, InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseStructure
rules: Optional[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntity]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBond]]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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponseRules]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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
class DesignResumeResponse: …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, 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 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 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[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)
class InputBinderSpecificationUniformlySampledBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecification]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponse: …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, InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelection]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseStructure
rules: Optional[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationStructureTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntity]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse: …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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
class InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
bonds: Optional[List[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBond]]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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …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: InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand 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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationNoTemplateBinderSpecResponseRules]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 InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponse: …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[InputBinderSpecificationUniformlySampledBinderSpecResponseBinderSpecificationBoltzCuratedBinderSpecResponseRules]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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
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]
ProteinSequence Redesign
Redesign selected protein residues in one fixed CIF structure. Use the top-level type discriminator to choose binder redesign, with target and binder chain roles, or generic redesign. Every chain in the input structure must be assigned exactly once. Binder results include binding and structure metrics; generic results include structure and secondary-structure metrics.
Start a protein sequence redesign run
List protein sequence redesign runs
Get protein sequence redesign run status
Get redesigned protein sequences
Stop a running protein sequence redesign run
Resume a stopped protein sequence redesign run
Delete protein sequence redesign run data
Estimate cost for a protein sequence redesign run
ModelsExpand Collapse
class SequenceRedesignStartResponse: …A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline instead.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class SequenceRedesignListResponse: …Summary of a protein sequence redesign run.
Summary of a protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline instead.
Deprecated. Use pipeline_version instead.
class SequenceRedesignRetrieveResponse: …A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline instead.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class BinderProteinDesignResult: …
entities: List[BinderProteinDesignResultEntity]Entities in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
class BinderProteinDesignResultEntityProteinEntity: …
class BinderProteinDesignResultEntityRnaEntity: …
class BinderProteinDesignResultEntityDnaEntity: …
metrics: BinderProteinDesignResultMetricsStructural and binding quality metrics for a designed protein binder
Structural and binding quality metrics for a designed protein binder
class GenericProteinDesignResult: …
entities: List[GenericProteinDesignResultEntity]Entities in the designed complex, including designed and fixed input entities.
Entities in the designed complex, including designed and fixed input entities.
class GenericProteinDesignResultEntityProteinEntity: …
class GenericProteinDesignResultEntityRnaEntity: …
class GenericProteinDesignResultEntityDnaEntity: …
class SequenceRedesignStopResponse: …A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline instead.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class SequenceRedesignResumeResponse: …A fixed-structure protein sequence redesign run.
A fixed-structure protein sequence redesign run.
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline instead.
Deprecated. Use pipeline_version instead.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once as target or binder.
Every chain in the input CIF, assigned exactly once as target or binder.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …A fixed target chain from the input CIF.
A fixed target chain from the input CIF.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]Residues to redesign. Omit this field to keep the binder chain fixed.
Residues to redesign. Omit this field to keep the binder chain fixed.
filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]Every chain in the input CIF, assigned exactly once.
Every chain in the input CIF, assigned exactly once.
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]Residues to redesign. Omit this field to keep the chain fixed.
Residues to redesign. Omit this field to keep the chain fixed.
filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]Filters applied to this motif in addition to global_design_filters.
Filters applied to this motif in addition to global_design_filters.
Number of unique filter-passing redesigned proteins to generate.
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.
class SequenceRedesignEstimateCostResponse: …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]
ProteinLibrary Screen
Screen an existing library of proteins against a target structure. Results are scored by binding confidence (likelihood of protein-protein interaction) and structure confidence.
Start a protein library screen
List protein library screens
Get protein library screen status
Get screened protein candidates
Stop a running protein library screen
Resume a stopped protein library screen
Delete protein library screen data
Estimate cost for a protein library screen
ModelsExpand Collapse
class LibraryScreenStartResponse: …A protein library screening pipeline run
A protein library screening pipeline run
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)
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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: Optional[Progress]
class LibraryScreenListResponse: …Summary of a protein library screening pipeline run (excludes input)
Summary of a protein library screening 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.
progress: Optional[Progress]
class LibraryScreenRetrieveResponse: …A protein library screening pipeline run
A protein library screening pipeline run
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)
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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: Optional[Progress]
class LibraryScreenListResultsResponse: …Result for a single screened protein
Result for a single screened protein
entities: List[Entity]Entities of the screened complex. Includes both screened and fixed entities from the input.
Entities of the screened complex. Includes both screened and fixed entities from the input.
class EntityProteinEntity: …
class EntityRnaEntity: …
class EntityDnaEntity: …
metrics: MetricsStructural and binding quality metrics for a screened protein
Structural and binding quality metrics for a screened protein
class LibraryScreenStopResponse: …A protein library screening pipeline run
A protein library screening pipeline run
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)
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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: Optional[Progress]
class LibraryScreenResumeResponse: …A protein library screening pipeline run
A protein library screening pipeline run
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)
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. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand 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 InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …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: InputTargetNoTemplateTargetResponseBondAtom2Ligand 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 InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …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.
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
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: …Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
progress: Optional[Progress]
class LibraryScreenEstimateCostResponse: …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) -> PathRun
client.protein.library_screen.run(*, proteins: Iterable[protein_library_screen_start_params.Protein], target: protein_library_screen_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