Start a protein de novo design run
Create a new design run that generates novel protein binder candidates
ParametersExpand Collapse
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
class BinderSpecificationStructureTemplateBinderSpec: …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 engine 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 engine run.
chain_selection: Dict[str, BinderSpecificationStructureTemplateBinderSpecChainSelection]Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the engine 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 engine 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 BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec: …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[Iterable[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[Iterable[BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotif]]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 BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif: …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.
design_length_range: BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotifDesignLengthRangeAllowed sequence length range for designed regions
Allowed sequence length range for designed regions
Maximum sequence length in residues. Must be >= min.
Minimum sequence length in residues
0-indexed end residue (inclusive)
0-indexed start residue (inclusive)
class BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif: …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.
design_length_range: BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotifDesignLengthRangeAllowed sequence length range for designed regions
Allowed sequence length range for designed regions
Maximum sequence length in residues. Must be >= min.
Minimum sequence length in residues
class BinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplateLigandChainSpec: …Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.
Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.
modality: Literal["peptide", "antibody", "nanobody", "custom_protein"]
structure: BinderSpecificationStructureTemplateBinderSpecStructureHow 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.
class BinderSpecificationStructureTemplateBinderSpecStructureURLSource: …
class BinderSpecificationStructureTemplateBinderSpecStructureCifBase64Source: …
Base64-encoded CIF file contents
Must be chemical/x-cif for CIF files
rules: Optional[BinderSpecificationStructureTemplateBinderSpecRules]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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
class BinderSpecificationNoTemplateBinderSpec: …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: Iterable[BinderSpecificationNoTemplateBinderSpecEntity]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 BinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntity: …Protein binder entity with designed and/or fixed segments.
Protein binder entity with designed and/or fixed segments.
Chain IDs to assign to this entity
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.
Whether the sequence is cyclic
modifications: Optional[Iterable[BinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class BinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class BinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class BinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntity: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
Chain IDs to assign to this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
modifications: Optional[Iterable[BinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class BinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class BinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class BinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntity: …
Chain IDs to assign to this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
modifications: Optional[Iterable[BinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class BinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class BinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class BinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntity: …
Chain IDs to assign to this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
modifications: Optional[Iterable[BinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class BinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class BinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class BinderSpecificationNoTemplateBinderSpecEntityFixedLigandSmilesEntity: …
Chain IDs to assign to this entity
SMILES string representing the ligand
class BinderSpecificationNoTemplateBinderSpecEntityFixedLigandCcdEntity: …
Chain IDs to assign to this entity
CCD code from RCSB PDB (e.g. 'ATP', 'ADP')
modality: Literal["peptide", "antibody", "nanobody", "custom_protein"]
bonds: Optional[Iterable[BinderSpecificationNoTemplateBinderSpecBond]]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: BinderSpecificationNoTemplateBinderSpecBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class BinderSpecificationNoTemplateBinderSpecBondAtom1LigandAtom: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class BinderSpecificationNoTemplateBinderSpecBondAtom1PolymerAtom: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
atom2: BinderSpecificationNoTemplateBinderSpecBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class BinderSpecificationNoTemplateBinderSpecBondAtom2LigandAtom: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class BinderSpecificationNoTemplateBinderSpecBondAtom2PolymerAtom: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
rules: Optional[BinderSpecificationNoTemplateBinderSpecRules]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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
class BinderSpecificationBoltzCuratedBinderSpec: …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[BinderSpecificationBoltzCuratedBinderSpecRules]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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
Number of protein designs to generate. Must be between 10 and 1,000,000.
Target specification (structure template or template-free)
Target specification (structure template or template-free)
class TargetStructureTemplateTarget: …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, TargetStructureTemplateTargetChainSelection]Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the engine run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the engine run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, and which are flexible.
class TargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec: …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[Iterable[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 engine run.
0-indexed residue indices to retain from this chain, or 'all' to keep all residues. Residues not listed are excluded from the engine run.
0-indexed residue indices to keep
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues.
0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues.
class TargetStructureTemplateTargetChainSelectionStructureTemplateTargetLigandChainSpec: …Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.
Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.
structure: TargetStructureTemplateTargetStructureHow 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.
class TargetStructureTemplateTargetStructureURLSource: …
class TargetStructureTemplateTargetStructureCifBase64Source: …
Base64-encoded CIF file contents
Must be chemical/x-cif for CIF files
class TargetNoTemplateTarget: …Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
entities: Iterable[TargetNoTemplateTargetEntity]Entities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
class TargetNoTemplateTargetEntityProteinEntity: …
Chain IDs for this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
modifications: Optional[Iterable[TargetNoTemplateTargetEntityProteinEntityModification]]Post-translational modifications. Optional; defaults to an empty list when omitted.
Post-translational modifications. Optional; defaults to an empty list when omitted.
class TargetNoTemplateTargetEntityProteinEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class TargetNoTemplateTargetEntityProteinEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class TargetNoTemplateTargetEntityRnaEntity: …
Chain IDs for this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
modifications: Optional[Iterable[TargetNoTemplateTargetEntityRnaEntityModification]]Chemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
class TargetNoTemplateTargetEntityRnaEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class TargetNoTemplateTargetEntityRnaEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class TargetNoTemplateTargetEntityDnaEntity: …
Chain IDs for this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
modifications: Optional[Iterable[TargetNoTemplateTargetEntityDnaEntityModification]]Chemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
class TargetNoTemplateTargetEntityDnaEntityModificationCcdModification: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class TargetNoTemplateTargetEntityDnaEntityModificationSmilesModification: …
0-based index of the residue to modify
SMILES string for the modification
class TargetNoTemplateTargetEntityLigandCcdEntity: …
Chain IDs for this ligand
CCD code (e.g., ATP, ADP)
class TargetNoTemplateTargetEntityLigandSmilesEntity: …
Chain IDs for this ligand
SMILES string representing the ligand
bonds: Optional[Iterable[TargetNoTemplateTargetBond]]Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: TargetNoTemplateTargetBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class TargetNoTemplateTargetBondAtom1LigandAtom: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class TargetNoTemplateTargetBondAtom1PolymerAtom: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
atom2: TargetNoTemplateTargetBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class TargetNoTemplateTargetBondAtom2LigandAtom: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class TargetNoTemplateTargetBondAtom2PolymerAtom: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
constraints: Optional[Iterable[TargetNoTemplateTargetConstraint]]Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
class TargetNoTemplateTargetConstraintPocketConstraint: …Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Chain ID of the binder molecule
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.
Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A.
Whether to force the constraint
class TargetNoTemplateTargetConstraintContactConstraint: …Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Maximum distance in Angstroms
token1: TargetNoTemplateTargetConstraintContactConstraintToken1Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class TargetNoTemplateTargetConstraintContactConstraintToken1PolymerContactToken: …
Chain ID
0-based residue index
class TargetNoTemplateTargetConstraintContactConstraintToken1LigandContactToken: …Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID
token2: TargetNoTemplateTargetConstraintContactConstraintToken2Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class TargetNoTemplateTargetConstraintContactConstraintToken2PolymerContactToken: …
Chain ID
0-based residue index
class TargetNoTemplateTargetConstraintContactConstraintToken2LigandContactToken: …Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID
Whether to force the constraint
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
Polymer chain residues where binder contact is desired (the epitope). Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices.
Client-provided key to prevent duplicate submissions on retries
Target workspace ID (admin keys only; ignored for workspace keys)
ReturnsExpand Collapse
class DesignStartResponse: …A protein design engine run that generates novel protein binders
A protein design engine run that generates novel protein binders
Unique ProteinDesignRun identifier
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Engine used for protein design
Engine version used for protein design
error: Optional[Error]
Machine-readable error code
Human-readable error message
Additional field-level error details keyed by input path, when available.
input: Optional[Input]Pipeline input (null if data deleted)
Pipeline input (null if data deleted)
binder_specification: InputBinderSpecificationBinder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, or boltz_curated for Boltz-managed nanobody and antibody defaults.
class InputBinderSpecificationStructureTemplateBinderSpecResponse: …Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the engine 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 engine 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 engine 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 engine 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.
design_length_range: InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotifDesignLengthRangeAllowed sequence length range for designed regions
Allowed sequence length range for designed regions
Maximum sequence length in residues. Must be >= min.
Minimum sequence length in residues
0-indexed end residue (inclusive)
0-indexed start residue (inclusive)
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.
design_length_range: InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotifDesignLengthRangeAllowed sequence length range for designed regions
Allowed sequence length range for designed regions
Maximum sequence length in residues. Must be >= min.
Minimum sequence length in residues
class InputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplateLigandChainSpec: …Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.
Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.
modality: Literal["peptide", "antibody", "nanobody", "custom_protein"]
structure: InputBinderSpecificationStructureTemplateBinderSpecResponseStructure
URL to download the file
When the presigned URL expires
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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
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.
Chain IDs to assign to this entity
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.
Whether the sequence is cyclic
modifications: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse: …A fixed protein entity whose sequence is not redesigned.
A fixed protein entity whose sequence is not redesigned.
Chain IDs to assign to this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
modifications: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse: …
Chain IDs to assign to this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
modifications: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse: …
Chain IDs to assign to this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
modifications: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModification]]Optional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedLigandSmilesEntityResponse: …
Chain IDs to assign to this entity
SMILES string representing the ligand
class InputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedLigandCcdEntityResponse: …
Chain IDs to assign to this entity
CCD code from RCSB PDB (e.g. 'ATP', 'ADP')
modality: Literal["peptide", "antibody", "nanobody", "custom_protein"]
bonds: Optional[List[InputBinderSpecificationNoTemplateBinderSpecResponseBond]]Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein "1..3C1..2", "C" is residue 1 (0-indexed) of the designed protein.
Covalent bond constraints between atoms in the binder complex. If defining bonds where an atom is part of a designed protein chain, assume residue indices count designed regions as the minimum length. Example: designed protein "1..3C1..2", "C" is residue 1 (0-indexed) of the designed protein.
atom1: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1PolymerAtomResponse: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
atom2: InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class InputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2PolymerAtomResponse: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
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)
Sequence motifs to exclude from designed regions. Designs containing any of these motifs are filtered out before scoring. Use X as a single-residue wildcard (e.g. "NGS", "NXS").
Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.
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 engine run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, and which are flexible.
Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the engine run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope 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 engine run.
0-indexed residue indices to retain from this chain, or 'all' to keep all residues. Residues not listed are excluded from the engine run.
0-indexed residue indices to keep
0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues.
0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues.
class InputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetLigandChainSpec: …Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.
Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.
structure: InputTargetStructureTemplateTargetResponseStructure
URL to download the file
When the presigned URL expires
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: …
Chain IDs for this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
modifications: Optional[List[InputTargetNoTemplateTargetResponseEntityProteinEntityResponseModification]]Post-translational modifications. Optional; defaults to an empty list when omitted.
Post-translational modifications. Optional; defaults to an empty list when omitted.
class InputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponse: …
Chain IDs for this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
modifications: Optional[List[InputTargetNoTemplateTargetResponseEntityRnaEntityResponseModification]]Chemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponse: …
Chain IDs for this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
modifications: Optional[List[InputTargetNoTemplateTargetResponseEntityDnaEntityResponseModification]]Chemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationCcdModificationResponse: …
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
class InputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationSmilesModificationResponse: …
0-based index of the residue to modify
SMILES string for the modification
class InputTargetNoTemplateTargetResponseEntityLigandCcdEntityResponse: …
Chain IDs for this ligand
CCD code (e.g., ATP, ADP)
class InputTargetNoTemplateTargetResponseEntityLigandSmilesEntityResponse: …
Chain IDs for this ligand
SMILES string representing the ligand
bonds: Optional[List[InputTargetNoTemplateTargetResponseBond]]Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: InputTargetNoTemplateTargetResponseBondAtom1Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class InputTargetNoTemplateTargetResponseBondAtom1PolymerAtomResponse: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
atom2: InputTargetNoTemplateTargetResponseBondAtom2Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse: …Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID containing the atom
class InputTargetNoTemplateTargetResponseBondAtom2PolymerAtomResponse: …
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
constraints: Optional[List[InputTargetNoTemplateTargetResponseConstraint]]Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse: …Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
Chain ID of the binder molecule
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.
Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A.
Whether to force the constraint
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponse: …Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Maximum distance in Angstroms
token1: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse: …
Chain ID
0-based residue index
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse: …Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID
token2: InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse: …
Chain ID
0-based residue index
class InputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse: …Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead.
Chain ID
Whether to force the constraint
Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).
Polymer chain residues where binder contact is desired (the epitope). Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices.
Client-provided key to prevent duplicate submissions on retries
Target workspace ID (admin keys only; ignored for workspace keys)
Whether this resource was created with a live API key.
progress: Optional[Progress]
Number of protein binders generated so far
Total number of protein binders requested
ID of the most recently generated result
status: Literal["pending", "running", "succeeded", 2 more]
Workspace ID
Client-provided idempotency key
Start a protein de novo design run
import os
from boltz_api import Boltz
client = Boltz(
api_key=os.environ.get("BOLTZ_API_KEY"), # This is the default and can be omitted
)
response = client.protein.design.start(
binder_specification={
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
}
},
"modality": "peptide",
"structure": {
"type": "url",
"url": "https://example.com",
},
"type": "structure_template",
},
num_proteins=10,
target={
"chain_selection": {
"A": {
"chain_type": "polymer",
"crop_residues": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
}
},
"structure": {
"type": "url",
"url": "https://example.com",
},
"type": "structure_template",
},
)
print(response.id){
"id": "id",
"completed_at": "2019-12-27T18:11:19.117Z",
"created_at": "2019-12-27T18:11:19.117Z",
"data_deleted_at": "2019-12-27T18:11:19.117Z",
"engine": "boltz-protein-design",
"engine_version": "engine_version",
"error": {
"code": "code",
"message": "message",
"details": {}
},
"input": {
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"num_proteins": 10,
"target": {
"chain_selection": {
"A": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12
],
"epitope_residues": [
10,
11,
12
],
"flexible_residues": [
5,
6,
7
]
}
},
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template"
},
"idempotency_key": "idempotency_key",
"workspace_id": "workspace_id"
},
"livemode": true,
"progress": {
"num_proteins_generated": 0,
"total_proteins_to_generate": 1,
"latest_result_id": "latest_result_id"
},
"started_at": "2019-12-27T18:11:19.117Z",
"status": "pending",
"stopped_at": "2019-12-27T18:11:19.117Z",
"workspace_id": "workspace_id",
"idempotency_key": "idempotency_key"
}Returns Examples
{
"id": "id",
"completed_at": "2019-12-27T18:11:19.117Z",
"created_at": "2019-12-27T18:11:19.117Z",
"data_deleted_at": "2019-12-27T18:11:19.117Z",
"engine": "boltz-protein-design",
"engine_version": "engine_version",
"error": {
"code": "code",
"message": "message",
"details": {}
},
"input": {
"binder_specification": {
"chain_selection": {
"B": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9
],
"design_motifs": [
{
"design_length_range": {
"max": 8,
"min": 4
},
"end_index": 5,
"start_index": 0,
"type": "replacement"
}
]
}
},
"modality": "peptide",
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template",
"rules": {
"excluded_amino_acids": [
"x"
],
"excluded_sequence_motifs": [
"string"
],
"max_hydrophobic_fraction": 0
}
},
"num_proteins": 10,
"target": {
"chain_selection": {
"A": {
"chain_type": "polymer",
"crop_residues": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12
],
"epitope_residues": [
10,
11,
12
],
"flexible_residues": [
5,
6,
7
]
}
},
"structure": {
"url": "https://example.com",
"url_expires_at": "2019-12-27T18:11:19.117Z"
},
"type": "structure_template"
},
"idempotency_key": "idempotency_key",
"workspace_id": "workspace_id"
},
"livemode": true,
"progress": {
"num_proteins_generated": 0,
"total_proteins_to_generate": 1,
"latest_result_id": "latest_result_id"
},
"started_at": "2019-12-27T18:11:19.117Z",
"status": "pending",
"stopped_at": "2019-12-27T18:11:19.117Z",
"workspace_id": "workspace_id",
"idempotency_key": "idempotency_key"
}