Start a protein de novo design run
Create a new design run that generates novel protein binder candidates
ParametersExpand Collapse
body ProteinDesignStartParams
BinderSpecification param.Field[ProteinDesignStartParamsBinderSpecificationUnion]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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpec struct{…}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.
ChainSelection map[string, ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion]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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion0-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.
DesignMotifs []ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifUnionoptionalOptional 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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif struct{…}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.
DesignLengthRange ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotifDesignLengthRangeAllowed 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)
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif struct{…}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.
DesignLengthRange ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotifDesignLengthRangeAllowed 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
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplateLigandChainSpec struct{…}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 ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecModality
Structure ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureUnionHow 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.
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureURLSource struct{…}
type ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureCifBase64Source struct{…}
Base64-encoded CIF file contents
Must be chemical/x-cif for CIF files
Rules ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecRulesoptionalConstraints 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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpec struct{…}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 []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityUnionBinder 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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntity struct{…}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 []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityDesignedProteinEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntity struct{…}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 []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedProteinEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntity struct{…}
Chain IDs to assign to this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedRnaEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntity struct{…}
Chain IDs to assign to this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedDnaEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedLigandSmilesEntity struct{…}
Chain IDs to assign to this entity
SMILES string representing the ligand
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecEntityFixedLigandCcdEntity struct{…}
Chain IDs to assign to this entity
CCD code from RCSB PDB (e.g. 'ATP', 'ADP')
Modality ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecModality
Bonds []ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondoptionalCovalent 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 ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom1UnionLigand 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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom1LigandAtom struct{…}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
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom1PolymerAtom struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Atom2 ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom2UnionLigand 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.
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom2LigandAtom struct{…}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
type ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecBondAtom2PolymerAtom struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Rules ProteinDesignStartParamsBinderSpecificationNoTemplateBinderSpecRulesoptionalConstraints 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.
type ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpec struct{…}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 ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpecBinderBoltz-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 ProteinDesignStartParamsBinderSpecificationBoltzCuratedBinderSpecRulesoptionalConstraints 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 param.Field[ProteinDesignStartParamsTargetUnion]Target specification (structure template or template-free)
Target specification (structure template or template-free)
type ProteinDesignStartParamsTargetStructureTemplateTarget struct{…}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.
ChainSelection map[string, ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion]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.
type ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion0-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.
type ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetLigandChainSpec struct{…}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 ProteinDesignStartParamsTargetStructureTemplateTargetStructureUnionHow 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.
type ProteinDesignStartParamsTargetStructureTemplateTargetStructureURLSource struct{…}
type ProteinDesignStartParamsTargetStructureTemplateTargetStructureCifBase64Source struct{…}
Base64-encoded CIF file contents
Must be chemical/x-cif for CIF files
type ProteinDesignStartParamsTargetNoTemplateTarget struct{…}Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
Entities []ProteinDesignStartParamsTargetNoTemplateTargetEntityUnionEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
type ProteinDesignStartParamsTargetNoTemplateTargetEntityProteinEntity struct{…}
Chain IDs for this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
Modifications []ProteinDesignStartParamsTargetNoTemplateTargetEntityProteinEntityModificationUnionoptionalPost-translational modifications. Optional; defaults to an empty list when omitted.
Post-translational modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartParamsTargetNoTemplateTargetEntityProteinEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsTargetNoTemplateTargetEntityProteinEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsTargetNoTemplateTargetEntityRnaEntity struct{…}
Chain IDs for this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartParamsTargetNoTemplateTargetEntityRnaEntityModificationUnionoptionalChemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartParamsTargetNoTemplateTargetEntityRnaEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsTargetNoTemplateTargetEntityRnaEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsTargetNoTemplateTargetEntityDnaEntity struct{…}
Chain IDs for this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartParamsTargetNoTemplateTargetEntityDnaEntityModificationUnionoptionalChemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartParamsTargetNoTemplateTargetEntityDnaEntityModificationCcdModification struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartParamsTargetNoTemplateTargetEntityDnaEntityModificationSmilesModification struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartParamsTargetNoTemplateTargetEntityLigandCcdEntity struct{…}
Chain IDs for this ligand
CCD code (e.g., ATP, ADP)
type ProteinDesignStartParamsTargetNoTemplateTargetEntityLigandSmilesEntity struct{…}
Chain IDs for this ligand
SMILES string representing the ligand
Bonds []ProteinDesignStartParamsTargetNoTemplateTargetBondoptionalCovalent 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 ProteinDesignStartParamsTargetNoTemplateTargetBondAtom1UnionLigand 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.
type ProteinDesignStartParamsTargetNoTemplateTargetBondAtom1LigandAtom struct{…}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
type ProteinDesignStartParamsTargetNoTemplateTargetBondAtom1PolymerAtom struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Atom2 ProteinDesignStartParamsTargetNoTemplateTargetBondAtom2UnionLigand 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.
type ProteinDesignStartParamsTargetNoTemplateTargetBondAtom2LigandAtom struct{…}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
type ProteinDesignStartParamsTargetNoTemplateTargetBondAtom2PolymerAtom struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Constraints []ProteinDesignStartParamsTargetNoTemplateTargetConstraintUnionoptionalStructural 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.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintPocketConstraint struct{…}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
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraint struct{…}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 ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken1UnionLigand 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.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken1PolymerContactToken struct{…}
Chain ID
0-based residue index
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken1LigandContactToken struct{…}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 ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken2UnionLigand 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.
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken2PolymerContactToken struct{…}
Chain ID
0-based residue index
type ProteinDesignStartParamsTargetNoTemplateTargetConstraintContactConstraintToken2LigandContactToken struct{…}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
type ProteinDesignStartResponse struct{…}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 ProteinDesignStartResponseError
Machine-readable error code
Human-readable error message
Additional field-level error details keyed by input path, when available.
Input ProteinDesignStartResponseInputPipeline input (null if data deleted)
Pipeline input (null if data deleted)
BinderSpecification ProteinDesignStartResponseInputBinderSpecificationUnionBinder 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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponse struct{…}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.
ChainSelection map[string, ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionUnion]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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion0-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.
DesignMotifs []ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifUnionoptionalOptional 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.
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotif struct{…}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.
DesignLengthRange ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifReplacementMotifDesignLengthRangeAllowed 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)
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotif struct{…}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.
DesignLengthRange ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplatePolymerChainSpecDesignMotifInsertionMotifDesignLengthRangeAllowed 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
type ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseChainSelectionStructureTemplateLigandChainSpec struct{…}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 ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseModality
Structure ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseStructure
URL to download the file
When the presigned URL expires
Rules ProteinDesignStartResponseInputBinderSpecificationStructureTemplateBinderSpecResponseRulesoptionalConstraints 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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponse struct{…}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 []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityUnionBinder 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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponse struct{…}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 []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityDesignedProteinEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponse struct{…}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 []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedProteinEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponse struct{…}
Chain IDs to assign to this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedRnaEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponse struct{…}
Chain IDs to assign to this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModificationUnionoptionalOptional polymer modifications. Defaults to [] when omitted.
Optional polymer modifications. Defaults to [] when omitted.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedDnaEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedLigandSmilesEntityResponse struct{…}
Chain IDs to assign to this entity
SMILES string representing the ligand
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseEntityFixedLigandCcdEntityResponse struct{…}
Chain IDs to assign to this entity
CCD code from RCSB PDB (e.g. 'ATP', 'ADP')
Modality ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseModality
Bonds []ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondoptionalCovalent 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 ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1UnionLigand 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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1LigandAtomResponse struct{…}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
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom1PolymerAtomResponse struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Atom2 ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2UnionLigand 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.
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2LigandAtomResponse struct{…}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
type ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseBondAtom2PolymerAtomResponse struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Rules ProteinDesignStartResponseInputBinderSpecificationNoTemplateBinderSpecResponseRulesoptionalConstraints 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.
type ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponse struct{…}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 ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponseBinderBoltz-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 ProteinDesignStartResponseInputBinderSpecificationBoltzCuratedBinderSpecResponseRulesoptionalConstraints 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 ProteinDesignStartResponseInputTargetUnionTarget specification (structure template or template-free)
Target specification (structure template or template-free)
type ProteinDesignStartResponseInputTargetStructureTemplateTargetResponse struct{…}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.
ChainSelection map[string, ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionUnion]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.
type ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpec struct{…}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.
CropResidues ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion0-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.
type ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseChainSelectionStructureTemplateTargetLigandChainSpec struct{…}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 ProteinDesignStartResponseInputTargetStructureTemplateTargetResponseStructure
URL to download the file
When the presigned URL expires
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponse struct{…}Target defined by sequences only, without a 3D structure template
Target defined by sequences only, without a 3D structure template
Entities []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityUnionEntities (proteins, RNA, DNA, ligands) defining the target complex.
Entities (proteins, RNA, DNA, ligands) defining the target complex.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponse struct{…}
Chain IDs for this entity
Amino acid sequence (one-letter codes)
Whether the sequence is cyclic
Modifications []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationUnionoptionalPost-translational modifications. Optional; defaults to an empty list when omitted.
Post-translational modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityProteinEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponse struct{…}
Chain IDs for this entity
RNA nucleotide sequence (A, C, G, U, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationUnionoptionalChemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityRnaEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponse struct{…}
Chain IDs for this entity
DNA nucleotide sequence (A, C, G, T, N)
Whether the sequence is cyclic
Modifications []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationUnionoptionalChemical modifications. Optional; defaults to an empty list when omitted.
Chemical modifications. Optional; defaults to an empty list when omitted.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationCcdModificationResponse struct{…}
0-based index of the residue to modify
CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine)
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityDnaEntityResponseModificationSmilesModificationResponse struct{…}
0-based index of the residue to modify
SMILES string for the modification
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityLigandCcdEntityResponse struct{…}
Chain IDs for this ligand
CCD code (e.g., ATP, ADP)
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseEntityLigandSmilesEntityResponse struct{…}
Chain IDs for this ligand
SMILES string representing the ligand
Bonds []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondoptionalCovalent 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 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom1UnionLigand 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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom1LigandAtomResponse struct{…}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
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom1PolymerAtomResponse struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Atom2 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom2UnionLigand 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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom2LigandAtomResponse struct{…}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
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseBondAtom2PolymerAtomResponse struct{…}
Standardized atom name (verifiable in CIF file on RCSB)
Chain ID containing the atom
0-based residue index
Constraints []ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintUnionoptionalStructural 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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintPocketConstraintResponse struct{…}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
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponse struct{…}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 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1UnionLigand 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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1PolymerContactTokenResponse struct{…}
Chain ID
0-based residue index
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken1LigandContactTokenResponse struct{…}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 ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2UnionLigand 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.
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2PolymerContactTokenResponse struct{…}
Chain ID
0-based residue index
type ProteinDesignStartResponseInputTargetNoTemplateTargetResponseConstraintContactConstraintResponseToken2LigandContactTokenResponse struct{…}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 ProteinDesignStartResponseProgress
Number of protein binders generated so far
Total number of protein binders requested
ID of the most recently generated result
Status ProteinDesignStartResponseStatus
Workspace ID
Client-provided idempotency key
Start a protein de novo design run
package main
import (
"context"
"fmt"
"github.com/boltz-bio/boltz-api-go"
"github.com/boltz-bio/boltz-api-go/option"
)
func main() {
client := boltzapi.NewClient(
option.WithAPIKey("My API Key"),
)
response, err := client.Protein.Design.Start(context.TODO(), boltzapi.ProteinDesignStartParams{
BinderSpecification: boltzapi.ProteinDesignStartParamsBinderSpecificationUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpec: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpec{
ChainSelection: map[string]boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion{
"B": boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpec{
CropResidues: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecChainSelectionStructureTemplatePolymerChainSpecCropResiduesUnion{
OfIntArray: []int64{0, 1, 2, 3, 4, 5, 6, 7, 8, 9},
},
},
},
},
Modality: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecModalityPeptide,
Structure: boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureUnion{
OfProteinDesignStartsBinderSpecificationStructureTemplateBinderSpecStructureURLSource: &boltzapi.ProteinDesignStartParamsBinderSpecificationStructureTemplateBinderSpecStructureURLSource{
URL: "https://example.com",
},
},
},
},
NumProteins: 10,
Target: boltzapi.ProteinDesignStartParamsTargetUnion{
OfProteinDesignStartsTargetStructureTemplateTarget: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTarget{
ChainSelection: map[string]boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion{
"A": boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionUnion{
OfProteinDesignStartsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpec{
CropResidues: boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetChainSelectionStructureTemplateTargetPolymerChainSpecCropResiduesUnion{
OfIntArray: []int64{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12},
},
},
},
},
Structure: boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetStructureUnion{
OfProteinDesignStartsTargetStructureTemplateTargetStructureURLSource: &boltzapi.ProteinDesignStartParamsTargetStructureTemplateTargetStructureURLSource{
URL: "https://example.com",
},
},
},
},
})
if err != nil {
panic(err.Error())
}
fmt.Printf("%+v\n", 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"
}