Stop a running protein design run

POST/compute/v1/protein/design/{id}/stop

Stop an in-progress protein design run early

Path ParametersExpand Collapse

id: string

ReturnsExpand Collapse

id: string

Unique ProteinDesignRun identifier

completed_at: string

formatdate-time

created_at: string

formatdate-time

data_deleted_at: string

When the input, output, and result data was permanently deleted. Null if data has not been deleted.

formatdate-time

Deprecatedengine: "boltzprot"

Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: "1.0"

Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: object { code, message, details }

code: string

Machine-readable error code

message: string

Human-readable error message

details: optional unknown

Additional field-level error details keyed by input path, when available.

input: object { binder_specification, num_proteins, target, 2 more }

Pipeline input (null if data deleted)

binder_specification: object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules } or object { binder_specifications, type }

Binder specification for protein design. Use no_template for sequence-defined binders, structure_template for uploaded binder structures, boltz_curated for Boltz-managed nanobody and antibody defaults, or uniformly_sampled_specifications to sample uniformly across multiple binder specifications.

One of the following:

StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more }

Binder specification starting from an existing 3D structure. Upload a CIF/PDB file and select which chains to include, which residues to keep, and which regions to redesign. Only chains included in chain_selection are part of the pipeline run.

chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]

Chains selected from the uploaded binder structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep (crop_residues). Omit design_motifs to include the chain as fixed scaffold context.

One of the following:

StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs }

Per-chain crop and design specification for a polymer chain in structure_template mode.

chain_type: "polymer"

crop_residues: array of number or "all"

0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.

One of the following:

array of number

"all"

design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type }

Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.

One of the following:

ReplacementMotif object { design_length_range, end_index, start_index, type }

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: object { max, min }

Allowed sequence length range for designed regions

max: number

Maximum sequence length in residues. Must be >= min.

minimum0

min: number

Minimum sequence length in residues

minimum0

end_index: number

0-indexed end residue (inclusive)

minimum0

start_index: number

0-indexed start residue (inclusive)

minimum0

type: "replacement"

InsertionMotif object { after_residue_index, design_length_range, type }

Insert a designed segment at a specific position in the sequence.

after_residue_index: number

0-indexed position after which to insert. Use -1 to insert before the first residue.

minimum-1

design_length_range: object { max, min }

Allowed sequence length range for designed regions

max: number

Maximum sequence length in residues. Must be >= min.

minimum0

min: number

Minimum sequence length in residues

minimum0

type: "insertion"

StructureTemplateLigandChainSpec object { chain_type }

Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.

chain_type: "ligand"

modality: "peptide" or "antibody" or "nanobody" or "custom_protein"

One of the following:

"peptide"

"antibody"

"nanobody"

"custom_protein"

structure: object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

type: "structure_template"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

NoTemplateBinderSpecResponse object { entities, modality, type, 2 more }

Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.

entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 more

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.

One of the following:

DesignedProteinEntityResponse object { chain_ids, type, value, 2 more }

Protein binder entity with designed and/or fixed segments.

chain_ids: array of string

Chain IDs to assign to this entity

type: "designed_protein"

value: string

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.

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedProteinEntityResponse object { chain_ids, type, value, 2 more }

A fixed protein entity whose sequence is not redesigned.

chain_ids: array of string

Chain IDs to assign to this entity

type: "protein"

value: string

Amino acid sequence (one-letter codes)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedRnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs to assign to this entity

type: "rna"

value: string

RNA nucleotide sequence (A, C, G, U, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedDnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs to assign to this entity

type: "dna"

value: string

DNA nucleotide sequence (A, C, G, T, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedLigandSmilesEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs to assign to this entity

type: "ligand_smiles"

value: string

SMILES string representing the ligand

FixedLigandCcdEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs to assign to this entity

type: "ligand_ccd"

value: string

CCD code from RCSB PDB (e.g. ‘ATP’, ‘ADP’)

modality: "peptide" or "antibody" or "nanobody" or "custom_protein"

One of the following:

"peptide"

"antibody"

"nanobody"

"custom_protein"

type: "no_template"

bonds: optional array of object { atom1, atom2 }

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: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters.

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

BoltzCuratedBinderSpecResponse object { binder, type, rules }

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: "boltz_nanobody" or "boltz_antibody"

Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.

One of the following:

"boltz_nanobody"

"boltz_antibody"

type: "boltz_curated"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

UniformlySampledBinderSpecResponse object { binder_specifications, type }

A collection of binder specifications sampled uniformly during protein design. This lets one run explore multiple binder definitions while keeping each generation request shape unchanged.

binder_specifications: array of object { chain_selection, modality, structure, 2 more } or object { entities, modality, type, 2 more } or object { binder, type, rules }

Binder specifications to sample uniformly when generating designs. Each generation samples one specification from this list; over larger runs this gives roughly equal representation.

One of the following:

StructureTemplateBinderSpecResponse object { chain_selection, modality, structure, 2 more }

chain_selection: map[object { chain_type, crop_residues, design_motifs } or object { chain_type } ]

One of the following:

StructureTemplatePolymerChainSpec object { chain_type, crop_residues, design_motifs }

Per-chain crop and design specification for a polymer chain in structure_template mode.

chain_type: "polymer"

crop_residues: array of number or "all"

0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are removed before design.

One of the following:

array of number

"all"

design_motifs: optional array of object { design_length_range, end_index, start_index, type } or object { after_residue_index, design_length_range, type }

Optional motifs (replacement or insertion) defining which regions to redesign on this chain. Omit this field to include the chain as fixed scaffold context.

One of the following:

ReplacementMotif object { design_length_range, end_index, start_index, type }

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: object { max, min }

Allowed sequence length range for designed regions

max: number

Maximum sequence length in residues. Must be >= min.

minimum0

min: number

Minimum sequence length in residues

minimum0

end_index: number

0-indexed end residue (inclusive)

minimum0

start_index: number

0-indexed start residue (inclusive)

minimum0

type: "replacement"

InsertionMotif object { after_residue_index, design_length_range, type }

Insert a designed segment at a specific position in the sequence.

after_residue_index: number

0-indexed position after which to insert. Use -1 to insert before the first residue.

minimum-1

design_length_range: object { max, min }

Allowed sequence length range for designed regions

max: number

Maximum sequence length in residues. Must be >= min.

minimum0

min: number

Minimum sequence length in residues

minimum0

type: "insertion"

StructureTemplateLigandChainSpec object { chain_type }

Per-chain specification for a ligand chain in structure_template mode. The full ligand is always included.

chain_type: "ligand"

modality: "peptide" or "antibody" or "nanobody" or "custom_protein"

One of the following:

"peptide"

"antibody"

"nanobody"

"custom_protein"

structure: object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

type: "structure_template"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

NoTemplateBinderSpecResponse object { entities, modality, type, 2 more }

Binder specification without a structural template. Define the binder from sequence components (fixed and designed segments) without providing a starting 3D structure.

entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 3 more

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.

One of the following:

DesignedProteinEntityResponse object { chain_ids, type, value, 2 more }

Protein binder entity with designed and/or fixed segments.

chain_ids: array of string

Chain IDs to assign to this entity

type: "designed_protein"

value: string

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedProteinEntityResponse object { chain_ids, type, value, 2 more }

A fixed protein entity whose sequence is not redesigned.

chain_ids: array of string

Chain IDs to assign to this entity

type: "protein"

value: string

Amino acid sequence (one-letter codes)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedRnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs to assign to this entity

type: "rna"

value: string

RNA nucleotide sequence (A, C, G, U, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedDnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs to assign to this entity

type: "dna"

value: string

DNA nucleotide sequence (A, C, G, T, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

Optional CCD polymer modifications. Defaults to [] when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

FixedLigandSmilesEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs to assign to this entity

type: "ligand_smiles"

value: string

SMILES string representing the ligand

FixedLigandCcdEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs to assign to this entity

type: "ligand_ccd"

value: string

CCD code from RCSB PDB (e.g. ‘ATP’, ‘ADP’)

modality: "peptide" or "antibody" or "nanobody" or "custom_protein"

One of the following:

"peptide"

"antibody"

"nanobody"

"custom_protein"

type: "no_template"

bonds: optional array of object { atom1, atom2 }

atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

BoltzCuratedBinderSpecResponse object { binder, type, rules }

binder: "boltz_nanobody" or "boltz_antibody"

Boltz-managed curated binder family. Boltz maintains and may update the underlying template lists on behalf of customers.

One of the following:

"boltz_nanobody"

"boltz_antibody"

type: "boltz_curated"

rules: optional object { excluded_amino_acids, excluded_sequence_motifs, max_hydrophobic_fraction }

Constraints applied during sequence design

excluded_amino_acids: optional array of string

Single-letter amino acid codes to exclude from design (e.g. [‘C’, ‘P’] to exclude cysteine and proline)

excluded_sequence_motifs: optional array of string

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”).

max_hydrophobic_fraction: optional number

Maximum allowed fraction of hydrophobic residues (I, L, V, M, F, W, Y) in designed regions. Designs exceeding this threshold are filtered out before scoring. Leave empty to disable.

minimum0

maximum1

type: "uniformly_sampled_specifications"

num_proteins: number

Number of protein designs to generate. Must be between 10 and 1,000,000.

minimum10

maximum1000000

target: object { chain_selection, structure, type } or object { entities, type, bonds, 4 more }

Target specification (structure template or template-free)

One of the following:

StructureTemplateTargetResponse object { chain_selection, structure, type }

Target defined by an uploaded 3D structure (CIF or PDB file). Only chains included in chain_selection are used.

chain_selection: map[object { chain_type, crop_residues, epitope_residues, 2 more } or object { chain_type } ]

Chains selected from the uploaded structure, keyed by chain ID. Only chains listed here are included in the pipeline run — any chains omitted from this mapping are ignored. Each value defines which residues to keep, which are epitope residues, which are non-binding residues, and which are flexible.

One of the following:

StructureTemplateTargetPolymerChainSpec object { chain_type, crop_residues, epitope_residues, 2 more }

Per-chain specification for a polymer (protein/RNA/DNA) chain in a structure template target.

chain_type: "polymer"

crop_residues: array of number or "all"

0-indexed residue indices to retain from this chain, or ‘all’ to keep all residues. Residues not listed are excluded from the pipeline run.

One of the following:

array of number

0-indexed residue indices to keep

"all"

epitope_residues: optional array of number

0-indexed residue indices where binder contact is desired (the epitope). All indices must be present in crop_residues and must not overlap non_binding_residues.

flexible_residues: optional array of number

0-indexed residue indices allowed to move during design (e.g. flexible loop regions). All indices must be present in crop_residues.

non_binding_residues: optional array of number

0-indexed residue indices where binder contact should be discouraged. All indices must be present in crop_residues and must not overlap epitope_residues.

StructureTemplateTargetLigandChainSpec object { chain_type }

Per-chain specification for a ligand chain in a structure template target. The full ligand is always included.

chain_type: "ligand"

structure: object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

type: "structure_template"

NoTemplateTargetResponse object { entities, type, bonds, 4 more }

Target defined by sequences only, without a 3D structure template

entities: array of object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or object { chain_ids, type, value, 2 more } or 2 more

Entities (proteins, RNA, DNA, ligands) defining the target complex.

One of the following:

ProteinEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs for this entity

type: "protein"

value: string

Amino acid sequence (one-letter codes)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

RnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs for this entity

type: "rna"

value: string

RNA nucleotide sequence (A, C, G, U, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

DnaEntityResponse object { chain_ids, type, value, 2 more }

chain_ids: array of string

Chain IDs for this entity

type: "dna"

value: string

DNA nucleotide sequence (A, C, G, T, N)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

CCD chemical modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

LigandCcdEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs for this ligand

type: "ligand_ccd"

value: string

CCD code (e.g., ATP, ADP)

LigandSmilesEntityResponse object { chain_ids, type, value }

chain_ids: array of string

Chain IDs for this ligand

type: "ligand_smiles"

value: string

SMILES string representing the ligand

type: "no_template"

bonds: optional array of object { atom1, atom2 }

Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.

atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtomResponse object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

PolymerAtomResponse object { atom_name, chain_id, residue_index, type }

atom_name: string

Standardized atom name (verifiable in CIF file on RCSB)

chain_id: string

Chain ID containing the atom

residue_index: number

0-based residue index

minimum0

type: "polymer_atom"

constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more }

Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.

One of the following:

PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more }

Constrains the binder to interact with specific pocket residues on the target.

binder_chain_id: string

Chain ID of the binder molecule

contact_residues: map[array of number]

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.

max_distance_angstrom: number

Maximum allowed distance in Angstroms between binder and pocket residues. Typical range: 4-8 A.

type: "pocket"

force: optional boolean

Whether to force the constraint

ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more }

Maximum-distance contact constraint between two polymer residues or ligand atoms.

max_distance_angstrom: number

Maximum distance in Angstroms

token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

PolymerContactTokenResponse object { chain_id, residue_index, type }

chain_id: string

Chain ID

residue_index: number

0-based residue index

minimum0

type: "polymer_contact"

LigandContactTokenResponse object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID

type: "ligand_contact"

token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

PolymerContactTokenResponse object { chain_id, residue_index, type }

chain_id: string

Chain ID

residue_index: number

0-based residue index

minimum0

type: "polymer_contact"

LigandContactTokenResponse object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

chain_id: string

Chain ID

type: "ligand_contact"

type: "contact"

force: optional boolean

Whether to force the constraint

epitope_ligand_chains: optional array of string

Chain IDs of ligand entities that are part of the binding epitope. Ligands are marked as epitope in full (no residue-level selection).

epitope_residues: optional map[array of number]

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. Residues must not overlap non_binding_residues on the same chain.

non_binding_residues: optional map[array of number]

Polymer chain residues where binder contact should be discouraged. Each key is a chain ID of a polymer entity, each value is an array of 0-indexed residue indices. Residues must not overlap epitope_residues on the same chain.

idempotency_key: optional string

Client-provided key to prevent duplicate submissions on retries

maxLength255

workspace_id: optional string

Target workspace ID (admin keys only; ignored for workspace keys)

livemode: boolean

Whether this resource was created with a live API key.

pipeline: "boltzprot"

Pipeline used for protein design

pipeline_version: "1.0"

Pipeline version used for protein design

progress: object { num_proteins_generated, total_proteins_to_generate, latest_result_id }

num_proteins_generated: number

Number of protein binders generated so far

minimum0

total_proteins_to_generate: number

Total number of protein binders requested

minimum1

latest_result_id: optional string

ID of the most recently generated result

started_at: string

formatdate-time

status: "pending" or "running" or "succeeded" or 2 more

One of the following:

"pending"

"running"

"succeeded"

"failed"

"stopped"

stopped_at: string

formatdate-time

workspace_id: string

Workspace ID

idempotency_key: optional string

Client-provided idempotency key

Stop a running protein design run

curl https://api.boltz.bio/compute/v1/protein/design/$ID/stop \
    -X POST \
    -H "x-api-key: $BOLTZ_API_KEY"

{
  "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": "boltzprot",
  "engine_version": "1.0",
  "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
          ],
          "non_binding_residues": [
            0,
            1,
            2
          ]
        }
      },
      "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,
  "pipeline": "boltzprot",
  "pipeline_version": "1.0",
  "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": "boltzprot",
  "engine_version": "1.0",
  "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
          ],
          "non_binding_residues": [
            0,
            1,
            2
          ]
        }
      },
      "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,
  "pipeline": "boltzprot",
  "pipeline_version": "1.0",
  "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"
}