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Protein

Sequence Redesign

Redesign selected protein residues in one fixed CIF structure. Use the top-level type discriminator to choose binder redesign, with target and binder chain roles, or generic redesign. Every chain in the input structure must be assigned exactly once. Binder results include binding and structure metrics; generic results include structure and secondary-structure metrics.

Start a protein sequence redesign run
protein.sequence_redesign.start(SequenceRedesignStartParams**kwargs) -> SequenceRedesignStartResponse
POST/compute/v1/protein/sequence-redesign
List protein sequence redesign runs
protein.sequence_redesign.list(SequenceRedesignListParams**kwargs) -> SyncCursorPage[SequenceRedesignListResponse]
GET/compute/v1/protein/sequence-redesign
Get protein sequence redesign run status
protein.sequence_redesign.retrieve(strid, SequenceRedesignRetrieveParams**kwargs) -> SequenceRedesignRetrieveResponse
GET/compute/v1/protein/sequence-redesign/{id}
Get redesigned protein sequences
protein.sequence_redesign.list_results(strid, SequenceRedesignListResultsParams**kwargs) -> SyncCursorPage[SequenceRedesignListResultsResponse]
GET/compute/v1/protein/sequence-redesign/{id}/results
Stop a running protein sequence redesign run
protein.sequence_redesign.stop(strid) -> SequenceRedesignStopResponse
POST/compute/v1/protein/sequence-redesign/{id}/stop
Resume a stopped protein sequence redesign run
protein.sequence_redesign.resume(strid) -> SequenceRedesignResumeResponse
POST/compute/v1/protein/sequence-redesign/{id}/resume
Delete protein sequence redesign run data
protein.sequence_redesign.delete_data(strid) -> SequenceRedesignDeleteDataResponse
POST/compute/v1/protein/sequence-redesign/{id}/delete-data
Estimate cost for a protein sequence redesign run
protein.sequence_redesign.estimate_cost(SequenceRedesignEstimateCostParams**kwargs) -> SequenceRedesignEstimateCostResponse
POST/compute/v1/protein/sequence-redesign/estimate-cost
ModelsExpand Collapse
class SequenceRedesignStartResponse: …

A fixed-structure protein sequence redesign run.

id: str

Unique ProteinSequenceRedesignRun identifier

completed_at: Optional[datetime]
formatdate-time
created_at: datetime
formatdate-time
data_deleted_at: Optional[datetime]

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

formatdate-time
Deprecatedengine: Literal["boltz-protein-redesign"]
Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: Literal["v2026-07-14"]
Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: Optional[Error]
code: str

Machine-readable error code

message: str

Human-readable error message

details: Optional[object]

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

input: Optional[Input]

Pipeline input (null if data deleted)

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once as target or binder.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …

A fixed target chain from the input CIF.

chain_id: str
minLength1
role: Literal["target"]
type: Literal["from_template"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
chain_id: str
minLength1
role: Literal["binder"]
type: Literal["from_template"]
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]

Residues to redesign. Omit this field to keep the binder chain fixed.

filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputBinderProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["binder"]
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once.

chain_id: str
minLength1
type: Literal["from_template"]
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]

Residues to redesign. Omit this field to keep the chain fixed.

filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputGenericProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["generic"]
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

livemode: bool

Whether this resource was created with a live API key.

pipeline: Literal["boltz-protein-redesign"]
pipeline_version: Literal["v2026-07-14"]
progress: Optional[Progress]
num_proteins_generated: int

Number of protein binders generated so far

minimum0
total_proteins_to_generate: int

Total number of protein binders requested

minimum1
latest_result_id: Optional[str]

ID of the most recently generated result

started_at: Optional[datetime]
formatdate-time
status: Literal["pending", "running", "succeeded", 2 more]
One of the following:
"pending"
"running"
"succeeded"
"failed"
"stopped"
stopped_at: Optional[datetime]
formatdate-time
workspace_id: str

Workspace ID

idempotency_key: Optional[str]

Client-provided idempotency key

class SequenceRedesignListResponse: …

Summary of a protein sequence redesign run.

id: str

Unique ProteinSequenceRedesignRunSummary identifier

completed_at: Optional[datetime]
formatdate-time
created_at: datetime
formatdate-time
data_deleted_at: Optional[datetime]

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

formatdate-time
Deprecatedengine: Literal["boltz-protein-redesign"]
Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: Literal["v2026-07-14"]
Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: Optional[Error]
code: str

Machine-readable error code

message: str

Human-readable error message

details: Optional[object]

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

livemode: bool

Whether this resource was created with a live API key.

pipeline: Literal["boltz-protein-redesign"]
pipeline_version: Literal["v2026-07-14"]
progress: Optional[Progress]
num_proteins_generated: int

Number of protein binders generated so far

minimum0
total_proteins_to_generate: int

Total number of protein binders requested

minimum1
latest_result_id: Optional[str]

ID of the most recently generated result

started_at: Optional[datetime]
formatdate-time
status: Literal["pending", "running", "succeeded", 2 more]
One of the following:
"pending"
"running"
"succeeded"
"failed"
"stopped"
stopped_at: Optional[datetime]
formatdate-time
workspace_id: str

Workspace ID

idempotency_key: Optional[str]

Client-provided idempotency key

class SequenceRedesignRetrieveResponse: …

A fixed-structure protein sequence redesign run.

id: str

Unique ProteinSequenceRedesignRun identifier

completed_at: Optional[datetime]
formatdate-time
created_at: datetime
formatdate-time
data_deleted_at: Optional[datetime]

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

formatdate-time
Deprecatedengine: Literal["boltz-protein-redesign"]
Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: Literal["v2026-07-14"]
Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: Optional[Error]
code: str

Machine-readable error code

message: str

Human-readable error message

details: Optional[object]

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

input: Optional[Input]

Pipeline input (null if data deleted)

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once as target or binder.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …

A fixed target chain from the input CIF.

chain_id: str
minLength1
role: Literal["target"]
type: Literal["from_template"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
chain_id: str
minLength1
role: Literal["binder"]
type: Literal["from_template"]
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]

Residues to redesign. Omit this field to keep the binder chain fixed.

filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputBinderProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["binder"]
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once.

chain_id: str
minLength1
type: Literal["from_template"]
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]

Residues to redesign. Omit this field to keep the chain fixed.

filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputGenericProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["generic"]
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

livemode: bool

Whether this resource was created with a live API key.

pipeline: Literal["boltz-protein-redesign"]
pipeline_version: Literal["v2026-07-14"]
progress: Optional[Progress]
num_proteins_generated: int

Number of protein binders generated so far

minimum0
total_proteins_to_generate: int

Total number of protein binders requested

minimum1
latest_result_id: Optional[str]

ID of the most recently generated result

started_at: Optional[datetime]
formatdate-time
status: Literal["pending", "running", "succeeded", 2 more]
One of the following:
"pending"
"running"
"succeeded"
"failed"
"stopped"
stopped_at: Optional[datetime]
formatdate-time
workspace_id: str

Workspace ID

idempotency_key: Optional[str]

Client-provided idempotency key

One of the following:
class BinderProteinDesignResult: …
id: str

Unique result ID.

artifacts: BinderProteinDesignResultArtifacts
archive: BinderProteinDesignResultArtifactsArchive
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
structure: Optional[BinderProteinDesignResultArtifactsStructure]
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
created_at: datetime
formatdate-time
entities: List[BinderProteinDesignResultEntity]

Entities in the designed complex, including designed and fixed input entities.

One of the following:
class BinderProteinDesignResultEntityProteinEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["protein"]
value: str

Amino acid sequence (one-letter codes)

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[BinderProteinDesignResultEntityProteinEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class BinderProteinDesignResultEntityRnaEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["rna"]
value: str

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

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[BinderProteinDesignResultEntityRnaEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class BinderProteinDesignResultEntityDnaEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["dna"]
value: str

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

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[BinderProteinDesignResultEntityDnaEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class BinderProteinDesignResultEntityLigandCcdEntity: …
chain_ids: List[str]

Chain IDs for this ligand

type: Literal["ligand_ccd"]
value: str

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

class BinderProteinDesignResultEntityLigandSmilesEntity: …
chain_ids: List[str]

Chain IDs for this ligand

type: Literal["ligand_smiles"]
value: str

SMILES string representing the ligand

metrics: BinderProteinDesignResultMetrics

Structural and binding quality metrics for a designed protein binder

binding_confidence: float

Confidence that the designed binder binds the target (0-1). Primary metric for hit discovery.

helix_fraction: float

Fraction of the designed sequence forming alpha helices (0-1).

minimum0
maximum1
iptm: float

Interface predicted TM score (0-1). Confidence in the protein-protein interface.

loop_fraction: float

Fraction of the designed sequence in coil/loop regions (0-1).

minimum0
maximum1
min_interaction_pae: float

Minimum predicted aligned error at the interface (Angstroms). Lower values indicate higher confidence.

sheet_fraction: float

Fraction of the designed sequence forming beta sheets (0-1).

minimum0
maximum1
structure_confidence: float

Confidence in the predicted 3D structure (0-1).

type: Literal["binder"]
warnings: Optional[List[BinderProteinDesignResultWarning]]

Warnings about potential quality issues with this result.

code: str

Machine-readable warning code (e.g. “low_confidence”, “unusual_geometry”)

message: str

Human-readable description of the warning

class GenericProteinDesignResult: …
id: str

Unique result ID.

artifacts: GenericProteinDesignResultArtifacts
archive: GenericProteinDesignResultArtifactsArchive
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
structure: Optional[GenericProteinDesignResultArtifactsStructure]
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
created_at: datetime
formatdate-time
entities: List[GenericProteinDesignResultEntity]

Entities in the designed complex, including designed and fixed input entities.

One of the following:
class GenericProteinDesignResultEntityProteinEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["protein"]
value: str

Amino acid sequence (one-letter codes)

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[GenericProteinDesignResultEntityProteinEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class GenericProteinDesignResultEntityRnaEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["rna"]
value: str

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

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[GenericProteinDesignResultEntityRnaEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class GenericProteinDesignResultEntityDnaEntity: …
chain_ids: List[str]

Chain IDs for this entity

type: Literal["dna"]
value: str

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

cyclic: Optional[bool]

Whether the sequence is cyclic

modifications: Optional[List[GenericProteinDesignResultEntityDnaEntityModification]]

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

residue_index: int

0-based index of the residue to modify

minimum0
type: Literal["ccd"]

Modification format. Only CCD polymer modifications are supported.

value: str

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

class GenericProteinDesignResultEntityLigandCcdEntity: …
chain_ids: List[str]

Chain IDs for this ligand

type: Literal["ligand_ccd"]
value: str

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

class GenericProteinDesignResultEntityLigandSmilesEntity: …
chain_ids: List[str]

Chain IDs for this ligand

type: Literal["ligand_smiles"]
value: str

SMILES string representing the ligand

metrics: GenericProteinDesignResultMetrics

Structure and design-quality metrics for a generic protein design.

helix_fraction: float

Fraction of the designed sequence forming alpha helices (0-1).

minimum0
maximum1
loop_fraction: float

Fraction of the designed sequence in coil/loop regions (0-1).

minimum0
maximum1
sheet_fraction: float

Fraction of the designed sequence forming beta sheets (0-1).

minimum0
maximum1
structure_confidence: float

Confidence in the predicted 3D structure (0-1).

type: Literal["generic"]
warnings: Optional[List[GenericProteinDesignResultWarning]]

Warnings about potential quality issues with this result.

code: str

Machine-readable warning code (e.g. “low_confidence”, “unusual_geometry”)

message: str

Human-readable description of the warning

class SequenceRedesignStopResponse: …

A fixed-structure protein sequence redesign run.

id: str

Unique ProteinSequenceRedesignRun identifier

completed_at: Optional[datetime]
formatdate-time
created_at: datetime
formatdate-time
data_deleted_at: Optional[datetime]

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

formatdate-time
Deprecatedengine: Literal["boltz-protein-redesign"]
Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: Literal["v2026-07-14"]
Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: Optional[Error]
code: str

Machine-readable error code

message: str

Human-readable error message

details: Optional[object]

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

input: Optional[Input]

Pipeline input (null if data deleted)

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once as target or binder.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …

A fixed target chain from the input CIF.

chain_id: str
minLength1
role: Literal["target"]
type: Literal["from_template"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
chain_id: str
minLength1
role: Literal["binder"]
type: Literal["from_template"]
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]

Residues to redesign. Omit this field to keep the binder chain fixed.

filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputBinderProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["binder"]
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once.

chain_id: str
minLength1
type: Literal["from_template"]
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]

Residues to redesign. Omit this field to keep the chain fixed.

filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputGenericProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["generic"]
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

livemode: bool

Whether this resource was created with a live API key.

pipeline: Literal["boltz-protein-redesign"]
pipeline_version: Literal["v2026-07-14"]
progress: Optional[Progress]
num_proteins_generated: int

Number of protein binders generated so far

minimum0
total_proteins_to_generate: int

Total number of protein binders requested

minimum1
latest_result_id: Optional[str]

ID of the most recently generated result

started_at: Optional[datetime]
formatdate-time
status: Literal["pending", "running", "succeeded", 2 more]
One of the following:
"pending"
"running"
"succeeded"
"failed"
"stopped"
stopped_at: Optional[datetime]
formatdate-time
workspace_id: str

Workspace ID

idempotency_key: Optional[str]

Client-provided idempotency key

class SequenceRedesignResumeResponse: …

A fixed-structure protein sequence redesign run.

id: str

Unique ProteinSequenceRedesignRun identifier

completed_at: Optional[datetime]
formatdate-time
created_at: datetime
formatdate-time
data_deleted_at: Optional[datetime]

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

formatdate-time
Deprecatedengine: Literal["boltz-protein-redesign"]
Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: Literal["v2026-07-14"]
Use pipeline_version instead.

Deprecated. Use pipeline_version instead.

error: Optional[Error]
code: str

Machine-readable error code

message: str

Human-readable error message

details: Optional[object]

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

input: Optional[Input]

Pipeline input (null if data deleted)

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponse: …
entities: List[InputBinderProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once as target or binder.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignTargetEntityResponse: …

A fixed target chain from the input CIF.

chain_id: str
minLength1
role: Literal["target"]
type: Literal["from_template"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponse: …
chain_id: str
minLength1
role: Literal["binder"]
type: Literal["from_template"]
design_motifs: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotif]]

Residues to redesign. Omit this field to keep the binder chain fixed.

filters: List[InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseEntityBinderSequenceRedesignBinderEntityResponseDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputBinderProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["binder"]
global_design_filters: Optional[List[InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputBinderProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

class InputGenericProteinSequenceRedesignRunInputResponse: …
entities: List[InputGenericProteinSequenceRedesignRunInputResponseEntity]

Every chain in the input CIF, assigned exactly once.

chain_id: str
minLength1
type: Literal["from_template"]
design_motifs: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotif]]

Residues to redesign. Omit this field to keep the chain fixed.

filters: List[InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilter]

Filters applied to this motif in addition to global_design_filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseEntityDesignMotifFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
residues: List[int]

0-indexed residues to redesign on this chain.

type: Literal["residues"]
num_proteins: int

Number of unique filter-passing redesigned proteins to generate.

minimum1
maximum1000
structure: InputGenericProteinSequenceRedesignRunInputResponseStructure
url: str

URL to download the file

formaturi
url_expires_at: datetime

When the presigned URL expires

formatdate-time
type: Literal["generic"]
global_design_filters: Optional[List[InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilter]]

Filters applied to every redesigned region. When omitted, cysteine is excluded. Pass [] to disable global filters.

One of the following:
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedAminoAcidsDesignFilterResponse: …
amino_acids: List[str]

Single-letter amino-acid codes that must not occur in the filtered designed region.

type: Literal["excluded_amino_acids"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterMaxHydrophobicFractionDesignFilterResponse: …
max_fraction: float
minimum0
maximum1
type: Literal["max_hydrophobic_fraction"]
class InputGenericProteinSequenceRedesignRunInputResponseGlobalDesignFilterExcludedSequenceMotifsDesignFilterResponse: …
motifs: List[str]

Sequence motifs that must not occur. X matches any single residue.

type: Literal["excluded_sequence_motifs"]
idempotency_key: Optional[str]
maxLength255
workspace_id: Optional[str]

Workspace to run this redesign in.

livemode: bool

Whether this resource was created with a live API key.

pipeline: Literal["boltz-protein-redesign"]
pipeline_version: Literal["v2026-07-14"]
progress: Optional[Progress]
num_proteins_generated: int

Number of protein binders generated so far

minimum0
total_proteins_to_generate: int

Total number of protein binders requested

minimum1
latest_result_id: Optional[str]

ID of the most recently generated result

started_at: Optional[datetime]
formatdate-time
status: Literal["pending", "running", "succeeded", 2 more]
One of the following:
"pending"
"running"
"succeeded"
"failed"
"stopped"
stopped_at: Optional[datetime]
formatdate-time
workspace_id: str

Workspace ID

idempotency_key: Optional[str]

Client-provided idempotency key

class SequenceRedesignDeleteDataResponse: …
id: str

ID of the resource whose data was deleted

data_deleted: Literal[true]
data_deleted_at: datetime

When the data was deleted

formatdate-time
class SequenceRedesignEstimateCostResponse: …

Estimate response with monetary values encoded as decimal strings to preserve precision.

breakdown: Breakdown

Cost breakdown for the billed application.

application: Literal["structure_and_binding", "small_molecule_design", "small_molecule_library_screen", 4 more]
One of the following:
"structure_and_binding"
"small_molecule_design"
"small_molecule_library_screen"
"protein_design"
"protein_redesign"
"protein_library_screen"
"adme"
cost_per_unit_usd: str

Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total.

num_units: int

Number of billable units in the estimate. The unit depends on the endpoint: samples for structure-and-binding, molecules for ADME, and requested proteins or molecules for design/screen endpoints.

disclaimer: str
estimated_cost_usd: str

Estimated total cost as a decimal string