Start a protein sequence redesign run

POST/compute/v1/protein/sequence-redesign

Create a protein sequence redesign run from selected residues in a fixed input structure

Body ParametersJSONExpand Collapse

body: object { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }

One of the following:

BinderProteinSequenceRedesignRunInput object { entities, num_proteins, structure, 4 more }

entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs }

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

One of the following:

BinderSequenceRedesignTargetEntity object { chain_id, role, type }

A fixed target chain from the input CIF.

chain_id: string

minLength1

role: "target"

type: "from_template"

BinderSequenceRedesignBinderEntity object { chain_id, role, type, design_motifs }

chain_id: string

minLength1

role: "binder"

type: "from_template"

design_motifs: optional array of object { filters, residues, type }

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

filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

Filters applied to this motif in addition to global_design_filters.

One of the following:

ExcludedAminoAcidsDesignFilter object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilter object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilter object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

residues: array of number

0-indexed residues to redesign on this chain.

type: "residues"

num_proteins: number

Number of unique filter-passing redesigned proteins to generate.

minimum1

maximum1000

structure: object { type, url } or object { data, media_type, type }

How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.

One of the following:

URLSource object { type, url }

type: "url"

url: string

formaturi

CifBase64Source object { data, media_type, type }

data: string

Base64-encoded CIF file contents

media_type: "chemical/x-cif"

Must be chemical/x-cif for CIF files

type: "base64"

type: "binder"

global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

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

One of the following:

ExcludedAminoAcidsDesignFilter object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilter object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilter object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

idempotency_key: optional string

maxLength255

workspace_id: optional string

Workspace to run this redesign in.

GenericProteinSequenceRedesignRunInput object { entities, num_proteins, structure, 4 more }

entities: array of object { chain_id, type, design_motifs }

Every chain in the input CIF, assigned exactly once.

chain_id: string

minLength1

type: "from_template"

design_motifs: optional array of object { filters, residues, type }

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

filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

Filters applied to this motif in addition to global_design_filters.

One of the following:

ExcludedAminoAcidsDesignFilter object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilter object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilter object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

residues: array of number

0-indexed residues to redesign on this chain.

type: "residues"

num_proteins: number

Number of unique filter-passing redesigned proteins to generate.

minimum1

maximum1000

structure: object { type, url } or object { data, media_type, type }

How to provide a CIF structure file. URLs are auto-detected; base64 uploads must use chemical/x-cif media type.

One of the following:

URLSource object { type, url }

type: "url"

url: string

formaturi

CifBase64Source object { data, media_type, type }

data: string

Base64-encoded CIF file contents

media_type: "chemical/x-cif"

Must be chemical/x-cif for CIF files

type: "base64"

type: "generic"

global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

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

One of the following:

ExcludedAminoAcidsDesignFilter object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilter object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilter object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

idempotency_key: optional string

maxLength255

workspace_id: optional string

Workspace to run this redesign in.

ReturnsExpand Collapse

id: string

Unique ProteinSequenceRedesignRun 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: "boltz-protein-redesign"

Use pipeline instead.

Deprecated. Use pipeline instead.

Deprecatedengine_version: "v2026-07-14"

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 { entities, num_proteins, structure, 4 more } or object { entities, num_proteins, structure, 4 more }

Pipeline input (null if data deleted)

One of the following:

BinderProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }

entities: array of object { chain_id, role, type } or object { chain_id, role, type, design_motifs }

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

One of the following:

BinderSequenceRedesignTargetEntityResponse object { chain_id, role, type }

A fixed target chain from the input CIF.

chain_id: string

minLength1

role: "target"

type: "from_template"

BinderSequenceRedesignBinderEntityResponse object { chain_id, role, type, design_motifs }

chain_id: string

minLength1

role: "binder"

type: "from_template"

design_motifs: optional array of object { filters, residues, type }

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

filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

Filters applied to this motif in addition to global_design_filters.

One of the following:

ExcludedAminoAcidsDesignFilterResponse object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilterResponse object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilterResponse object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

residues: array of number

0-indexed residues to redesign on this chain.

type: "residues"

num_proteins: number

Number of unique filter-passing redesigned proteins to generate.

minimum1

maximum1000

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: "binder"

global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

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

One of the following:

ExcludedAminoAcidsDesignFilterResponse object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilterResponse object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilterResponse object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

idempotency_key: optional string

maxLength255

workspace_id: optional string

Workspace to run this redesign in.

GenericProteinSequenceRedesignRunInputResponse object { entities, num_proteins, structure, 4 more }

entities: array of object { chain_id, type, design_motifs }

Every chain in the input CIF, assigned exactly once.

chain_id: string

minLength1

type: "from_template"

design_motifs: optional array of object { filters, residues, type }

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

filters: array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

Filters applied to this motif in addition to global_design_filters.

One of the following:

ExcludedAminoAcidsDesignFilterResponse object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilterResponse object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilterResponse object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

residues: array of number

0-indexed residues to redesign on this chain.

type: "residues"

num_proteins: number

Number of unique filter-passing redesigned proteins to generate.

minimum1

maximum1000

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: "generic"

global_design_filters: optional array of object { amino_acids, type } or object { max_fraction, type } or object { motifs, type }

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

One of the following:

ExcludedAminoAcidsDesignFilterResponse object { amino_acids, type }

amino_acids: array of string

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

type: "excluded_amino_acids"

MaxHydrophobicFractionDesignFilterResponse object { max_fraction, type }

max_fraction: number

minimum0

maximum1

type: "max_hydrophobic_fraction"

ExcludedSequenceMotifsDesignFilterResponse object { motifs, type }

motifs: array of string

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

type: "excluded_sequence_motifs"

idempotency_key: optional string

maxLength255

workspace_id: optional string

Workspace to run this redesign in.

livemode: boolean

Whether this resource was created with a live API key.

pipeline: "boltz-protein-redesign"

pipeline_version: "v2026-07-14"

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

Start a protein sequence redesign run

curl https://api.boltz.bio/compute/v1/protein/sequence-redesign \
    -H 'Content-Type: application/json' \
    -H "x-api-key: $BOLTZ_API_KEY" \
    -d '{
          "entities": [
            {
              "chain_id": "x",
              "role": "target",
              "type": "from_template"
            },
            {
              "chain_id": "x",
              "role": "target",
              "type": "from_template"
            }
          ],
          "num_proteins": 1,
          "structure": {
            "type": "url",
            "url": "https://example.com"
          },
          "type": "binder"
        }'

{
  "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-redesign",
  "engine_version": "v2026-07-14",
  "error": {
    "code": "code",
    "message": "message",
    "details": {}
  },
  "input": {
    "entities": [
      {
        "chain_id": "x",
        "role": "target",
        "type": "from_template"
      },
      {
        "chain_id": "x",
        "role": "target",
        "type": "from_template"
      }
    ],
    "num_proteins": 1,
    "structure": {
      "url": "https://example.com",
      "url_expires_at": "2019-12-27T18:11:19.117Z"
    },
    "type": "binder",
    "global_design_filters": [
      {
        "amino_acids": [
          "x"
        ],
        "type": "excluded_amino_acids"
      }
    ],
    "idempotency_key": "idempotency_key",
    "workspace_id": "workspace_id"
  },
  "livemode": true,
  "pipeline": "boltz-protein-redesign",
  "pipeline_version": "v2026-07-14",
  "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-redesign",
  "engine_version": "v2026-07-14",
  "error": {
    "code": "code",
    "message": "message",
    "details": {}
  },
  "input": {
    "entities": [
      {
        "chain_id": "x",
        "role": "target",
        "type": "from_template"
      },
      {
        "chain_id": "x",
        "role": "target",
        "type": "from_template"
      }
    ],
    "num_proteins": 1,
    "structure": {
      "url": "https://example.com",
      "url_expires_at": "2019-12-27T18:11:19.117Z"
    },
    "type": "binder",
    "global_design_filters": [
      {
        "amino_acids": [
          "x"
        ],
        "type": "excluded_amino_acids"
      }
    ],
    "idempotency_key": "idempotency_key",
    "workspace_id": "workspace_id"
  },
  "livemode": true,
  "pipeline": "boltz-protein-redesign",
  "pipeline_version": "v2026-07-14",
  "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"
}