API Reference

Predictions

Copy Markdown

Open in Claude

Open in ChatGPT

Open in Cursor

---

Copy Markdown

View as Markdown

Structure And Binding

Predict 3D structure coordinates, per-residue confidence scores, and binding metrics for a molecular complex. Supports optional template-guided folding and per-protein MSA control.

Start a structure and binding prediction

POST/compute/v1/predictions/structure-and-binding

List structure and binding predictions

GET/compute/v1/predictions/structure-and-binding

Retrieve a structure and binding prediction

GET/compute/v1/predictions/structure-and-binding/{id}

Delete prediction data

POST/compute/v1/predictions/structure-and-binding/{id}/delete-data

Estimate cost for a structure and binding prediction

POST/compute/v1/predictions/structure-and-binding/estimate-cost

ModelsExpand Collapse

StructureAndBindingStartResponse object { id, completed_at, created_at, 12 more }

id: string

Unique prediction identifier

completed_at: string

formatdate-time

created_at: string

formatdate-time

data_deleted_at: string

When the input/output data was deleted, or null if still available

formatdate-time

error: object { code, message, details }

Error details when failed

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.

expires_at: string

When this resource and its associated data will be permanently deleted. Null while still in progress.

formatdate-time

input: object { entities, binding, bonds, 4 more }

Prediction input (null if data deleted)

entities: array of object { chain_ids, type, value, 3 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) forming the complex to predict. Order determines chain assignment.

One of the following:

Boltz2ProteinEntityResponse object { chain_ids, type, value, 3 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)

msa: optional object { format, source, type } or object { type }

Optional protein MSA control. Omit msa on all protein entities to use automatic MSA generation. Use custom for user-provided A3M/CSV files, or empty for single-sequence mode. Custom MSA and automatic MSA cannot be mixed in one request.

One of the following:

Boltz2CustomMsaResponse object { format, source, type }

Use a user-provided MSA for this protein entity. If any protein entity uses a custom MSA, every other protein entity must use either custom or empty MSA; automatic MSA generation cannot be mixed with custom MSAs in the same request.

format: "a3m" or "csv"

Custom MSA file format. Base64 uploads must use media_type text/x-a3m for A3M or text/csv for CSV.

One of the following:

"a3m"

"csv"

source: 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: "custom"

Boltz2EmptyMsaResponse object { type }

Run this protein entity in single-sequence mode without an MSA. Use this for chains that should not use automatic MSA generation, including non-homologous chains in a request that also includes custom MSAs.

type: "empty"

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

binding: optional object { binder_chain_id, type } or object { binder_chain_ids, type }

One of the following:

LigandProteinBindingResponse object { binder_chain_id, type }

binder_chain_id: string

Chain ID of the ligand binder (must have exactly 1 copy, at most 2048 heavy atoms, and only ligands+proteins in entities)

type: "ligand_protein_binding"

ProteinProteinBindingResponse object { binder_chain_ids, type }

binder_chain_ids: array of string

Chain IDs of the protein binders

type: "protein_protein_binding"

bonds: optional array of object { atom1, atom2 }

Bond constraints between atoms. 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

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

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"

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

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

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

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

type: "ligand_contact"

type: "contact"

force: optional boolean

Whether to force the constraint

model_options: optional object { recycling_steps, sampling_steps, step_scale }

recycling_steps: optional number

The number of recycling steps to use for prediction. Default is 3.

minimum1

sampling_steps: optional number

The number of sampling steps to use for prediction. Default is 200.

minimum50

step_scale: optional number

Diffusion step scale (temperature). Controls sampling diversity — higher values produce more varied structures. Default is 1.638.

minimum1.3

maximum2

num_samples: optional number

Number of structure samples to generate (1-10)

minimum1

maximum10

templates: optional array of object { template_chains, template_structure, force_threshold_angstroms }

Template structure files to guide protein-chain prediction. Supports up to 4 CIF or PDB templates from HTTPS URLs or base64 uploads. Use template_chains to map request chains to template-file chains.

template_chains: array of object { input_chain_id, template_chain_id }

Request-to-template chain mappings. Each input_chain_id and template_chain_id must be unique within this template.

input_chain_id: string

Chain ID in this prediction request

template_chain_id: string

Corresponding chain ID in the template structure file

template_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

force_threshold_angstroms: optional number

Force the template reference potential with this distance threshold in angstroms. Omit to use the template without force.

minimum0

livemode: boolean

Whether this resource was created with a live API key.

model: "boltz-2.1"

Model used for prediction

output: object { all_sample_results, best_sample, archive, binding_metrics }

Prediction output when succeeded

all_sample_results: array of object { metrics, structure, ligand_structure }

Per-sample structure results

metrics: object { complex_ipde, complex_iplddt, complex_pde, 6 more }

complex_ipde: number

Complex interface predicted distance error. Lower is better.

complex_iplddt: number

Complex interface pLDDT (0-1 float). Confidence at inter-chain interfaces.

complex_pde: number

Complex predicted distance error. Lower is better.

complex_plddt: number

Complex pLDDT (0-1 float). Per-residue confidence averaged over the complex.

iptm: number

Interface predicted TM score (0-1). Confidence in domain interfaces.

ligand_iptm: number

Ligand interface pTM (0-1). Only present when ligands are included.

protein_iptm: number

Protein-protein interface pTM (0-1). Only present for multi-protein complexes.

ptm: number

Predicted TM score (0-1). Global structure quality.

structure_confidence: number

Overall structure confidence (0-1).

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

ligand_structure: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

best_sample: object { metrics, structure, ligand_structure }

metrics: object { complex_ipde, complex_iplddt, complex_pde, 6 more }

complex_ipde: number

Complex interface predicted distance error. Lower is better.

complex_iplddt: number

Complex interface pLDDT (0-1 float). Confidence at inter-chain interfaces.

complex_pde: number

Complex predicted distance error. Lower is better.

complex_plddt: number

Complex pLDDT (0-1 float). Per-residue confidence averaged over the complex.

iptm: number

Interface predicted TM score (0-1). Confidence in domain interfaces.

ligand_iptm: number

Ligand interface pTM (0-1). Only present when ligands are included.

protein_iptm: number

Protein-protein interface pTM (0-1). Only present for multi-protein complexes.

ptm: number

Predicted TM score (0-1). Global structure quality.

structure_confidence: number

Overall structure confidence (0-1).

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

ligand_structure: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

archive: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

binding_metrics: optional object { binding_confidence, optimization_score, type } or object { binding_confidence, type }

One of the following:

LigandProteinBindingMetrics object { binding_confidence, optimization_score, type }

binding_confidence: number

Confidence that binding occurs (0-1). Primary metric for hit discovery.

optimization_score: number

Binding strength ranking score for lead optimization. Higher values indicate stronger predicted binding.

type: "ligand_protein_binding_metrics"

ProteinProteinBindingMetrics object { binding_confidence, type }

binding_confidence: number

Confidence that binding occurs (0-1). Primary metric for hit discovery.

type: "protein_protein_binding_metrics"

started_at: string

formatdate-time

status: "pending" or "running" or "succeeded" or "failed"

One of the following:

"pending"

"running"

"succeeded"

"failed"

version: string

Model version used for prediction

workspace_id: string

Workspace ID

idempotency_key: optional string

Client-provided idempotency key

StructureAndBindingListResponse object { id, completed_at, created_at, 10 more }

id: string

Unique prediction identifier

completed_at: string

formatdate-time

created_at: string

formatdate-time

data_deleted_at: string

When the input/output data was deleted, or null if still available

formatdate-time

error: object { code, message, details }

Error details when failed

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.

expires_at: string

When this resource and its associated data will be permanently deleted. Null while still in progress.

formatdate-time

livemode: boolean

Whether this resource was created with a live API key.

model: "boltz-2.1"

Model used for prediction

started_at: string

formatdate-time

status: "pending" or "running" or "succeeded" or "failed"

One of the following:

"pending"

"running"

"succeeded"

"failed"

version: string

Model version used for prediction

workspace_id: string

Workspace ID

idempotency_key: optional string

Client-provided idempotency key

StructureAndBindingRetrieveResponse object { id, completed_at, created_at, 12 more }

id: string

Unique prediction identifier

completed_at: string

formatdate-time

created_at: string

formatdate-time

data_deleted_at: string

When the input/output data was deleted, or null if still available

formatdate-time

error: object { code, message, details }

Error details when failed

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.

expires_at: string

When this resource and its associated data will be permanently deleted. Null while still in progress.

formatdate-time

input: object { entities, binding, bonds, 4 more }

Prediction input (null if data deleted)

entities: array of object { chain_ids, type, value, 3 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) forming the complex to predict. Order determines chain assignment.

One of the following:

Boltz2ProteinEntityResponse object { chain_ids, type, value, 3 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)

msa: optional object { format, source, type } or object { type }

Optional protein MSA control. Omit msa on all protein entities to use automatic MSA generation. Use custom for user-provided A3M/CSV files, or empty for single-sequence mode. Custom MSA and automatic MSA cannot be mixed in one request.

One of the following:

Boltz2CustomMsaResponse object { format, source, type }

Use a user-provided MSA for this protein entity. If any protein entity uses a custom MSA, every other protein entity must use either custom or empty MSA; automatic MSA generation cannot be mixed with custom MSAs in the same request.

format: "a3m" or "csv"

Custom MSA file format. Base64 uploads must use media_type text/x-a3m for A3M or text/csv for CSV.

One of the following:

"a3m"

"csv"

source: 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: "custom"

Boltz2EmptyMsaResponse object { type }

Run this protein entity in single-sequence mode without an MSA. Use this for chains that should not use automatic MSA generation, including non-homologous chains in a request that also includes custom MSAs.

type: "empty"

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

binding: optional object { binder_chain_id, type } or object { binder_chain_ids, type }

One of the following:

LigandProteinBindingResponse object { binder_chain_id, type }

binder_chain_id: string

Chain ID of the ligand binder (must have exactly 1 copy, at most 2048 heavy atoms, and only ligands+proteins in entities)

type: "ligand_protein_binding"

ProteinProteinBindingResponse object { binder_chain_ids, type }

binder_chain_ids: array of string

Chain IDs of the protein binders

type: "protein_protein_binding"

bonds: optional array of object { atom1, atom2 }

Bond constraints between atoms. 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

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

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"

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

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

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

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

type: "ligand_contact"

type: "contact"

force: optional boolean

Whether to force the constraint

model_options: optional object { recycling_steps, sampling_steps, step_scale }

recycling_steps: optional number

The number of recycling steps to use for prediction. Default is 3.

minimum1

sampling_steps: optional number

The number of sampling steps to use for prediction. Default is 200.

minimum50

step_scale: optional number

Diffusion step scale (temperature). Controls sampling diversity — higher values produce more varied structures. Default is 1.638.

minimum1.3

maximum2

num_samples: optional number

Number of structure samples to generate (1-10)

minimum1

maximum10

templates: optional array of object { template_chains, template_structure, force_threshold_angstroms }

Template structure files to guide protein-chain prediction. Supports up to 4 CIF or PDB templates from HTTPS URLs or base64 uploads. Use template_chains to map request chains to template-file chains.

template_chains: array of object { input_chain_id, template_chain_id }

Request-to-template chain mappings. Each input_chain_id and template_chain_id must be unique within this template.

input_chain_id: string

Chain ID in this prediction request

template_chain_id: string

Corresponding chain ID in the template structure file

template_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

force_threshold_angstroms: optional number

Force the template reference potential with this distance threshold in angstroms. Omit to use the template without force.

minimum0

livemode: boolean

Whether this resource was created with a live API key.

model: "boltz-2.1"

Model used for prediction

output: object { all_sample_results, best_sample, archive, binding_metrics }

Prediction output when succeeded

all_sample_results: array of object { metrics, structure, ligand_structure }

Per-sample structure results

metrics: object { complex_ipde, complex_iplddt, complex_pde, 6 more }

complex_ipde: number

Complex interface predicted distance error. Lower is better.

complex_iplddt: number

Complex interface pLDDT (0-1 float). Confidence at inter-chain interfaces.

complex_pde: number

Complex predicted distance error. Lower is better.

complex_plddt: number

Complex pLDDT (0-1 float). Per-residue confidence averaged over the complex.

iptm: number

Interface predicted TM score (0-1). Confidence in domain interfaces.

ligand_iptm: number

Ligand interface pTM (0-1). Only present when ligands are included.

protein_iptm: number

Protein-protein interface pTM (0-1). Only present for multi-protein complexes.

ptm: number

Predicted TM score (0-1). Global structure quality.

structure_confidence: number

Overall structure confidence (0-1).

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

ligand_structure: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

best_sample: object { metrics, structure, ligand_structure }

metrics: object { complex_ipde, complex_iplddt, complex_pde, 6 more }

complex_ipde: number

Complex interface predicted distance error. Lower is better.

complex_iplddt: number

Complex interface pLDDT (0-1 float). Confidence at inter-chain interfaces.

complex_pde: number

Complex predicted distance error. Lower is better.

complex_plddt: number

Complex pLDDT (0-1 float). Per-residue confidence averaged over the complex.

iptm: number

Interface predicted TM score (0-1). Confidence in domain interfaces.

ligand_iptm: number

Ligand interface pTM (0-1). Only present when ligands are included.

protein_iptm: number

Protein-protein interface pTM (0-1). Only present for multi-protein complexes.

ptm: number

Predicted TM score (0-1). Global structure quality.

structure_confidence: number

Overall structure confidence (0-1).

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

ligand_structure: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

archive: optional object { url, url_expires_at }

url: string

URL to download the file

formaturi

url_expires_at: string

When the presigned URL expires

formatdate-time

binding_metrics: optional object { binding_confidence, optimization_score, type } or object { binding_confidence, type }

One of the following:

LigandProteinBindingMetrics object { binding_confidence, optimization_score, type }

binding_confidence: number

Confidence that binding occurs (0-1). Primary metric for hit discovery.

optimization_score: number

Binding strength ranking score for lead optimization. Higher values indicate stronger predicted binding.

type: "ligand_protein_binding_metrics"

ProteinProteinBindingMetrics object { binding_confidence, type }

binding_confidence: number

Confidence that binding occurs (0-1). Primary metric for hit discovery.

type: "protein_protein_binding_metrics"

started_at: string

formatdate-time

status: "pending" or "running" or "succeeded" or "failed"

One of the following:

"pending"

"running"

"succeeded"

"failed"

version: string

Model version used for prediction

workspace_id: string

Workspace ID

idempotency_key: optional string

Client-provided idempotency key

StructureAndBindingDeleteDataResponse object { id, data_deleted, data_deleted_at }

id: string

ID of the resource whose data was deleted

data_deleted: true

data_deleted_at: string

When the data was deleted

formatdate-time

StructureAndBindingEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd }

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

breakdown: object { application, cost_per_unit_usd, num_units }

Cost breakdown for the billed application.

application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 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: string

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: number

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: string

estimated_cost_usd: string

Estimated total cost as a decimal string