Predictions
Run prediction models on molecular inputs. Each application is available as its own endpoint with application-specific inputs and outputs.
PredictionsStructure 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
List structure and binding predictions
Retrieve a structure and binding prediction
Delete prediction data
Estimate cost for a structure and binding prediction
ModelsExpand Collapse
StructureAndBindingStartResponse object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { entities, binding, bonds, 4 more } Prediction input (null if data deleted)
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 3 moreEntities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Entities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Boltz2ProteinEntityResponse object { chain_ids, type, value, 3 more }
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.
CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.
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.
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.
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.
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.
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues.
Branched glycan represented as an explicit graph of CCD monosaccharide residues.
bonds: array of object { atom1, atom2 } Covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
binding: optional object { binder_chain_id, type } or object { binder_chain_ids, type }
bonds: optional array of object { atom1, atom2 } Covalent bonds between entities. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand.
Covalent bonds between entities. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand.
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_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.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
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.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
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.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
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.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
model_options: optional object { recycling_steps, sampling_steps, step_scale }
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 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.
output: object { all_sample_results, best_sample, archive, binding_metrics } Prediction output when succeeded
Prediction output when succeeded
all_sample_results: array of object { metrics, structure, ligand_structure } Per-sample structure results
Per-sample structure results
best_sample: object { metrics, structure, ligand_structure }
StructureAndBindingListResponse object { id, completed_at, created_at, 10 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
StructureAndBindingRetrieveResponse object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { entities, binding, bonds, 4 more } Prediction input (null if data deleted)
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 3 moreEntities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Entities (proteins, RNA, DNA, ligands, and glycans) forming the complex to predict. Order determines chain assignment.
Boltz2ProteinEntityResponse object { chain_ids, type, value, 3 more }
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.
CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.
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.
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.
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.
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.
RnaEntityResponse object { chain_ids, type, value, 2 more }
DnaEntityResponse object { chain_ids, type, value, 2 more }
GlycanEntityResponse object { bonds, chain_ids, residues, type } Branched glycan represented as an explicit graph of CCD monosaccharide residues.
Branched glycan represented as an explicit graph of CCD monosaccharide residues.
bonds: array of object { atom1, atom2 } Covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
Covalent bonds connecting the glycan residues. A single-residue glycan uses an empty array.
binding: optional object { binder_chain_id, type } or object { binder_chain_ids, type }
bonds: optional array of object { atom1, atom2 } Covalent bonds between entities. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand.
Covalent bonds between entities. Use ccd_atom with a glycan residue ID, smiles_atom with a numeric SMILES atom-map, or ligand_atom for a single-residue ligand.
atom1: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
atom2: object { atom_name, chain_id, residue_index, type } or object { atom_id, chain_id, residue_id, type } or object { atom_map, chain_id, type } or object { atom_name, chain_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
CcdAtomResponse object { atom_id, chain_id, residue_id, type } Atom reference for a specific CCD residue in a glycan graph.
Atom reference for a specific CCD residue in a glycan graph.
SmilesAtomResponse object { atom_map, chain_id, type } Atom reference using an explicit numeric atom-map in the input SMILES.
Atom reference using an explicit numeric atom-map in the input SMILES.
LigandAtomResponse object { atom_name, chain_id, type } Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_atom.
Atom reference for a single-residue ligand_ccd or an explicitly atom-mapped SMILES ligand. Glycan bonds use ccd_atom; new SMILES bonds should use smiles_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.
Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.
PocketConstraintResponse object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } Constrains the binder to interact with specific pocket residues on the target.
Constrains the binder to interact with specific pocket residues on the target.
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.
ContactConstraintResponse object { max_distance_angstrom, token1, token2, 2 more } Maximum-distance contact constraint between two polymer residues or ligand atoms.
Maximum-distance contact constraint between two polymer residues or ligand atoms.
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.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
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.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
LigandContactTokenResponse object { atom_name, chain_id, type } Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.
model_options: optional object { recycling_steps, sampling_steps, step_scale }
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 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.
output: object { all_sample_results, best_sample, archive, binding_metrics } Prediction output when succeeded
Prediction output when succeeded
all_sample_results: array of object { metrics, structure, ligand_structure } Per-sample structure results
Per-sample structure results
best_sample: object { metrics, structure, ligand_structure }
StructureAndBindingEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd } Estimate response with monetary values encoded as decimal strings to preserve precision.
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.
Cost breakdown for the billed application.
application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 4 more
PredictionsAdme
Predict Tier 1 ADME summary values for a batch of small molecules specified by SMILES.
Start an ADME prediction
List ADME predictions
Retrieve an ADME prediction
Delete ADME prediction data
Estimate cost for an ADME prediction
ModelsExpand Collapse
AdmeStartResponse object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { molecules } Prediction input (null if data deleted)
Prediction input (null if data deleted)
output: object { molecules } Prediction output when succeeded
Prediction output when succeeded
molecules: array of object { id, adme, error, 3 more } or object { id, adme, error, 3 more } Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
AdmeListResponse object { id, completed_at, created_at, 10 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
AdmeRetrieveResponse object { id, completed_at, created_at, 12 more }
When the input/output data was deleted, or null if still available
When this resource and its associated data will be permanently deleted. Null while still in progress.
input: object { molecules } Prediction input (null if data deleted)
Prediction input (null if data deleted)
output: object { molecules } Prediction output when succeeded
Prediction output when succeeded
molecules: array of object { id, adme, error, 3 more } or object { id, adme, error, 3 more } Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
Per-molecule results in the same order as the request. Successful molecules carry an adme summary. Failed molecules carry status: "failed" and a non-null error.
AdmeEstimateCostResponse object { breakdown, disclaimer, estimated_cost_usd } Estimate response with monetary values encoded as decimal strings to preserve precision.
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.
Cost breakdown for the billed application.