# Design ## Start **post** `/compute/v1/small-molecule/design` Create a new design run that generates novel small molecule candidates for a protein target ### Body Parameters - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: object { entities, bonds, constraints, 2 more }` Target protein with binding pocket for small molecule design or screening - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"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 } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom = 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 - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom = 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 - `type: "polymer_atom"` - `"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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint = 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"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraint = object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `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. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `chemical_space: optional "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key: optional string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter = object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `"lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter = object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `"rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilter = object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter = object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `"smarts_catalog_filter"` - `SmilesRegexFilter = object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `id: string` Unique SmDesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `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 { num_molecules, target, chemical_space, 3 more }` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: object { entities, bonds, constraints, 2 more }` Target protein with binding pocket for small molecule design or screening - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"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 } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `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"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraintResponse = object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `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. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `chemical_space: optional "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key: optional string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse = object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `"lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse = object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `"rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse = object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse = object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse = object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: object { num_molecules_generated, total_molecules_to_generate, latest_result_id }` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design \ -H 'Content-Type: application/json' \ -H "x-api-key: $BOLTZ_API_KEY" \ -d '{ "num_molecules": 10, "target": { "entities": [ { "chain_ids": [ "string" ], "type": "protein", "value": "value" } ] } }' ``` ## List **get** `/compute/v1/small-molecule/design` List small molecule design runs, optionally filtered by workspace ### Query Parameters - `after_id: optional string` Return results after this ID - `before_id: optional string` Return results before this ID - `limit: optional number` Max items to return. Defaults to 100. - `workspace_id: optional string` Filter by workspace ID. Only used with admin API keys. If not provided, defaults to the workspace associated with the API key, or the default workspace for admin keys. ### Returns - `data: array of object { id, completed_at, created_at, 11 more }` - `id: string` Unique SmDesignRunSummary identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `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. - `livemode: boolean` Whether this resource was created with a live API key. - `progress: object { num_molecules_generated, total_molecules_to_generate, latest_result_id }` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key - `first_id: string` ID of the first item. Use as before_id for the previous page. - `has_more: boolean` - `last_id: string` ID of the last item. Use as after_id for the next page. ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design \ -H "x-api-key: $BOLTZ_API_KEY" ``` ## Retrieve **get** `/compute/v1/small-molecule/design/{id}` Retrieve a design run by ID, including progress and status ### Path Parameters - `id: string` ### Query Parameters - `workspace_id: optional string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `id: string` Unique SmDesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `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 { num_molecules, target, chemical_space, 3 more }` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: object { entities, bonds, constraints, 2 more }` Target protein with binding pocket for small molecule design or screening - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"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 } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `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"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraintResponse = object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `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. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `chemical_space: optional "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key: optional string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse = object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `"lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse = object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `"rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse = object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse = object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse = object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: object { num_molecules_generated, total_molecules_to_generate, latest_result_id }` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design/$ID \ -H "x-api-key: $BOLTZ_API_KEY" ``` ## List Results **get** `/compute/v1/small-molecule/design/{id}/results` Retrieve paginated results from a design run ### Path Parameters - `id: string` ### Query Parameters - `after_id: optional string` Return results after this ID - `before_id: optional string` Return results before this ID - `limit: optional number` Max results to return. Defaults to 100. - `workspace_id: optional string` Workspace ID. Only used with admin API keys. Ignored (or validated) for workspace-scoped keys. ### Returns - `data: array of object { id, artifacts, created_at, 3 more }` - `id: string` Unique result ID - `artifacts: object { archive, structure }` - `archive: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `structure: object { url, url_expires_at }` - `url: string` URL to download the file - `url_expires_at: string` When the presigned URL expires - `created_at: string` - `metrics: object { binding_confidence, complex_iplddt, complex_plddt, 4 more }` Scoring metrics for a designed small molecule - `binding_confidence: number` Confidence that the molecule binds the target (0-1). Primary metric for hit discovery. - `complex_iplddt: number` Interface pLDDT for the complex (0-1 float). Confidence at the binding interface. - `complex_plddt: number` pLDDT for the full complex (0-1 float). - `iptm: number` Interface predicted TM score (0-1). Confidence in relative positioning of ligand and protein. - `optimization_score: number` Binding strength ranking score for lead optimization. Higher values indicate stronger predicted binding. - `ptm: number` Predicted TM score (0-1). Global structure quality metric. - `structure_confidence: number` Confidence in the predicted 3D structure (0-1). - `smiles: string` SMILES string of the designed molecule - `warnings: optional array of object { code, message }` Warnings about potential quality issues with this result. - `code: string` Machine-readable warning code (e.g. "low_confidence", "unusual_geometry") - `message: string` Human-readable description of the warning - `first_id: string` ID of the first item. Use as before_id for the previous page. - `has_more: boolean` - `last_id: string` ID of the last item. Use as after_id for the next page. ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design/$ID/results \ -H "x-api-key: $BOLTZ_API_KEY" ``` ## Stop **post** `/compute/v1/small-molecule/design/{id}/stop` Stop an in-progress design run early ### Path Parameters - `id: string` ### Returns - `id: string` Unique SmDesignRun identifier - `completed_at: string` - `created_at: string` - `data_deleted_at: string` When the input, output, and result data was permanently deleted. Null if data has not been deleted. - `engine: "boltz-sm-design"` Engine used for small molecule design - `"boltz-sm-design"` - `engine_version: string` Engine version used for small molecule design - `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 { num_molecules, target, chemical_space, 3 more }` Pipeline input (null if data deleted) - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: object { entities, bonds, constraints, 2 more }` Target protein with binding pocket for small molecule design or screening - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"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 } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModificationResponse = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtomResponse = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"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 - `type: "polymer_atom"` - `"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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `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"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraintResponse = object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `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. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactTokenResponse = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactTokenResponse = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `chemical_space: optional "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key: optional string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilterResponse = object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `"lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilterResponse = object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `"rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilterResponse = object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilterResponse = object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `"smarts_catalog_filter"` - `SmilesRegexFilterResponse = object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) - `livemode: boolean` Whether this resource was created with a live API key. - `progress: object { num_molecules_generated, total_molecules_to_generate, latest_result_id }` - `num_molecules_generated: number` Number of molecules generated so far - `total_molecules_to_generate: number` Total number of molecules requested - `latest_result_id: optional string` ID of the most recently generated result - `started_at: string` - `status: "pending" or "running" or "succeeded" or 2 more` - `"pending"` - `"running"` - `"succeeded"` - `"failed"` - `"stopped"` - `stopped_at: string` - `workspace_id: string` Workspace ID - `idempotency_key: optional string` Client-provided idempotency key ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design/$ID/stop \ -X POST \ -H "x-api-key: $BOLTZ_API_KEY" ``` ## Delete Data **post** `/compute/v1/small-molecule/design/{id}/delete-data` Permanently delete the input, output, and result data associated with this design run. The design run record itself is retained with a `data_deleted_at` timestamp. This action is irreversible. ### Path Parameters - `id: string` ### Returns - `id: string` ID of the resource whose data was deleted - `data_deleted: true` - `true` - `data_deleted_at: string` When the data was deleted ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design/$ID/delete-data \ -X POST \ -H "x-api-key: $BOLTZ_API_KEY" ``` ## Estimate Cost **post** `/compute/v1/small-molecule/design/estimate-cost` Estimate the billed cost of a small molecule design run without creating any resource or consuming GPU. Includes the SynFlowNet generation charges implied by the scheduler iteration cap plus Boltz2 scoring for each requested molecule. ### Body Parameters - `num_molecules: number` Number of molecules to generate. Must be between 10 and 1,000,000. - `target: object { entities, bonds, constraints, 2 more }` Target protein with binding pocket for small molecule design or screening - `entities: array of object { chain_ids, type, value, 2 more }` Protein entities defining the target structure. Each entity represents a protein chain. - `chain_ids: array of string` Chain IDs for this entity - `type: "protein"` - `"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 } or object { residue_index, type, value }` Post-translational modifications. Optional; defaults to an empty list when omitted. - `CcdModification = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "ccd"` - `"ccd"` - `value: string` CCD code from RCSB PDB (e.g. 'MSE' for selenomethionine, 'SEP' for phosphoserine) - `SmilesModification = object { residue_index, type, value }` - `residue_index: number` 0-based index of the residue to modify - `type: "smiles"` - `"smiles"` - `value: string` SMILES string for the modification - `bonds: optional array of object { atom1, atom2 }` Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom = 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 - `type: "polymer_atom"` - `"polymer_atom"` - `atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `LigandAtom = object { atom_name, chain_id, type }` Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Standardized atom name (verifiable in CIF file on RCSB). Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID containing the atom - `type: "ligand_atom"` - `"ligand_atom"` - `PolymerAtom = 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 - `type: "polymer_atom"` - `"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). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported. - `PocketConstraint = 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"` - `"pocket"` - `force: optional boolean` Whether to force the constraint - `ContactConstraint = object { max_distance_angstrom, token1, token2, 2 more }` Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `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. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `PolymerContactToken = object { chain_id, residue_index, type }` - `chain_id: string` Chain ID - `residue_index: number` 0-based residue index - `type: "polymer_contact"` - `"polymer_contact"` - `LigandContactToken = object { atom_name, chain_id, type }` Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported. - `atom_name: string` Atom name. Atom-level references to ligand_smiles entities are currently unsupported; use ligand_ccd instead. - `chain_id: string` Chain ID - `type: "ligand_contact"` - `"ligand_contact"` - `type: "contact"` - `"contact"` - `force: optional boolean` Whether to force the constraint - `pocket_residues: optional 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 binding pocket on that chain. When provided, these residues guide pocket extraction and add a derived pocket constraint during affinity predictions. That derived constraint remains separate from any explicit pocket constraints in target.constraints. When omitted, the model auto-detects the pocket. - `reference_ligands: optional array of string` Reference ligands as SMILES strings that help the model identify the binding pocket. When omitted, a set of drug-like default ligands is used for pocket detection. - `chemical_space: optional "enamine_real"` Chemical space to constrain generated molecules. Currently only 'enamine_real' (Enamine REAL chemical space) is supported. Additional options may be added in the future. - `"enamine_real"` - `idempotency_key: optional string` Client-provided key to prevent duplicate submissions on retries - `molecule_filters: optional object { boltz_smarts_catalog_filter_level, custom_filters }` Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters. - `boltz_smarts_catalog_filter_level: optional "recommended" or "extra" or "aggressive" or "disabled"` Controls the stringency of Boltz's built-in SMARTS structural alert filtering, which removes molecules matching known problematic substructures. 'recommended' (default): applies a curated set of alerts balancing safety and hit rate. 'extra': adds additional alerts beyond the recommended set for stricter filtering. 'aggressive': applies the most comprehensive alert set — may reject viable molecules. 'disabled': turns off Boltz SMARTS filtering entirely; only custom_filters will be applied. - `"recommended"` - `"extra"` - `"aggressive"` - `"disabled"` - `custom_filters: optional array of object { max_hba, max_hbd, max_logp, 3 more } or object { type, fraction_csp3, mol_logp, 8 more } or object { patterns, type } or 2 more` Custom filters to apply. Molecules must pass all filters (AND logic). - `LipinskiFilter = object { max_hba, max_hbd, max_logp, 3 more }` Lipinski's Rule of Five filter. Rejects molecules that violate drug-likeness criteria based on molecular weight, LogP, hydrogen bond donors, and hydrogen bond acceptors. - `max_hba: number` Maximum number of hydrogen bond acceptors. Lipinski threshold: 10 - `max_hbd: number` Maximum number of hydrogen bond donors. Lipinski threshold: 5 - `max_logp: number` Maximum LogP. Lipinski threshold: 5 - `max_mw: number` Maximum molecular weight (Da). Lipinski threshold: 500 - `type: "lipinski_filter"` - `"lipinski_filter"` - `allow_single_violation: optional boolean` If true, one rule violation is allowed (classic Rule of Five). Defaults to false (all rules must pass). - `RdkitDescriptorFilter = object { type, fraction_csp3, mol_logp, 8 more }` Filter molecules by RDKit molecular descriptors. Each descriptor is constrained to a min/max range. Only descriptors you provide are checked — omitted descriptors are unconstrained. - `type: "rdkit_descriptor_filter"` - `"rdkit_descriptor_filter"` - `fraction_csp3: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_logp: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `mol_wt: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_aromatic_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_acceptors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_h_donors: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_heteroatoms: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rings: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `num_rotatable_bonds: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `tpsa: optional object { max, min }` Min/max range constraint for an RDKit molecular descriptor - `max: optional number` Maximum allowed value (inclusive) - `min: optional number` Minimum allowed value (inclusive) - `SmartsCustomFilter = object { patterns, type }` Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected. - `patterns: array of string` SMARTS patterns. Molecules matching any pattern are rejected. - `type: "smarts_custom_filter"` - `"smarts_custom_filter"` - `SmartsCatalogFilter = object { catalog, type }` Filter molecules using a predefined SMARTS catalog of structural alerts. - `catalog: "PAINS" or "PAINS_A" or "PAINS_B" or 11 more` Predefined SMARTS catalog to apply. PAINS, BRENK, ChEMBL, and NIH catalogs reject known problematic substructures. - `"PAINS"` - `"PAINS_A"` - `"PAINS_B"` - `"PAINS_C"` - `"BRENK"` - `"CHEMBL"` - `"CHEMBL_BMS"` - `"CHEMBL_Dundee"` - `"CHEMBL_Glaxo"` - `"CHEMBL_Inpharmatica"` - `"CHEMBL_LINT"` - `"CHEMBL_MLSMR"` - `"CHEMBL_SureChEMBL"` - `"NIH"` - `type: "smarts_catalog_filter"` - `"smarts_catalog_filter"` - `SmilesRegexFilter = object { patterns, type }` Filter molecules by regex patterns on their SMILES representation. - `patterns: array of string` Regex patterns applied to SMILES strings. Molecules matching any pattern are rejected. - `type: "smiles_regex_filter"` - `"smiles_regex_filter"` - `workspace_id: optional string` Target workspace ID (admin keys only; ignored for workspace keys) ### Returns - `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 3 more` - `"structure_and_binding"` - `"small_molecule_design"` - `"small_molecule_library_screen"` - `"protein_design"` - `"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 units shown for the estimate. For structure-and-binding, this is the requested number of samples. For protein and small-molecule design/screen endpoints, this is the requested number of proteins or molecules. - `disclaimer: string` - `estimated_cost_usd: string` Estimated total cost as a decimal string ### Example ```http curl https://api.boltz.bio/compute/v1/small-molecule/design/estimate-cost \ -H 'Content-Type: application/json' \ -H "x-api-key: $BOLTZ_API_KEY" \ -d '{ "num_molecules": 10, "target": { "entities": [ { "chain_ids": [ "string" ], "type": "protein", "value": "value" } ] } }' ```