Design
Generate novel small molecules optimized for binding to a protein target. Results are scored by binding confidence (likelihood of binding, for hit discovery), optimization score (binding strength ranking, for lead optimization), and structure confidence.
Start a small molecule de novo design run
List small molecule design runs
Get small molecule design run status
Get generated small molecule designs
Stop a running small molecule design run
Delete small molecule design run data
Estimate cost for a small molecule design run
ModelsExpand Collapse
DesignStartResponse { id, completed_at, created_at, 14 more } A small molecule design pipeline run that generates novel molecules
A small molecule design pipeline run that generates novel molecules
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Input | nullPipeline input (null if data deleted)
Pipeline input (null if data deleted)
Number of molecules to generate. Must be between 10 and 1,000,000.
target: Target { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: Array<Entity>Protein entities defining the target structure. Each entity represents a protein chain.
Protein entities defining the target structure. Each entity represents a protein chain.
bonds?: Array<Bond>Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints?: Array<PocketConstraintResponse { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } | ContactConstraintResponse { 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.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
PocketConstraintResponse { 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 { 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.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token2: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
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.
Chemical space to constrain generated molecules. Currently only ‘enamine_real’ (Enamine REAL chemical space) is supported. Additional options may be added in the future.
molecule_filters?: MoleculeFilters { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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.
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.
custom_filters?: Array<LipinskiFilterResponse { max_hba, max_hbd, max_logp, 3 more } | RdkitDescriptorFilterResponse { type, fraction_csp3, mol_logp, 8 more } | SmartsCustomFilterResponse { patterns, type } | 2 more>Custom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse { 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.
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.
RdkitDescriptorFilterResponse { 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.
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.
fraction_csp3?: FractionCsp3 { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings?: NumAromaticRings { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors?: NumHAcceptors { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms?: NumHeteroatoms { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
DesignListResponse { id, completed_at, created_at, 13 more } Summary of a small molecule design pipeline run (excludes input)
Summary of a small molecule design pipeline run (excludes input)
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
DesignRetrieveResponse { id, completed_at, created_at, 14 more } A small molecule design pipeline run that generates novel molecules
A small molecule design pipeline run that generates novel molecules
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Input | nullPipeline input (null if data deleted)
Pipeline input (null if data deleted)
Number of molecules to generate. Must be between 10 and 1,000,000.
target: Target { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: Array<Entity>Protein entities defining the target structure. Each entity represents a protein chain.
Protein entities defining the target structure. Each entity represents a protein chain.
bonds?: Array<Bond>Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints?: Array<PocketConstraintResponse { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } | ContactConstraintResponse { 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.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
PocketConstraintResponse { 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 { 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.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token2: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
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.
Chemical space to constrain generated molecules. Currently only ‘enamine_real’ (Enamine REAL chemical space) is supported. Additional options may be added in the future.
molecule_filters?: MoleculeFilters { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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.
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.
custom_filters?: Array<LipinskiFilterResponse { max_hba, max_hbd, max_logp, 3 more } | RdkitDescriptorFilterResponse { type, fraction_csp3, mol_logp, 8 more } | SmartsCustomFilterResponse { patterns, type } | 2 more>Custom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse { 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.
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.
RdkitDescriptorFilterResponse { 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.
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.
fraction_csp3?: FractionCsp3 { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings?: NumAromaticRings { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors?: NumHAcceptors { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms?: NumHeteroatoms { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
DesignListResultsResponse { id, artifacts, created_at, 4 more } A single designed small molecule result
A single designed small molecule result
artifacts: Artifacts { archive, structure, ligand_structure }
metrics: Metrics { binding_confidence, complex_iplddt, complex_plddt, 4 more } Scoring metrics for a designed small molecule
Scoring metrics for a designed small molecule
Confidence that the molecule binds the target (0-1). Primary metric for hit discovery.
Interface pLDDT for the complex (0-1 float). Confidence at the binding interface.
Interface predicted TM score (0-1). Confidence in relative positioning of ligand and protein.
DesignStopResponse { id, completed_at, created_at, 14 more } A small molecule design pipeline run that generates novel molecules
A small molecule design pipeline run that generates novel molecules
When the input, output, and result data was permanently deleted. Null if data has not been deleted.
Deprecated. Use pipeline_version instead.
input: Input | nullPipeline input (null if data deleted)
Pipeline input (null if data deleted)
Number of molecules to generate. Must be between 10 and 1,000,000.
target: Target { entities, bonds, constraints, 3 more } Target protein sequences for small molecule design or screening.
Target protein sequences for small molecule design or screening.
entities: Array<Entity>Protein entities defining the target structure. Each entity represents a protein chain.
Protein entities defining the target structure. Each entity represents a protein chain.
bonds?: Array<Bond>Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
Covalent bond constraints between atoms in the target complex. Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
atom1: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
atom2: LigandAtomResponse { atom_name, chain_id, type } | PolymerAtomResponse { atom_name, chain_id, residue_index, type } Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand atom reference. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
constraints?: Array<PocketConstraintResponse { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } | ContactConstraintResponse { 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.
Structural constraints (pocket and contact). Atom-level ligand references currently support ligand_ccd only; ligand_smiles is unsupported.
PocketConstraintResponse { 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 { 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.
Contact constraint between two tokens. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token1: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
token2: PolymerContactTokenResponse { chain_id, residue_index, type } | LigandContactTokenResponse { atom_name, chain_id, type } Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
Ligand contact token. Atom-level ligand references currently support ligand_ccd entities only; ligand_smiles is unsupported.
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.
Chemical space to constrain generated molecules. Currently only ‘enamine_real’ (Enamine REAL chemical space) is supported. Additional options may be added in the future.
molecule_filters?: MoleculeFilters { boltz_smarts_catalog_filter_level, custom_filters } Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
Molecule filtering configuration. Controls both Boltz built-in SMARTS filtering and custom filters.
boltz_smarts_catalog_filter_level?: "recommended" | "extra" | "aggressive" | "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.
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.
custom_filters?: Array<LipinskiFilterResponse { max_hba, max_hbd, max_logp, 3 more } | RdkitDescriptorFilterResponse { type, fraction_csp3, mol_logp, 8 more } | SmartsCustomFilterResponse { patterns, type } | 2 more>Custom filters to apply. Molecules must pass all filters (AND logic).
Custom filters to apply. Molecules must pass all filters (AND logic).
LipinskiFilterResponse { 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.
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.
RdkitDescriptorFilterResponse { 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.
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.
fraction_csp3?: FractionCsp3 { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_aromatic_rings?: NumAromaticRings { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_h_acceptors?: NumHAcceptors { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
num_heteroatoms?: NumHeteroatoms { max, min } Min/max range constraint for an RDKit molecular descriptor
Min/max range constraint for an RDKit molecular descriptor
SmartsCustomFilterResponse { patterns, type } Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
Filter molecules by custom SMARTS patterns. Molecules matching any pattern are rejected.
DesignEstimateCostResponse { 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: Breakdown { application, cost_per_unit_usd, num_units } Cost breakdown for the billed application.
Cost breakdown for the billed application.