API Reference

Small Molecule

Library Screen

Copy Markdown

Open in Claude

Open in ChatGPT

Open in Cursor

---

Copy Markdown

View as Markdown

Estimate cost for a small molecule library screen

POST/compute/v1/small-molecule/library-screen/estimate-cost

Estimate the cost of a small molecule library screen without creating any resource or consuming GPU.

Body ParametersJSONExpand Collapse

molecules: array of object { smiles, id }

List of small molecules to screen.

smiles: string

SMILES string of the molecule

id: optional string

Optional identifier for this molecule

target: object { entities, bonds, constraints, 3 more }

Target protein sequences 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"

value: string

Amino acid sequence (one-letter codes)

cyclic: optional boolean

Whether the sequence is cyclic

modifications: optional array of object { residue_index, type, value }

CCD post-translational modifications. Optional; defaults to an empty list when omitted. SMILES modifications are not supported.

residue_index: number

0-based index of the residue to modify

minimum0

type: "ccd"

Modification format. Only CCD polymer modifications are supported.

value: string

CCD code from RCSB PDB (e.g. ‘MSE’ for selenomethionine, ‘SEP’ for phosphoserine)

bonds: optional array of object { atom1, atom2 }

Covalent bond constraints between atoms in the target complex. Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.

atom1: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtom object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters.

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

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

minimum0

type: "polymer_atom"

atom2: object { atom_name, chain_id, type } or object { atom_name, chain_id, residue_index, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

LigandAtom object { atom_name, chain_id, type }

Ligand atom reference for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters.

chain_id: string

Chain ID containing the atom

type: "ligand_atom"

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

minimum0

type: "polymer_atom"

constraints: optional array of object { binder_chain_id, contact_residues, max_distance_angstrom, 2 more } or object { max_distance_angstrom, token1, token2, 2 more }

Structural constraints (pocket and contact). Ligand atom references support CCD atom names and explicitly atom-mapped SMILES atoms.

One of the following:

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"

force: optional boolean

Whether to force the constraint

ContactConstraint object { max_distance_angstrom, token1, token2, 2 more }

Maximum-distance contact constraint between two polymer residues or ligand atoms.

max_distance_angstrom: number

Maximum distance in Angstroms

token1: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

PolymerContactToken object { chain_id, residue_index, type }

chain_id: string

Chain ID

residue_index: number

0-based residue index

minimum0

type: "polymer_contact"

LigandContactToken object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters.

chain_id: string

Chain ID

type: "ligand_contact"

token2: object { chain_id, residue_index, type } or object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

One of the following:

PolymerContactToken object { chain_id, residue_index, type }

chain_id: string

Chain ID

residue_index: number

0-based residue index

minimum0

type: "polymer_contact"

LigandContactToken object { atom_name, chain_id, type }

Ligand contact token for a CCD atom or an explicitly atom-mapped SMILES atom.

atom_name: string

Atom name. For ligand_ccd, use the standardized CIF atom name. For ligand_smiles, explicitly label the atom with numeric atom-map notation: [C:1] is referenced as C1 and [O:2] as O2. The resulting name must be unique within the molecule and at most four characters.

chain_id: string

Chain ID

type: "ligand_contact"

type: "contact"

force: optional boolean

Whether to force the constraint

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.

type: optional "no_template"

Target is defined directly by protein sequences rather than a structure template.

idempotency_key: optional string

Client-provided key to prevent duplicate submissions on retries

maxLength255

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.

One of the following:

"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).

One of the following:

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"

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"

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"

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.

One of the following:

"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"

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"

workspace_id: optional string

Target workspace ID (admin keys only; ignored for workspace keys)

ReturnsExpand Collapse

breakdown: object { application, cost_per_unit_usd, num_units }

Cost breakdown for the billed application.

application: "structure_and_binding" or "small_molecule_design" or "small_molecule_library_screen" or 4 more

One of the following:

"structure_and_binding"

"small_molecule_design"

"small_molecule_library_screen"

"protein_design"

"protein_redesign"

"protein_library_screen"

"adme"

cost_per_unit_usd: string

Estimated cost per displayed unit as a decimal string, rounded up to 4 decimal places. This may include token-size multipliers or generation overhead; estimated_cost_usd is the authoritative total.

num_units: number

Number of billable units in the estimate. The unit depends on the endpoint: samples for structure-and-binding, molecules for ADME, and requested proteins or molecules for design/screen endpoints.

disclaimer: string

estimated_cost_usd: string

Estimated total cost as a decimal string

Estimate cost for a small molecule library screen

HTTP

HTTP

TypeScript

Python

Go

CLI Tool

curl https://api.boltz.bio/compute/v1/small-molecule/library-screen/estimate-cost \
    -H 'Content-Type: application/json' \
    -H "x-api-key: $BOLTZ_API_KEY" \
    -d '{
          "molecules": [
            {
              "smiles": "smiles"
            }
          ],
          "target": {
            "entities": [
              {
                "chain_ids": [
                  "string"
                ],
                "type": "protein",
                "value": "value"
              }
            ]
          }
        }'

200 example

{
  "breakdown": {
    "application": "structure_and_binding",
    "cost_per_unit_usd": "0.0500",
    "num_units": 1
  },
  "disclaimer": "This is an estimate only and may differ from your actual charges. Final billing is based on exact token counts computed at run time. For large library screens, the estimate is extrapolated from a sample and may be less accurate for highly variable inputs.",
  "estimated_cost_usd": "0.0500"
}

Returns Examples

200 example

{
  "breakdown": {
    "application": "structure_and_binding",
    "cost_per_unit_usd": "0.0500",
    "num_units": 1
  },
  "disclaimer": "This is an estimate only and may differ from your actual charges. Final billing is based on exact token counts computed at run time. For large library screens, the estimate is extrapolated from a sample and may be less accurate for highly variable inputs.",
  "estimated_cost_usd": "0.0500"
}