BoltzMol-1

BoltzMol-1 webserver overview

BoltzMol-1 proposes small molecules for a protein target by searching a make-on-demand catalog such as Enamine REAL, then scoring each proposal against the target. A job returns a ranked table of SMILES with Boltz's scores and a predicted complex for each entry.

ProteinIQ sends the job to the hosted Boltz API pipeline and publishes the finished table, structures and records. To score a list of molecules you already have, use Boltz Small Molecule Screen instead.

Pricing

BoltzMol-1 costs a flat rate per requested molecule, so the price follows the Molecules setting. The total is rounded once for the whole job.

Molecules	Credits
10	507
50	2,532
100	5,064
500	25,317
1,000	50,633

Target size, chemical space, reference ligands and filters do not change the price. The exact quote is calculated before submission. If Boltz estimates a noticeably higher cost when the job starts, the run is not started and the credits are refunded.

Inputs

Input	Accepted formats	Limits and behavior
Target protein	FASTA text, .fasta, .fa or .txt file, or a UniProt sequence	Required. Up to 10 chains, files up to 10 MB, one sequence each. Chain IDs are assigned A, B, C in submission order.
Reference ligand	One SMILES string, a .smi or .smiles file, or a PubChem compound	Optional. Up to 10 known binders that guide the search.

Each target input accepts 1 to 10 copies, and each copy becomes its own chain. Job name is an optional label for the saved run.

Settings

Search

Parameter	Type	Default	Description
Molecules (num_molecules)	integer	50	Molecules to return, from 10 to 1,000. Each one is billed.
Chemical space (chemical_space)	enum	enamine_real	enamine_real, wuxi_galaxi or none. none lifts the catalog constraint, so results need not be purchasable.
Pocket residues (pocket_residues)	string	optional	Binding-pocket residues as 1-based positions, for example A:45,48-52. Without a chain prefix the first target chain is used.

Molecule filters

Parameter	Type	Default	Description
Structural alert filter (structural_alert_filter)	enum	recommended	Boltz's own SMARTS catalog filter level: recommended, extra, aggressive or disabled.
Lipinski filter (lipinski_filter)	boolean	false	Removes molecules that break Lipinski's rule of five.
Maximum molecular weight (lipinski_max_mw)	number	500	Largest molecular weight kept, in Da. Applies when the Lipinski filter is on.
Maximum LogP (lipinski_max_logp)	number	5	Largest LogP kept. Applies when the Lipinski filter is on.
Maximum H-bond donors (lipinski_max_hbd)	integer	5	Most hydrogen-bond donors kept. Applies when the Lipinski filter is on.
Maximum H-bond acceptors (lipinski_max_hba)	integer	10	Most hydrogen-bond acceptors kept. Applies when the Lipinski filter is on.
Allow one violation (lipinski_allow_single_violation)	boolean	false	Keeps molecules that break at most one Lipinski rule.
Additional alert catalog (alert_catalog)	enum	none	One RDKit structural-alert catalog: PAINS, PAINS A, PAINS B, PAINS C, BRENK, NIH, or a CHEMBL catalog.
Excluded SMARTS (excluded_smarts)	string	optional	SMARTS patterns to exclude, one per line or comma-separated.

Outputs

Viewer shows the predicted complexes. Results lists the ranked molecules. Files holds the downloads.

Download	Contents
boltzmol_0001_<name>.cif onwards	Predicted complex for each returned molecule, numbered by rank.
boltzmol_results.csv	The results table.
boltzmol_results.json	Boltz's run and per-result records.

The scored molecules, the CSV table and the predicted complexes can be passed to other tools in workflows.

Understanding results

Each row carries a rank, the molecule ID, its SMILES, Boltz's own metric columns, any warnings Boltz attached and the matching structure file. Ranks follow the order Boltz returns, so rank 1 is its top-scoring entry. Nested metrics are flattened into columns joined by underscores.

Scores order candidates within one run and are not measured affinities. Molecules from a make-on-demand catalog are synthesis proposals, so check availability with the supplier before ordering.