Boltz Small Molecule Screen

Boltz Small Molecule Screen webserver overview

Boltz Small Molecule Screen scores a SMILES list you supply against a protein target and returns the molecules ranked, each with a predicted complex. A job takes up to 1,000 molecules.

ProteinIQ sends the job to the hosted Boltz API pipeline and publishes the finished table, structures and records. To search a make-on-demand catalog instead of your own list, use BoltzMol-1. To sample a much larger library under a fixed budget, use Boltz Small Molecule Explore.

Pricing

The screen costs a flat rate per molecule submitted. The total is rounded once for the whole job.

Molecules	Credits
1	51
10	507
100	5,064
500	25,317
1,000	50,633

Target size, molecule size, reference ligands and filters do not change the price. Filters remove molecules from the results, not from the quote. 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.
Molecules to screen	Pasted text, or a .csv, .tsv, .smi, .smiles or .txt file	Required. One list per job, up to 1,000 molecules and 50 MB.
Reference ligand	One SMILES string, a .smi or .smiles file, or a PubChem compound	Optional. Up to 10 known binders that guide scoring.

The molecule list can take any of these forms:

• One SMILES per line. Molecules are named mol_1, mol_2 and so on.
• name<TAB>SMILES or name,SMILES on each line.
• A CSV or TSV table whose header has a smiles column. The id or name column, when present, supplies the molecule IDs.

For a drug repurposing screen, choose Load from dataset in the upload menu and pick molecules from the FDA-approved drug library. They arrive as a named list, and the picker stops at the job's molecule limit.

Repeated names get a numeric suffix such as _2 so each row stays traceable. 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

Target

Parameter	Type	Default	Description
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
boltz_sm_screen_0001_<name>.cif onwards	Predicted complex for each scored molecule, numbered by rank.
boltz_sm_screen_results.csv	The results table.
boltz_sm_screen_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.

Molecules removed by the filters do not appear in the results, so the row count can be lower than the number submitted. The run summary reports both numbers. Scores order candidates within one run and are not measured affinities.