BoltzProt-1

BoltzProt-1 webserver overview

BoltzProt-1 designs protein binders for a target sequence. The binder can be a mini-protein, a peptide, or a nanobody or antibody built on Boltz's curated scaffolds. A job returns each design's sequence, Boltz's scores and a predicted complex with the target.

ProteinIQ sends the job to the hosted Boltz API pipeline and publishes the finished sequences, structures and records. To score binder sequences you already have, use Boltz Protein Screen. To change chosen residues on an existing structure, use Boltz Sequence Redesign.

Pricing

BoltzProt-1 is billed per design, and each design is priced by the size of the target plus binder complex in tokens. A token is about one residue, so the complex size is the total target length plus the binder length. A mini-protein or peptide counts as its maximum length, a nanobody as 130 and an antibody as 250.

Complex size (tokens)	10 designs	20 designs	100 designs	500 designs
Up to 256	507	1,013	5,064	25,317
257 to 512	1,013	2,026	10,127	50,633
513 to 1,024	2,026	4,051	20,254	101,266
1,025 to 2,048	4,051	8,102	40,507	202,532
More than 2,048	8,102	16,203	81,013	405,064

For example, a 150-residue target with the default 100-residue maximum binder length is 250 tokens, so 20 designs cost 1,013 credits. The same target with a nanobody binder is 280 tokens and costs 2,026 credits. The total is rounded once for the whole job. Epitope selection and the sequence 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.

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

Binder

Parameter	Type	Default	Description
Binder type (binder_type)	enum	custom_protein	custom_protein (mini-protein), peptide, nanobody or antibody. Nanobody and antibody designs use Boltz's curated scaffolds.
Minimum binder length (binder_min_length)	integer	60	Shortest designed binder in residues, from 4 to 400. Shown for mini-protein and peptide binders.
Maximum binder length (binder_max_length)	integer	100	Longest designed binder in residues, from 4 to 400, and never below the minimum. Shown for mini-protein and peptide binders.
Designs (num_designs)	integer	20	Designs to return, from 10 to 500. Each one is billed.

Target site

Parameter	Type	Default	Description
Epitope residues (epitope_residues)	string	optional	Target residues the binder should contact, as 1-based positions, for example A:10,12-15; B:3. Without a chain prefix the first target chain is used.
Non-binding residues (non_binding_residues)	string	optional	Target residues the binder should avoid, in the same format. A position cannot appear in both lists.

Sequence filters

Parameter	Type	Default	Description
Excluded amino acids (excluded_amino_acids)	string	C	Amino acids never placed in designed positions, as single-letter codes separated by commas.
Maximum hydrophobic fraction (max_hydrophobic_fraction)	number	1	Largest fraction of hydrophobic residues in a design, from 0 to 1. 1 turns the filter off.
Excluded sequence motifs (excluded_motifs)	string	optional	Motifs designs must not contain, one per line or comma-separated.

Outputs

Viewer shows the predicted complexes. Results lists the designs. Files holds the downloads.

Download	Contents
boltzprot_0001_<name>.cif onwards	Predicted complex for each design, numbered by rank.
boltzprot_sequences.fasta	Designed binder sequences, with the chain IDs in each header.
boltzprot_results.csv	The results table.
boltzprot_results.json	Boltz's run and per-result records.

The FASTA sequences and the predicted complexes can be passed to other tools in workflows, for example to score the designs with Boltz Protein Screen.

Understanding results

Each row carries a rank, the design ID, the designed sequence and chains, 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 design. Nested metrics are flattened into columns joined by underscores. The table and the FASTA file hold the designed binder only, not the target chains.

Scores order designs within one run. They are model confidence values, not measured binding, so designs still need experimental validation.