Boltz Sequence Redesign

Boltz Sequence Redesign webserver overview

Boltz Sequence Redesign proposes new amino acids for chosen residues of a fixed structure, keeping the rest of the structure as it is. It can redesign a binder chain against the remaining chains, or positions anywhere in the structure. Each design comes back with its sequence, Boltz's scores and a predicted complex.

ProteinIQ sends the job to the hosted Boltz API pipeline and publishes the finished sequences, structures and records. To design a new binder from a target sequence instead, use BoltzProt-1. For open-source inverse folding, see ProteinMPNN and LigandMPNN.

Pricing

Sequence Redesign is billed per design, and each design is priced by the size of the submitted structure in tokens: one per polymer residue in every chain, plus one per non-water ligand heavy atom. The number of redesigned positions does not change the price.

Structure size (tokens)	10 designs	50 designs	200 designs
Up to 256	507	2,532	10,127
257 to 512	1,013	5,064	20,254
513 to 1,024	2,026	10,127	40,507
1,025 to 2,048	4,051	20,254	81,013
More than 2,048	8,102	40,507	162,026

The total is rounded once for the whole job. The design mode 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
Structure	One .cif, .pdb or .ent file, or a structure fetched from RCSB	Required. One structure per job, one model, up to 50 MB, with at least one polymer chain. PDB files are converted to mmCIF before submission.

Hydrogens and empty chains are removed before the structure is sent. Job name is an optional label for the saved run.

Settings

Redesign

Parameter	Type	Default	Description
Residues to redesign (redesign_residues)	string	required	Positions to redesign per chain, 1-based, for example B:26-33. The chain prefix can be omitted only when the structure has one chain.
Design mode (design_mode)	enum	binder	binder redesigns binder chains against the remaining target chains. generic redesigns positions anywhere in the structure.
Binder chains (binder_chains)	string	conditional	Chains treated as the binder, comma-separated. Required in binder mode.
Designs (num_designs)	integer	10	Sequences to return, from 10 to 200. Each one is billed.

Binder mode also requires that every redesigned position sits on a binder chain, that at least one chain is left as the target, and that at least five residues are redesigned in total.

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
boltz_redesign_0001_<name>.cif onwards	Predicted complex for each design, numbered by rank.
boltz_redesign_sequences.fasta	Designed sequences, with the chain IDs in each header.
boltz_redesign_results.csv	The results table.
boltz_redesign_results.json	Boltz's run and per-result records.

The FASTA sequences and the predicted complexes can be passed to other tools in workflows.

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.

Positions outside the redesigned selection keep their original amino acids, so comparing a design against the input sequence shows exactly what changed. Scores order designs within one run and are not measured stability or binding.