BoltzGen

BoltzGen webserver overview

BoltzGen v0.3.2 designs peptide, protein, nanobody, and Fab binders against protein structures, redesigns selected regions of protein complexes, and designs proteins around small-molecule targets. ProteinIQ runs the complete native pipeline and returns ranked complexes, native metrics, binder-only refolds when available, sequence files, reports, and run provenance.

The BoltzGen guide explains the method, workflow, result interpretation, validation, and common mistakes. This reference lists the accepted inputs, settings, pricing behavior, and output files.

Pricing

BoltzGen temporarily reserves an estimated number of credits before submission, with a minimum reservation of 500 credits. This reservation is calculated from the uploaded target and selected settings, and it limits the maximum runtime available to the job. It is not the final charge. Completed jobs are charged 45 credits per minute of actual metered runtime, up to the reserved amount, and unused reserved credits are returned. Metered runtime is capped at 12 hours, equivalent to 32,400 credits at the current rate. The table below shows example reservation amounts, not final charges.

The examples below use one 200-residue protein target, a uniform binder length, one sequence per backbone, inverse folding enabled, and native sampling and filtering defaults.

Protocol	Binder assumption	1 design	10 designs	30 designs	100 designs
Peptide binder	12 residues	500	500	545	1,352
Protein binder	100 residues	500	500	989	2,832
Nanobody (~130 residues)	Bundled scaffold	500	500	748	1,961
Antibody / Fab CDR (~450 residues)	All bundled scaffolds	500	609	1,537	4,785

The quote can increase with target size, binder length, candidate count, Sequences per backbone, variable binder length, and protocol-specific folding or affinity stages. Budget changes how many candidates are retained but does not currently increase the runtime estimate independently of Number of designs. Binding-site and structure constraints, checkpoint choice, filters, metric weights, and size buckets do not currently change the reservation. Skipping inverse folding lowers the estimate.

Inputs

Input	Accepted value	Limit	Used by
Target protein	.pdb, .ent, .cif, or .mmcif upload, or RCSB PDB ID	One structure, 50 MB, protein atoms required	Peptide, protein, redesign, nanobody, and Fab protocols
Nanobody framework	.pdb, .ent, .cif, or .mmcif upload	One structure, 10 MB, protein atoms required	Custom nanobody framework only
Target ligand	SMILES, CCD code, or PubChem result	One ligand	Protein-small molecule protocol

For mmCIF inputs, chain and residue controls use label_asym_id and 1-based label_seq_id, not author numbering.

Settings

Protocol and campaign

Parameter	Type	Default	Description
Protocol	enum	Peptide binder	Selects peptide, protein, protein redesign, nanobody, Fab, or protein-small molecule design.
Antibody scaffold	enum	All scaffolds (diverse sampling)	Selects all bundled Fab scaffolds or one named therapeutic scaffold; Fab protocol only.
Nanobody framework	enum	BoltzGen scaffold library	Uses bundled scaffolds or an uploaded VHH framework; nanobody protocol only.
Framework chain	string	conditional	Required for a custom nanobody framework; accepts an alphanumeric chain ID.
CDR design regions	string	conditional	Required for a custom framework; comma-separated 1-based canonical residues or closed ranges such as 26..34,52..59,98..118.
Sample CDR lengths	boolean	false	Allows selected custom CDR segments to be replaced by sampled-length insertions.
Variable CDR segments	string	conditional	Required when CDR length sampling is enabled; uses removed_range:replacement_range, such as 26..28:1..5.
Number of designs	integer	30	Generates 1 to 100 candidates before filtering.
Budget	integer	30	Retains 1 to 100 candidates after quality and diversity selection and cannot exceed the generated count.

Binder geometry and target selection

Parameter	Type	Default	Description
Uniform binder size	boolean	true	Uses one exact binder length for direct peptide, protein, and protein-small molecule design.
Binder length	integer	12	Exact direct-binder length from 5 to 500 residues.
Minimum length	integer	10	Minimum sampled direct-binder length from 8 to 150 when uniform size is off.
Maximum length	integer	14	Maximum sampled direct-binder length from 8 to 150 and must not be below the minimum.
Binding site (optional)	string	optional	Target residues in chain:residue_spec form, such as A:12,14,61; empty allows automatic site selection.
Cyclic peptide	boolean	false	Enables backbone cyclization for the peptide protocol.
Target chains (optional)	string	optional	Comma-separated chains such as A,B; empty includes all target chains.
Redesign regions	string	conditional	Required for protein redesign; one chain per line using A:10, A:10..20, A:..30, or A:55...

Sequence generation and final selection

Parameter	Type	Default	Description
Skip inverse folding	boolean	false	Skips sequence redesign and its runtime stage.
Sequences per backbone	integer	1	Generates 1 to 10 inverse-folded sequence variants for each backbone.
Avoid amino acids	string	optional	Excludes supplied one-letter amino-acid codes; empty preserves the protocol policy.
Quality vs diversity (alpha)	number	native	Optional value from 0 to 1; empty preserves 0.01 for peptide design and 0.001 for other protocols.
Filter biased compositions	boolean	true	Applies the native amino-acid composition filter.
Refolding RMSD threshold (Å)	number	native	Optional value from 0.5 to 5.0 Å; empty preserves 2.0 Å for peptides and 2.5 Å for other protocols.
Custom filters	string	optional	One strict metric<value or metric>value expression per line.
Metrics weights	string	optional	One metric=value override per line; metric=none removes a metric from ranking.
Size buckets	string	optional	One min-max:count cap per line for the final selected set.

Diffusion and structural constraints

Parameter	Type	Default	Description
Step scale	number	native	Optional value from 0 to 3; empty preserves the native per-stage schedule.
Noise scale	number	native	Optional value from 0 to 1; empty preserves the native per-stage schedule.
Model checkpoint	enum	Both (diverse + adherence)	Uses both native checkpoints or only the diverse or adherence checkpoint.
Secondary structure	string	optional	One chain:start-end:HELIX, SHEET, or LOOP constraint per line for direct binders.
Disulfide bonds	string	optional	One chain:residue,chain:residue pair per line for direct binders.
Staple bonds	string	optional	One chain:residue:atom,chain:residue:atom pair per line for direct binders.
Fixed sequence regions	string	optional	One chain:start-end:sequence region per line; requires a uniform direct-binder length and non-overlapping ranges.
Binding residues	string	optional	Binder positions that must contact the target in chain:residue1,residue2 form.
Non-binding residues	string	optional	Binder positions that must not contact the target in chain:residue1,residue2 form.
Design insertions	string	optional	Protein-redesign insertions in chain:position:min..max[:secondary_structure] form.
Residue constraints	string	optional	Inverse-folding rules in chain:position:allowed|disallowed:amino_acids form.

Direct binder constraints use chain B for peptide and protein targets and chain A for small-molecule targets. Malformed or protocol-inapplicable constraints are rejected before compute starts.

Outputs

Output	Format	Description
Ranked binder-target complex	.cif	Native final refold for each retained design in final-rank order.
Binder-only refold	.cif	Native isolated-binder refold when the selected protocol produces it.
Designed chain sequence	.fasta	One additive per-design FASTA projected from native full-chain sequence columns. Fab runs use source-proven heavy_chain and light_chain roles; other modes retain neutral native asym labels.
Final and all-design metrics	.csv	Native final-set and all-design tables without renamed columns.
Aggregate and per-target analysis	.csv	Native analysis tables when produced.
Results overview	.pdf	Native BoltzGen plots when produced.
Run provenance	.yaml	Native steps.yaml and generated configuration files.
Run log	.log	Curated protocol, campaign, scientific phase, resolved Fab scaffold, result metric, warning, and failure summary.
Reference inputs	Original format	Uploaded target and custom framework structures, or ligand reference.

Completed runs omit high-volume intermediate CIF and NPZ families. If a campaign reaches its reserved runtime limit, completed designs and native artifacts produced before execution stops are returned when available.

Understanding results

Field	Meaning
Binder pTM	Native design_ptm, a predicted quality score for the designed component; higher is better.
Binder-target iPTM	Native design_to_target_iptm, confidence for interactions between designed residues and the target; higher is better.
Minimum binder-target PAE (Å)	Native min_design_to_target_pae, the most confident predicted design-target contact; lower is better.
Delta SASA (Ų)	Native delta_sasa_refolded, the change in solvent-accessible surface area after complex formation; larger values indicate more buried surface.
Normalized rank score	Native quality_score used by final ranking; compare it only within the same run and settings.
Sequence	Native designed residue sequence for the retained candidate.

No single confidence or interface score proves binding, affinity, specificity, expression, solubility, or biological activity. Inspect the complete native metrics, structures, sequence diversity, and independent experimental evidence before selecting candidates.