Example walkthrough: Ubiquitin

Target structure

Loaded from RCSB via 3Dmol.js — no compute spent on your click.

  Target: PDB 1UBQ
  · cartoon in cool slate ·
  ● epitope sticks (gold)
  · loaded directly from RCSB, no Aikium cache

What a /design submission for this target would look like

The four inputs · the integrated ensemble · the output schema.

1

The submission

Target: 1UBQ (Ubiquitin)
Epitope hint: Ile44 patch residues 8, 44, 68, 70
Tier: anonymous (≤ $10) or magic-link (full ensemble)

2

What the pipeline would do

Up to 6 generators (anonymous: 2-tool subset · magic-link: full ensemble). Boltz-2 folds every candidate against the target structure. fold_confidence (ESMFold per-region pLDDT) + canonical-VHH gate. k-mer cluster dedup at J≥0.7.

3

What you'd download

Top-N ranked VHHs · CSV + FASTA
Folded complex PDB per design
Per-design developability-score breakdown
CDR-source provenance manifest

Honest framing

What this walkthrough doesn't show. Aikium's existing pipeline outputs (sequences, scores, selections from internal work) are intentionally not displayed on this public demo. Submit your own target at /design to see a real run end-to-end — your designs, your output, never cached.

What designs aren't. Designs from this pipeline are developability-screened and structurally validated. They are not predicted binders. Wet-lab affinity assays are required. Expected hit rate without a positive prior is typically ≤5%.

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