Ariax.bio

Ariax.bio

BoltzGen Project Setup

7. BoltzGen Project Setup

Looking for the BindCraft workflow instead? See 6. BindCraft Project Setup.

7.1 Overview

BoltzGen is an all‑atom generative model for universal binder design. On Ariax, you can launch the following BoltzGen project types:

  • VHH (nanobody)
  • Miniprotein
  • Peptide
  • Cyclic‑Peptide
  • Helicon
  • Miniprotein + Small Molecule (design against a small‑molecule ligand via CCD or SMILES)

7.2 Inputs

  • Protein targets: Upload a .pdb or .cif, or search RCSB by PDB ID/keyword directly from the setup page.
  • Small‑molecule targeting (miniprotein + small molecule):
    • Provide exactly one: CCD (3‑letter) or SMILES.
    • No target structure file is required in this mode.

Canonical indexing and residue masks

BoltzGen uses canonical residue numbering under the hood (mmCIF label indices when available). The viewer and logs display helpful shift messages when author vs label indices differ.

You can define binding rules per chain:

  • “Bind anywhere” (equivalent to all)
  • binding and/or not_binding masks using:
    • comma lists: 5,13,21
    • ranges: 50..60
    • the keyword all
      Validation will flag invalid tokens, out‑of‑range residues, and overlaps between binding and not_binding.

7.3 Project Type–specific fields

  • VHH / Helicon: Length fields are hidden (not required).
  • Miniprotein / Peptide / Cyclic‑Peptide: Configure Min Length and Max Length.
    • Miniprotein: min ≥ 31 (typical defaults 65–150)
    • Peptide/Cyclic‑Peptide: 8–30

7.4 Design Settings

  • # Final Designs (num_designs): Target the number of final, ranked designs to return (e.g., 10,000+ recommended by authors for robust down‑selection).
  • Budget: Must be ≤ num_designs. Determines the number of designs included in the final ranked folder.

7.5 GPU Selection & Turbo Mode

  • Mode: Performance (fastest) or Cost (cheapest).
  • Primary GPUs: Select at least one of H100, A100, or L40/L40S (required for availability).
  • Additional GPUs: B200, H200, RTX 6000 Pro/Ada (optional).
  • Turbo Mode (2×/4×/8×): Runs in parallel across multiple GPUs to accelerate campaigns. Pricing remains transparent: base GPU rate + $1/hr per extra GPU.

7.6 Validate & Start

Click Validate Settings to check structure parsing, chain selection, mask syntax, length rules, GPU availability, and Turbo options. Once validated, click Start BoltzGen. Your job appears on the dashboard immediately, streaming logs and results as they become available.

7.7 Outputs & Files

Results stream into organized folders:

  • Final Ranked Designs: A timestamped directory containing the final ranked CIFs; a subfolder final_<N>_designs is selected based on your budget.
  • Intermediate Designs and Inverse Folded Designs: Optional folders for additional inspection (when produced by the pipeline).
  • ZIP archives: Per‑tab .zip bundles are created for quick download; large files include CLI download suggestions (cURL/wget/aria2c).

Per‑step progress bars indicate pipeline stages and percent complete. For viewing structures, CIF files may be converted to PDB for a consistent viewer experience.

7.8 Helpful Links