BoltzGen

Paths and expectations

• Arguments are passed verbatim to the boltzgen entry point.
• Design YAML plus referenced structures live under /inputs; keep relative paths consistent.
• Results land in /outputs (look for final_ranked_designs/, all_designs_metrics.csv, results_overview.pdf).
• --cache=/ref keeps downloads inside the shared reference volume to skip re-fetching weights.

Quickstart

Sanity-check with the upstream vanilla protein template:

run
/inputs/example/vanilla_protein.yaml
--output=/outputs/protein_anything_quickstart
--protocol=protein-anything
--num_designs=10
--budget=2
--cache=/ref

Example YAML to pair with it:

entities:
  binder:
    id: B
    sequence: 90-130
targets:
  - file: /inputs/targets/1g13prot.cif
    chains: [A]
protocol: protein-anything
output:
  path: /outputs/protein_anything_quickstart

Targeted peptide scan

Short run that stops after design plus inverse folding:

run
/inputs/peptide_site.yaml
--output=/outputs/site_scan
--protocol=peptide-anything
--num_designs=24
--budget=4
--steps=design,inverse_folding
--cache=/ref

Rerank existing designs

Filtering only; explore different budgets without regenerating designs:

run
/inputs/long_run.yaml
--output=/outputs/reranked_budget10
--steps=filtering
--budget=10
--alpha=0.2
--cache=/ref

Submit

Start jobs from New Job -> BoltzGen. Keep design YAML and assets under /inputs.