v2.0 by Ayushman Mallick

Build, auto-clean templates for, and submit hosted Boltz-2 API predictions — binary, ternary, or N-body — directly from your browser. Define entities, drop in CIF/PDB templates (BoltzYML repairs the metadata that breaks the parser), set sampling options, then submit with your own API key. Your key stays in your browser and is forwarded only through BoltzYML's open-source proxy to Boltz — never stored. No setup needed.

Need the local-CLI version: 1 YAML (Protein + Ligand + Protein)? → BoltzYML v1 (CLI generator)

BoltzYML v2.0 workflow: define a complex and clean templates in the browser, submit through a stateless Cloudflare Worker proxy to the Boltz-2 API, then download the complete results.

1 Entities

Chain IDs must be unique single letters. Mark a ligand as binder to emit a ligand_protein_binding block (affinity/pose scoring).

1 Templates — optional, up to 4 chain mappings

On upload, BoltzYML rewrites _struct_asym to drop phantom chains, strips waters/ligands, repairs modified residues (e.g. OCY→CYS), and removes _pdbx_poly_seq_scheme/_struct_conn records — the exact fixes a raw RCSB/ChimeraX CIF needs before Boltz will accept it.

1 Sampling options

1 Payload preview

2 Submit with your API key

Submissions go through BoltzYML's open-source proxy, which forwards your key to Boltz and stores nothing. Your key is never sent to GitHub Pages or anyone else. You only need your own Boltz API key — no setup required.

3 Jobs & results

⏳ Please be patient. Predictions take a few minutes. Running jobs (spinner) refresh automatically, so you do not need to click Poll repeatedly. Each check spends one request from a shared free-tier budget, so over-polling reduces the free capacity that keeps this tool free for everyone.

Submitted jobs appear here. They poll themselves; when one succeeds, View 3D opens the structure here, or download a results .zip (all sample CIFs + metrics.json) plus the best structure by ipTM.

Feedback / report a bug