Protein Design (BoltzGen)

Overview

This skill runs the FastFold BoltzGen workflow in the same flow used by the Composer:

1. Prepare or generate design-spec YAMLs (single-spec or multi-spec).
2. Fetch/clean CIF inputs or reuse existing references.
3. Create a draft workflow.
4. Upload files and upsert the full workflow graph (workflow.yml) in one transaction.
5. Share the full Composer link and a draft review summary (inputs + params + YAML previews) after non-empty graph upsert.
6. Ask user to validate and confirm.
7. Execute, wait, and summarize candidate metrics + structure links.

It is based on:

• BoltzGen upstream repository and README: https://github.com/HannesStark/boltzgen
• BoltzGen paper (bioRxiv DOI 10.1101/2025.11.20.689494): https://www.biorxiv.org/content/10.1101/2025.11.20.689494v1.full