{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "jwohlwend-boltz--predict-a-protein-complex-structure-with-boltz",
 "repo": "jwohlwend/boltz",
 "repo_url": "https://github.com/jwohlwend/boltz",
 "repo_slug": "jwohlwend-boltz",
 "title": "Predict a protein complex structure with Boltz",
 "page_title": "How to predict a protein complex structure with Boltz with Boltz",
 "summary": "Describe your biomolecules in a YAML file and let Boltz predict the structure of the complex.",
 "who": "A structural biologist who wants a quick open-source structure model of a complex before setting up experiments.",
 "problem": "Getting a structure prediction for a complex usually means a hosted service, a queue or a closed model.",
 "outcome": "Predicted complex structures written by the latest Boltz model on your own machine.",
 "steps": [
  "Create a fresh Python environment, as the README recommends",
  "Install with `pip install boltz[cuda] -U` (drop [cuda] on CPU-only or non-CUDA GPU hardware)",
  "Write an input YAML file describing the biomolecules you want to model, following docs/prediction.md",
  "Run `boltz predict input_path --use_msa_server` with input_path pointing at the YAML file",
  "Check every option with `boltz predict --help`"
 ],
 "agent_prompt": "Using jwohlwend/boltz, install it in a fresh environment, write an input YAML for <protein sequences and ligands> following docs/prediction.md, and run `boltz predict input_path --use_msa_server`. Tell me where the predicted structures were written.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Intermediate",
 "time": "1 hour",
 "basis": "readme",
 "caveat": "Predictions are model outputs, not experimental structures; validate anything you act on.",
 "category": "Security and science",
 "tags": [
  "Security and science"
 ],
 "lang": "python",
 "requirements": [
  "Python in a fresh environment and pip",
  "An NVIDIA GPU for the [cuda] install; CPU-only works but is significantly slower",
  "Input YAML files describing the biomolecules (format in docs/prediction.md)",
  "Network access for the optional MSA server (--use_msa_server)"
 ],
 "risk": "none",
 "seen_in_the_wild": false,
 "mentioned_publicly": false,
 "risks": [
  {
   "tag": "platform",
   "notice": "The CPU version is significantly slower than the GPU version, so large complexes realistically need an NVIDIA GPU."
  }
 ],
 "best": true,
 "score": 1.0,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/jwohlwend-boltz/predict-a-protein-complex-structure-with-boltz/",
 "md": "https://dedupedai.com/use-cases/jwohlwend-boltz/predict-a-protein-complex-structure-with-boltz/index.md",
 "disclaimer": "Deduped lists open-source repositories that belong to other people. We do not own, maintain, audit, or vouch for any of them, and a repo appearing here is not an endorsement or a safety check. The use cases, steps, and prompts are written by AI and may be incomplete, outdated, or just wrong. Where a use case is marked \"Seen in the wild\", we link to public posts where someone described something similar, but we have not verified those posts and the use case itself is still our AI's own write-up. Use all of this at your own risk. Only run code, commands, or agents on systems and accounts you are authorized to use, and read the code and every command before you run it, especially anything that touches credentials, files, or the network. Nothing here is professional, security, legal, or financial advice. All trademarks and project names belong to their respective owners, and their use here does not imply affiliation. Content is provided as is, without warranties of any kind. Found a mistake, a safety problem, or something you want removed? Email hello@dedupedai.com and we will look at it promptly.",
 "api": "https://dedupedai.com/api/v1/usecases/jwohlwend-boltz--predict-a-protein-complex-structure-with-boltz.json",
 "api_version": "v1"
}