{
 "schema_version": 1,
 "generated": "2026-10-31",
 "id": "rosettacommons-rfdiffusion--scaffold-a-functional-motif-with-rfdiffusion",
 "repo": "RosettaCommons/RFdiffusion",
 "repo_url": "https://github.com/RosettaCommons/RFdiffusion",
 "repo_slug": "rosettacommons-rfdiffusion",
 "title": "Scaffold a functional motif into a new protein",
 "page_title": "How to scaffold a functional motif into a new protein with RFdiffusion",
 "summary": "Hold a motif from an input PDB fixed and let diffusion build the protein around it.",
 "who": "An enzyme or epitope designer who needs a motif presented in a new scaffold.",
 "problem": "Grafting a motif into a stable fold by hand is slow and often fails.",
 "outcome": "Designs that keep your motif geometry inside a newly built protein.",
 "steps": [
  "Set up the repo, weights and SE3nv environment as in the installation section",
  "Point the run at your structure with `inference.input_pdb=path/to/file.pdb`",
  "Describe the build with a contig such as `'contigmap.contigs=[5-15/A10-25/30-40]'`, where A10-25 is the motif and the numbers are residues to build",
  "For very small motifs add `inference.ckpt_override_path=models/ActiveSite_ckpt.pt`, and see ./examples/design_motifscaffolding.sh"
 ],
 "agent_prompt": "Using RosettaCommons/RFdiffusion, scaffold residues <my motif range> of <my pdb> with contigs like 'contigmap.contigs=[5-15/A10-25/30-40]' and tell me how to check the motif stayed in place.",
 "agents": [
  "claude-code",
  "codex",
  "cursor",
  "gemini-cli"
 ],
 "difficulty": "Advanced",
 "time": "4 hours",
 "basis": "readme",
 "caveat": "A chain break is written as /0 with the space included, which is easy to get wrong in a shell command.",
 "category": "Security and science",
 "tags": [
  "Security and science"
 ],
 "lang": "",
 "requirements": [
  "A clone of the repo plus the model weights downloaded into its models folder",
  "Anaconda or Miniconda, and NVIDIA's SE(3)-Transformer installed from the env folder",
  "An NVIDIA GPU; the provided environment file targets CUDA 11.1 and may need adapting",
  "Docker as an alternative to the conda setup, using the provided docker/Dockerfile"
 ],
 "risk": "none",
 "seen_in_the_wild": false,
 "mentioned_publicly": false,
 "risks": [],
 "best": false,
 "score": 0.8,
 "evidence": [],
 "url": "https://dedupedai.com/use-cases/rosettacommons-rfdiffusion/scaffold-a-functional-motif-with-rfdiffusion/",
 "md": "https://dedupedai.com/use-cases/rosettacommons-rfdiffusion/scaffold-a-functional-motif-with-rfdiffusion/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/rosettacommons-rfdiffusion--scaffold-a-functional-motif-with-rfdiffusion.json",
 "api_version": "v1"
}