DEDUPED Hot AI repos. Real use cases. What people build. Get the Monday 5

How to scaffold a functional motif into a new protein with RFdiffusion

Hold a motif from an input PDB fixed and let diffusion build the protein around it.

Short answer: Set up the repo, weights and SE3nv environment as in the installation section; then 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. All steps.

Who it is forAn enzyme or epitope designer who needs a motif presented in a new scaffold.

The problemGrafting a motif into a stable fold by hand is slow and often fails.

The outcomeDesigns that keep your motif geometry inside a newly built protein.

What you need first

  • 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

Steps

  1. Set up the repo, weights and SE3nv environment as in the installation section
  2. Point the run at your structure with inference.input_pdb=path/to/file.pdb
  3. 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
  4. For very small motifs add inference.ckpt_override_path=models/ActiveSite_ckpt.pt, and see ./examples/design_motifscaffolding.sh

Prompt for your agent

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.

Caveat. A chain break is written as /0 with the space included, which is easy to get wrong in a shell command.

Use this in your AI agent

Ask your agent

Using the Deduped MCP, get the setup steps for RosettaCommons/RFdiffusion and "Scaffold a functional motif into a new protein"

Add Deduped to Claude Code once

claude mcp add --transport http deduped https://dedupedai.com/mcp

Cursor, ChatGPT, others

Share: X LinkedIn Hacker News Email Copy link

Third-party repos we don't own. AI-written use cases can be wrong. Disclaimer