RosettaCommons / RosettaCommons/RFdiffusion
RFdiffusion small binder generation
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- Dominant language
- Python
- Stars
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Description
Hello, I'm a beginner with RFdiffusion.
I'm trying to generate a small binder to inhibit the interaction between proteins A and B. However, none of the small binder sequences I've obtained so far have been effective in disrupting their interaction. Protein A is 1071 amino acids, and protein B is 216 amino acids.
For the input, I set contigs = A:50 and specified the interaction sites as hotspots. When I ran protein A, B, and the small binder sequences through AlphaFold 3, none of the binders were able to inhibit the interaction.
How should I adjust the input parameters to generate a more effective small binder sequence? If you were in my position, how would you modify the inputs? I’d really appreciate your help.
Best regards,
Yoo
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No file, test, or entry point is named. Start by reviewing RFdiffusion's contigs and hotspot inputs, then compare the generated binders using the stated AlphaFold 3 evaluation; completion would require a reproducible input adjustment that produces an effective binder.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100