RosettaCommons / RosettaCommons/RFdiffusion
RFPpeptides protocol
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- Dominant language
- Python
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Description
Hi everybody, I am trying to follow the procedure in the SI of the RFPeptides paper to design macrocyclic binders against a target protein. I have correctly launched RFDiffusion with the cyclic flags, and obtain .pdbs of the complex of my protein and the binder. Then I run ProteinMPNN with the options listed in the paper.
But now the procedure tells to run FastRelax, however i do not know how to generate the .pdb of the complex with the ProteinMPNN sequence instead the polyG and they do not tell how they model this. Any advise?
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First steps
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Research direction
Start with the RFdiffusion cyclic-design procedure in the linked RFPeptides paper's supplementary information, then trace the generated complex through ProteinMPNN and FastRelax. Document how the ProteinMPNN sequence replaces polyG before relaxation, including the expected complex PDB input and a reproducible validation step.
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Assessment
- Tech stack
- python
- Domain
- documentation, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100