RosettaCommons / RosettaCommons/RFdiffusion
How to generate compact binders?
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- Python
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Description
Thank you for your great work. I have been using rfdiffusion to design protein binders in my project, but I am having difficulty generating compact binders. I took an example in paper, IL7 Receptor α (PDB: 3DI3), I cannot reproduce the results(see my options below), Despite trying binder_ROG, the majority of designs still have long helices. Could you please provide the command line used in your paper's experiment to achieve better conformations? I appreciate your assistance with this matter.
Thanks
run_inference.py inference.output_prefix=test/rf inference.input_pdb=3di3.pdb contigmap.contigs=[B17-209/0 90-90] inference.num_designs=10 diffuser.T=50 ppi.hotspot_res=[B58, B80, B139] potentials.guiding_potentials=["type:binder_ROG,min_dist:5"]
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Research direction
Start with the run_inference.py invocation and options included in the issue, then compare them with the RFdiffusion experiment described in the paper. Done would be a documented, reproducible command or clear usage guidance for generating the requested compact binders.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100