How to generate compact binders?
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"]
I'm wondering if you could generate compact binders. @bzhousd