Just to make sure I understand correctly the hotspots are specified at the contacts of the green "experimentally determined" binder?

hi @0merle0 Could you please add some sample runs for binder design? I could not find binder_design.sh within the examples folder. Thanks, Renzhi

Here's a sample script of how I ran these jobs (except for hotspot residues and length of chain A, everything else is the same for all cases):
python /path/to/protein_generator/inference.py \ --num_designs 2 \ --out output/2b1n \ --pdb 2b1n.pdb \ --T 10 \ --save_best_plddt \ --contigs A1-227,0 6-8 \ --hotspots A19,A65,A166,A147,A21,A64 \ --checkpoint /path/to/protein_generator/SEQDIFF_221219_equalTASKS_nostrSELFCOND_mod30.pt

Thank you. I tried this pipeline. For my target, when I use alphafold3 to check the designed binders, the ipTM score is very low despite the high pLDDT in protein_generator, and not binding to the hotspots that I specified. Do you have the same problem?

Actually I haven't tried that. Will try and let you know the results.