Oliver Kanders

@joewatchwell, Thanks so much for the help! Currently, I am using the SS of my target, but I would like my binder to be smaller... how would you recommend I...

@nrbennet, Hi, The pdb I sent above was the output of MPNN (I just MPNN used). Here are my outputs from RFDiffusion and the AF2 initial guess from pdb_interfaceAF2.py: [InsulinDesign_RFDiff_a2pred.zip](https://github.com/RosettaCommons/RFdiffusion/files/12163917/InsulinDesign_RFDiff_a2pred.zip)...

@nrbennet, yes of course. I made some edits to the dl_interface_design.py, but none that should have effected the target sequence. **RFDiffusion (example provided as script):** `../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/ppi_test/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]'...

@nrbennet Unfortunately, I do not have access to pyrosetta... I am trying to look into a Biopython substitute for this MPNN sequencing if that is possible (is this translation to...

@nrbennet I was wondering what is wrong with my MPNN output? The target has the same sequence and coordinates as from the RFDiffusion output. Do you modify the target, which...

@nrbennet , Hi Nathaniel, I was wondering what your PDB file looks like after ProteinMPNN, as mine is just backbone + encoded sequence, which does not seem to be enough...