ColabDesign icon indicating copy to clipboard operation
ColabDesign copied to clipboard

homo-oligomeric binders

Open thomas-tugwell opened this issue 3 months ago • 0 comments

I was wondering if there is currently a way to generate homo-oligomeric binders for homo-oligomeric targets? When I try something like this, where i supply a binder scaffold:

af_model = mk_afdesign_model(protocol="binder", data_dir="/params")
af_model.prep_inputs(
    pdb_filename="../pdbs/toy_complex.pdb",
    num_model=1,
    use_multimer=True,
    chain="A,B,C,D,E",
    binder_chain="F,G,H,I,J",
    copies=5,
    homooligomer=True
)

af_model.design_3stage()   
af_model.save_pdb("designed_output.pdb")

I get my target returned with five non-identical binders that are not arranged symmetrically. Any advice on how to do something like this? I would also eventually like to do the case where I dont have to supply a binder scaffold.

thomas-tugwell avatar Sep 22 '25 17:09 thomas-tugwell