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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.
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