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baker-laboratory / rf_diffusion_all_atom

Public RFDiffusionAA repo
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Diffusion of protein binder including a ligand #24

Open BJHardy opened 3 months ago

BJHardy commented 3 months ago

Thank you for this incredible software, and for making it freely available!

I would like to know if it is possible to diffuse protein binders using RFdiffusion all-atom, specifically where one or both of the proteins includes ligands.

I have tried this but get an error saying "AssertionError: contig_list with >1 element not curently supported: ['A1-A112/0', '50-100,B249,50-100/0']", making me think this is not possible.

Could you please confirm whether this function is indeed to available, or if there is another way to perform this kind of design?

LiorZ commented 2 weeks ago

Try and rename the ligand on both structure to have the same name (e.g. "LIG") inside the PDB. When both have the same name, you can use it in the "inference.ligand=" command line parameter