Diffusion of protein binder including a ligand

[BJHardy]

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]

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

[anton-bushuiev]

@LiorZ Thank you for your comment! Does it generate meaningful designs when both ligands are named LIG? I assume RFdiffusionAA was not trained on this kind of data, where "one ligand" contains of several disjoint molecules.