Using sequence in potentials

[geraseva]

I am trying to make a custom potential that needs not only backbone coordinates, but also a sequence matrix. Now I am using LigandMPNN inside my potential, but it is a quite complicated way. Could sequence generated by RFDiffusion be used instead, and, if so, which functions should be rewritten to provide its use?

[roccomoretti]

RFdiffusion is primary concerned with generating backbone coordinates, not sequence identities. It would likely be a substantial re-write to have it generate sequence information for the newly generated residues. (Note, though, that it can take sequence information for input residues.)

If you're looking to do joint sequence/structure generation, take a look at ProteinGenerator (https://doi.org/10.1038/s41587-024-02395-w).

[geraseva]

Thank you!