Only applicable to protein (amino acids) part or not?

[SimonYYS]

Hi there, thanks for posting the powerful LigandMPNN. I am wondering if it is possible to design (or optimize) the nucleic acid sequence given a DNA/RNA-protein complex with LigandMPNN, instead of designing the aa sequence of protein? Thanks!

[roccomoretti]

Yes, it is possible to do something similar as LigandMPNN, but with design of nucleic acids. However, LigandMPNN itself isn't trained that way, and its outputs are only parameterized to change the protein portion of the complex.

However, the Baker lab also has NA-MPNN (preprint) (repo) which is designed to do exactly that.