Allow excluding amino acids in sequence generation

[Hartree42]

Hi everyone!

Since this new version of Diffusion outputs a backbone with a sequence already included, I would like to know if there is a way to configure the sequence generation part that fits the backbone. Specifically, I would like to avoid certain amino acids in the proposed sequence (for example, I don't want HIS or CYS).

Is this possible? And if so, how?

Grazie mille!

Cosimo

[rclune]

I'm not sure if there is an easy way to do this with the current version of RFD3, however it can be accomplished by using the RFD3 output structures as the inputs to a follow up MPNN calculation. You can 'bias' the sequence generation towards or away from specific residues. (See 9 and 10 in the LigandMPNN README)