Is there a way to set a maximum number of mutations per designed sequence? about proteinmpnn

[dauparas]

You could add bias toward the input sequence. The stronger the bias the less number of mutations will be made. https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/make_bias_per_res_dict.py

[noah-c-noah-do]

Hi Justas,

Thanks for the quick reply! If I'm grokking that code correctly, then you're suggesting I just edit the code:

if chain == 'A':
residues = [A, B,...Z]
amino_acids = [5]
for res in residues:
for aa in amino_acids:
bias_per_residue[res, aa] = 100

So that A-Z equals each Glycine residue index in the WT sequence and then add a sub-block for each other amino acid type? Wouldn't that result in just the native sequence being returned? Or would I avoid that through specifying the positions to design by using the --specify_non_fixed flag?