Open kjogr12 opened 6 months ago
It's hard to say, you could try adding negative bias to K, and E amino acids when designing. It is known that the model has a bias towards polar residues like K, E for the surface residues when used with low sampling temperatures (0.1). You could also try to increase the sampling temperature.
Thank you for your insightful response. I appreciate your suggestion to add a negative bias to K and E amino acids and to consider adjusting the sampling temperature. When employing a negative bias, do you have any recommended setting for each amino acid? I am considering configuring the settings based on the amino acid distribution of PDBbench shown in SPDesign(https://www.biorxiv.org/content/10.1101/2023.12.14.571651v1).
I would be grateful if you could share any recommendations you might have.
Dear ProteinMPNN team, Thank you very much for your great efforts.I want to know why the designed amino acid sequence contains a large amount of E/K(i.g. EEKEKELKKYAEKLKKEVKDIESIDVKDGEITVKAKKLTEKTKKAI...). It’s looks unusual. The input file(pdb) was utilizes a backbone constructed using RFdiffusion. Is there any solution available? Thank you for your helps in advance