Binder Design Size

[JA-Hull]

There's a good amount of detail about RF diffusion followed by ProteinMPNN-FastRelax in terms of selecting target sites, truncating proteins, scale, and filtering. However, there's not really any discussion about how long to design the binder. I have reasonably good in silico success with 25 and 30mer peptides (getting interaction PAE ~5) when I have really small protein pockets. Is there a general guidance on how long these proteins should be? Is it just guess and check or are there suggested minimum/maximums?

[kjogr12]

I'm also interested in binder design for peptide/small proteins(< 20 AA).
Is there a size limitation for proteins with this method? Or could you inform me about the protein size range that has been validated with this approach?

[xinran1129305]

Hi there.
I'm wondering that if I want to design small binders, do I need to set and try different symmetry settings? Almost all of my designs failed, since they cannot meet the criteria of in silico success:(
Thanks in advance!