In lab experiment, binding affinity is pretty strong, but pae_interaction is only around 28

So, I have an example protein A that is very similar to my protein B I aim to study. The protein A has a binder A-binder, and I use A-binder as a scaffold to design my binder B-binder to my protein B.

As I learned here, at the last step, I will use af2_initial_guess/predict.py to assess designed binders and pick binders whose pae_interaction<10 .

However, pae_interaction~=28 between protein A and A-binder. I feel confused about it a lot, because its binding affinity is very strong in lab experiment.

I worked very hard to think of how to improve pae_interaction below 10. Unfortunately, over 95% pae_interaction is around 26~28. Should I still work hard to look for pae_interaction<10 ?

I don't understand these two scenarios: 1) why pae_interaction is bad, but binding affinity is very good in lab experiment? 2) Is pae_interaction<10 very important? Is there any other criteria I should to consider when I assess my designed binders?

Thanks a lot!!!

Start with af2_initial_guess/predict.py and the linked dl_binder_design guidance for how pae_interaction is calculated and used. Compare the reported pae_interaction values with the experimental binding-affinity example, then document whether the threshold is appropriate and which additional binder-assessment criteria are supported.