Comparing the binding affinity of three chains vs two chains


I hope this message finds you well. What is the best way to compare the binding affinity of a complex with three unique chains to a complex with two unique chains using PRODIGY? Should I run PRODIGY with each chain being Interactor 1 and the remaining chains being Interactor 2, and then add all the resulting binding affinities for a given protein complex together? I am not sure if there is a standard procedure or formula to do this correctly.

Thank you!

It all depends on which interfaces you want to evaluate…

If a homotrimer I would go for the interface between A and BC

If a heterotrimer, indeed how to best do it… Not sure adding the affinities would be a good approach.

You could tray A with BC, and all combinations and take the average. Or the weakest affinity since this might well be defining the breaking point.