This is a two-sided design drawback, the place we will design the sequence of each binding companions. The aim is to design a pair of proteins that may self-associate in resolution. This is very helpful for bioengineering purposes the place we’d need to use a brief peptide as a “sign” that may be acknowledged by its binding associate. Although the quick peptide could also be versatile in resolution, we wish to bind it within the form of beta strand, so the goal spine has been frozen as a beta strand. However, you should still change the sidechains of the strand goal to any amino acid you need!

AlphaFold predictions are enabled for the designed binder. Once you’ve got designed a binder for the strand goal, add your resolution for AlphaFold utilizing the AlphaFold prediction instrument. AlphaFold will predict the construction of your binder chain solely (i.e. within the unbound state, within the absence of the strand goal). If you load this prediction, then Foldit will try and align the prediction together with your resolution (i.e. within the sure state, making an interface with the strand goal). If you proceed working off of the AlphaFold prediction, you might have to make changes on the interface the place the binder interacts with the goal. See the puzzle feedback for added Objectives.