I'm working with a transmembrane protein and I'm interested in understanding the folding differences between its variants. I've used AlphaFold and some other tools to generate predictions, but this protein folds in the lipid bilayer, which doesn't seem to be supported. I've read here (https://www.frontiersin.org/articles/10.3389/fmolb.2022.906437/full) that AlphaFold's prediction of membrane proteins is surprisingly good. Can anyone confirm this or explain it? It seems that the protein's secondary structure would be very different in water.
