Perhaps you should have the option to not save the current protein you are working on when you close, so you don't have a bunch of unwanted autosaves.

Also, an ability to easily port proteins you are working on between computers would be very nice. I might experiment with this by manually moving around files, such as the .pdb files, which appear to be related to (or are) the protein save-files. If anyone has managed to successfully move proteins around from computer to computer, please comment!