Many suggestions going in this direction, I think it would be the best to generally allow custom templates.
With this you could also save a special form of a protein part when you want to work an a neighboring part and the saved region together to get a new form.
related issues:
http://fold.it/portal/node/987708 Partial alignment– first thoughts (drag&drop request)
http://fold.it/portal/node/988107 combine recipes
I second that.
Regarding to recipes:
If we could save and load them as .lua-files,
we could include one recipe in another (as the include-function does in PHP).
Or, if direct file access isn't intended, we could include scripts not by calling their file- but their recipe-name.
Important is, when using multiple recipes, that per script all variables and saveslots must be stored on several layers of scope.
Here is a discussion about loading and saving parts of a puzzle:
http://fold.it/portal/node/992730