A fold is said to be stable when its score will remain the same despite a given manipulation. Thus, a fold is "shake stable" if shaking it results in no change in score. A fold is "wiggle stable" if a Wiggle does not change the score. This terminology can be applied to rebuilds and also to nudges, although it can be hard to talk about nudge stability with precision, since there are a nearly infinite number of different possible nudges, making generalization difficult. Mojo can often be thought of as a relative degree of nudge stability.
- Unstable proteins often present areas that can be improved significantly, but it can be a challenge to find them. When you find an area that is unstable with regard to wiggle or shake, it is often a good idea to apply what you know about the amino acids in that area, and try to make it live up to its potential.
- When a protein is shake unstable, and loses points during a shake, it is often an indication that you weren't really done wiggling it yet. Control-z your shake, wiggle it some more, and see if it stabilizes.