Mojo is the tendency of any folded protein to revert to its current state after a disturbance. A given fold may be said to have high or low mojo, depending on whether it is likely or unlikely to revert in this way. Those that are high in mojo can stand up to more nudges, wiggles, and other alterations than those that are low in it. In technical terms, structures that have high mojo are close to a local minimum in energy; in other words, they are resistant to change because it's energetically unfavorable to perturb them (see Folding funnel for more information on this concept).

  • Mojo tends to increase as a score goes up, but there are exceptions, and sometimes even a high-scoring protein may become unstable.
  • One way to lower the mojo of a protein is to adjust the orientation of the sidechains. This (for reasons not always clear) will often cause nudge and wiggle to gain many new points, a condition that would not happen if the protein had higher mojo. The opposite tends to happen when using Local Wiggle Strategy; this strategy tends to make the protein's overall configuration harder to change.

The concept of mojo is also useful in that it suggests that players should be more rather than less inclined to make large alterations as their scores increase: They are unlikely to do as much damage, owing to the mojo.