Table II.

Types of perturbations

Type	Parameter	Continuous	Residues affected	Where usually found
Shear*	Primary shear angle	Yes	4	Helices
Backrub	Primary backrub angle	Yes	3	β sheets, loops
Loop closure adjustment*	Solution from discrete set	No	3	Loops
Secondary structure adjustment*	Solution from discrete set	No	3–4	Loop-helix or loop-sheet borders
Partial structure switch	Structure from discrete set	No	As desired	Anywhere
Full structure switch	Structure from discrete set	No	All	Entire protein
Proline flip	Boolean: flip or no flip	No	1	Prolines

^*These perturbations cannot, to our knowledge, be performed by any previous protein design algorithm. DEEPer also offers novel combinations of perturbations that have been modeled previously; for example, no previous provable algorithm modeled overlapping backrubs. DEEPer is also novel in combining these perturbations with continuous sidechain flexibility, which is represented as orthogonal to perturbations in conformational space.