Physical review. E, Statistical, nonlinear, and soft matter physics

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure we want to find a sequence that has a certain structure as its ground state. If such a sequence exists, the structure is called designable. We have implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer as to whether such a sequence exists. The bounds required by the branch-and-bound algorithm… Expand