# RNA secondary structure design.

@article{Burghardt2007RNASS, title={RNA secondary structure design.}, author={Bernd Burghardt and Alexander K. Hartmann}, journal={Physical review. E, Statistical, nonlinear, and soft matter physics}, year={2007}, volume={75 2 Pt 1}, pages={ 021920 } }

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…

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