RNA secondary structure design.

  title={RNA secondary structure design.},
  author={Bernd Burghardt and Alexander K. Hartmann},
  journal={Physical review. E, Statistical, nonlinear, and soft matter physics},
  volume={75 2 Pt 1},
  • B. BurghardtA. Hartmann
  • Published 15 September 2006
  • Computer Science
  • 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… 

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