NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots

  • Ján Maňuch
  • Chris Thachuk
  • Ladislav Stacho
  • Anne Condon
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5877)


Knowledge of energy barriers between pairs of secondary structures for a given DNA or RNA molecule is useful, both in understanding RNA function in biological settings and in design of programmed molecular systems. Current heuristics are not guaranteed to find the exact energy barrier, raising the question whether the energy barrier can be calculated efficiently. In this paper, we study the computational complexity of a simple formulation of the energy barrier problem, in which each base pair contributes an energy of − 1 and only base pairs in the initial and final structures may be used on a folding pathway from initial to final structure. We show that this problem is NP-complete.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Ján Maňuch
    • 1
  • Chris Thachuk
    • 2
  • Ladislav Stacho
    • 1
  • Anne Condon
    • 2
  1. 1.School of Computing Science and Department of MathematicsSimon Fraser UniversityCanada
  2. 2.Department of Computer ScienceUniversity of British ColumbiaCanada

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