Revolutions in RNA secondary structure prediction

J Mol Biol. 2006 Jun 9;359(3):526-32. doi: 10.1016/j.jmb.2006.01.067. Epub 2006 Feb 6.


RNA structure formation is hierarchical and, therefore, secondary structure, the sum of canonical base-pairs, can generally be predicted without knowledge of the three-dimensional structure. Secondary structure prediction algorithms evolved from predicting a single, lowest free energy structure to their current state where statistics can be determined from the thermodynamic ensemble. This article reviews the free energy minimization technique and the salient revolutions in the dynamic programming algorithm methods for secondary structure prediction. Emphasis is placed on highlighting the recently developed method, which statistically samples structures from the complete Boltzmann ensemble.

Publication types

  • Review

MeSH terms

  • Algorithms
  • Base Pairing
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Sequence Analysis, RNA
  • Thermodynamics


  • RNA