ProbKnot: fast prediction of RNA secondary structure including pseudoknots

RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.


It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at:

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Base Sequence
  • Computational Biology
  • Computer Simulation
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • RNA / genetics
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • Software
  • Thermus thermophilus / genetics


  • RNA, Bacterial
  • RNA