NUPACK: Analysis and design of nucleic acid systems

J Comput Chem. 2011 Jan 15;32(1):170-3. doi: 10.1002/jcc.21596.


The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server ( currently enables:

Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands.

Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA / chemistry
  • Models, Molecular
  • Nucleic Acid Conformation*
  • Nucleic Acids / chemistry*
  • RNA / chemistry
  • Software*


  • Nucleic Acids
  • RNA
  • DNA