title: NUPACK: Analysis and design of nucleic acid systems.
abstract: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables:
  
  
  METHODS
  thermodynamic analysis of dilute solutions of interacting nucleic acid strands.
  
  
  METHODS
  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.
authors.affiliation: Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Zadeh
authors.forename: Conrad D
authors.initials: CD
authors.lastname: Steenberg
authors.forename: Justin S
authors.initials: JS
authors.lastname: Bois
authors.forename: Brian R
authors.initials: BR
authors.lastname: Wolfe
authors.forename: Marshall B
authors.initials: MB
authors.lastname: Pierce
authors.forename: Asif R
authors.initials: AR
authors.lastname: Khan
authors.forename: Robert M
authors.initials: RM
authors.lastname: Dirks
authors.forename: Niles A
authors.initials: NA
authors.lastname: Pierce
mesh_terms: D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012984:Software
chemical_list: D009696:Nucleic Acids; D012313:RNA; D004247:DNA