NUPACK: Analysis and design of nucleic acid systems.
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.
Zadeh
Joseph N
JN
Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.
Steenberg
Conrad D
CD
Bois
Justin S
JS
Wolfe
Brian R
BR
Pierce
Marshall B
MB
Khan
Asif R
AR
Dirks
Robert M
RM
Pierce
Niles A
NA
D004247:DNA / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012984:Software
D009696:Nucleic Acids; D012313:RNA; D004247:DNA