NUPACK: Analysis and design of nucleic acid systems

Joseph N. Zadeh, Conrad D. Steenberg, Justin S. Bois, Brian R. Wolfe, Marshall B. Pierce, Asif R. Khan, Robert M. Dirks, Niles A. Pierce
2010 Journal of Computational Chemistry  
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: • 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
more » ... id strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.
doi:10.1002/jcc.21596 pmid:20645303 fatcat:izrwy3b2u5b2hjfprkxlaebpxm