NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems

NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms have pioneered the treatment of complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these fields. The all-new NUPACK 4 scientific code base offers enhanced physical models (coaxial and dangle stacking subensembles), dramatic speedups (20-120x for test tube analysis), increased scalability for large complexes (e.g., 30,000 nt), mixed materials (specified at nucleotide resolution), and diverse hard and soft sequence constraints for design. The all-new NUPACK web app (nupack.org) facilitates rapid job submission and result inspection with NUPACK 4 algorithms running in parallel on a hybrid cloud compute cluster that scales dynamically in response to user demand. NUPACK 4 algorithms can also be run locally using the all-new NUPACK Python module. Analysis and design of multi-tube ensembles enable reaction pathway engineering of dynamic hybridization cascades and structural engineering including the possibility of pseudoknots.