The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems.[1] Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally for non-commercial academic use.[2] NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.
^Zadeh, J.N., C.D. Steenberg, J.S. Bois, B.R. Wolfe, A.R. Khan, M.B. Pierce, R.M. Dirks, and N.A. Pierce, NUPACK: analysis and design of nucleic acid systems. Journal of Computational Chemistry
(NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. Jobs can be run online on the NUPACK webserver or NUPACK source...
NET_Framework. The Outercurve Foundation initially created it under the name NuPack. Since its introduction in 2010, NuGet has evolved into a larger ecosystem...
sonnets of William Shakespeare in DNA. More generally, algorithms such as NUPACK, ViennaRNA, Ribosome Binding Site Calculator, Cello, and Non-Repetitive...
stacking and phosphate anion-base interactions. Yes No sourcecode webserver NUPACK Computes the full unpseudoknotted partition function of interacting strands...
nucleic acid structure prediction. Dirks wrote the initial code for the NUPACK suite of nucleic acid design and analysis tools, which generates base pairing...
Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A. (17 November 2010). "NUPACK: Analysis and design of nucleic acid systems". Journal of Computational...
computationally costly. Software for thermodynamic modeling of nucleic acids includes Nupack, mfold/UNAFold, and Vienna. A related approach, inverse secondary structure...
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