(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...
8 KB (975 words) - 19:19, 28 December 2020
Framework. The Outercurve Foundation initially created it under the name NuPack. Since its introduction in 2010, NuGet has evolved into a larger ecosystem...
5 KB (366 words) - 11:03, 25 June 2024
sonnets of William Shakespeare in DNA. More generally, algorithms such as NUPACK, ViennaRNA, Ribosome Binding Site Calculator, Cello, and Non-Repetitive...
151 KB (18,342 words) - 12:08, 30 August 2024
stacking and phosphate anion-base interactions. Yes No sourcecode webserver NUPACK Computes the full unpseudoknotted partition function of interacting strands...
152 KB (8,419 words) - 09:22, 27 August 2024
Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A. (17 November 2010). "NUPACK: Analysis and design of nucleic acid systems". Journal of Computational...
7 KB (628 words) - 03:54, 27 March 2024
nucleic acid structure prediction. Dirks wrote the initial code for the NUPACK suite of nucleic acid design and analysis tools, which generates base pairing...
20 KB (1,886 words) - 17:57, 31 August 2024
computationally costly. Software for thermodynamic modeling of nucleic acids includes Nupack, mfold/UNAFold, and Vienna. A related approach, inverse secondary structure...
19 KB (2,110 words) - 22:43, 3 December 2023