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NUPACK

NUPACK

(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

NUPACK

NuGet

.NET package manager

Framework. The Outercurve Foundation initially created it under the name NuPack. Since its introduction in 2010, NuGet has evolved into a larger ecosystem

NuGet

List of computational chemistry software

Molekel Molecular visualization Open-source Ms2 Molecular modeling Free NUPACK Nucleic acid structure modeling Open-source ParaSurf Surface analysis /

List of computational chemistry software

List_of_computational_chemistry_software

List of free and open-source software packages

CS-ROSETTA ECCE Folding@home Jmol MODELLER Molecular Modelling Toolkit Molekel NUPACK QuteMol RasMol ShelXle Chimera VMD VOTCA Avogadro Biskit Chemistry Development

List of free and open-source software packages

List_of_free_and_open-source_software_packages

Robert Dirks

American computational chemist killed in 2015 train wreck

nucleic acid structure prediction. Dirks wrote the initial code for the NUPACK suite of nucleic acid design and analysis tools, which generates base pairing

Robert Dirks

Robert_Dirks

Synthetic biology

Interdisciplinary branch of biology and engineering

sonnets of William Shakespeare in DNA. More generally, algorithms such as NUPACK, ViennaRNA, Ribosome Binding Site Calculator, Cello, and Non-Repetitive

Synthetic biology

Synthetic_biology

List of software developed at universities

Software projects developed at universities

photonic band structures (MIT) NAMD – molecular dynamics software (Illinois) NUPACK – nucleic acid analysis and design software suite (Caltech) PARI/GP – computer

List of software developed at universities

List_of_software_developed_at_universities

Niles Pierce

Khan, Asif R.; Dirks, Robert M.; Pierce, Niles A. (17 November 2010). "NUPACK: Analysis and design of nucleic acid systems". Journal of Computational

Niles Pierce

Niles_Pierce

Nucleic acid design

Generative process for base sequences

computationally costly. Software for thermodynamic modeling of nucleic acids includes Nupack, mfold/UNAFold, and Vienna. A related approach, inverse secondary structure

Nucleic acid design

Nucleic_acid_design

List of RNA structure prediction software

stacking and phosphate anion-base interactions. Yes No sourcecode webserver NUPACK Computes the full unpseudoknotted partition function of interacting strands

List of RNA structure prediction software

List_of_RNA_structure_prediction_software