ArticleACS synthetic biology2026
NUPACK: Computational Nucleic Acid Analysis and Design.
Article in ACS synthetic biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- Charge-screening dominates signal transduction in electrochemical nucleic acid sensors for aminoglycosides.bioRxiv : the preprint server for biology · 2026Article
- Nucleic acid aptamers: new methods for selection, target validation, molecular diagnostics and therapeutics.Signal transduction and targeted therapy · 2026Review
- Enabling molecular signaling with temperature and ionic-strength independence or programmable dependence.Nature communications · 2026Article
- A computational framework for designing micron-scale crisscross DNA megastructures.Nature communications · 2026Article
- Crowdsourced riboregulators reveal design principles for programmable RNA switching.bioRxiv : the preprint server for biology · 2026Article
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. Analysis and design of multitube ensembles enable reaction pathway engineering of dynamic hybridization cascades and structural engineering including the possibility of pseudoknots. The all-new NUPACK 4 scientific code base offers enhanced physical models (coaxial and dangle stacking subensembles), dramatic speedups (20-120× 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.