ArticleMolecules (Basel, Switzerland)2022
3dDNA: A Computational Method of Building DNA 3D Structures.
Article in Molecules (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Aptamers Structure Flexibility Is Crucial to EGFR Inhibition Function.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Aptamer-based nanoparticle drug delivery system designed for targeting GPC3-positive liver cancer.Journal of pharmaceutical analysis · 2026Article
- Ultrasensitive Detection of Porcine Epidemic Diarrhea Virus Infections Using Multivalent DNA Nanostructure-Enabled Lateral Flow Assay.Advanced healthcare materials · 2026Article
- Slfn4-mediated Stat3 signaling promotes suppressive bone marrow monocytes in a murine second-hit sepsis model.Molecular medicine (Cambridge, Mass.) · 2026Article
- Biomarker-targeted functionalized magnetic nanoparticles: synthesis and aptamer conjugation optimization toward Alzheimer's disease biosensing.Nanoscale advances · 2026Article
- Determining the Optimal Heparin Binding Domain Distance in VEGFInternational journal of molecular sciences · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Chromosome-level genome assembly of Trichogramma ostriniae Pang & Chen (Hymenoptera: Trichogrammatidae).Scientific data · 2025Article
- Chromosome-level genome assembly of Hippophae neurocarpa.Scientific data · 2025Article
- From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid.BMC plant biology · 2025Article
- DNA aptamer AptScientific reports · 2025Article
- Enhancing aptamer selection in alzheimer's disease: integrating structure prediction and molecular dynamics simulations.Scientific reports · 2025Article
- Chromosome-level assembly and annotation of the yellow-shelled fish (Barbodes Wynaadensis).Scientific data · 2025Article
- Functional aptamer evolution-enabled elucidation of a melanoma migration-related bioactive epitope.Acta pharmaceutica Sinica. B · 2025Article
- Macrophage ATF6 accelerates corticotomy-assisted orthodontic tooth movement through promoting Tnfα transcription.International journal of oral science · 2025Article
- Chromosome-level genome assembly of an endoparasitoid Cotesia ruficrus.Scientific data · 2025Article
- Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Design and development of an aptamer targeting C-type lectin-like molecule-1 as a biomarker for acute myeloid leukemia: a SELEX approach.Frontiers in bioengineering and biotechnology · 2025Article
- Article
- Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA.Molecules (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains.
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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.