ArticleNature protocols2008
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
Article in Nature protocols, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 347 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.
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Who cites it
347 citing papers in PubMed.
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- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- Molecular basis of UV lesion binding and repair inhibition by ETS-family transcription factors.Nucleic acids research · 2026Article
- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.eLife · 2026Article
- Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics.Communications biology · 2026Article
- DNA twist at high alkali ion concentrations: evidence against C-form DNA in solution.Nucleic acids research · 2026Article
- PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation.Nature communications · 2026Article
- Zinc-finger transcription factor Fzf1 binds to its target DNA in a non-canonical manner.Nucleic acids research · 2026Article
- Loop of fate: structural and mechanistic insights into hnRNPA1 binding to the hepatitis C virus RNA.RNA (New York, N.Y.) · 2026Article
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Enhanced i-Motif Stability through Consecutive 2',2'-Difluorocytidine Incorporation.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase.Nature communications · 2025Article
- Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome.Nature communications · 2025Article
- GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability.Mathematical biosciences · 2025Article
- The Effect of 2'F-RNA on I-Motif Structure and Stability.Molecules (Basel, Switzerland) · 2025Article
- Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning.Nucleic acids research · 2025Article
- Interfacing B-DNA and DNA Mimic Foldamers.Angewandte Chemie (International ed. in English) · 2025Article
287 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases and so on. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.
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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.