ArticleJournal of visualized experiments : JoVE2013
Analyzing and building nucleic acid structures with 3DNA.
Article in Journal of visualized experiments : JoVE, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
37 citing papers in PubMed.
- Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites.Genome research · 2025Article
- A Multi-Input Neural Network Model for Accurate MicroRNA Target Site Detection.Non-coding RNA · 2025Article
- Circular oligomeric particles formed by Ros/MucR family members mediate DNA organization in α-proteobacteria.Nucleic acids research · 2024Article
- Relative genotoxicity of polycyclic aromatic hydrocarbons inferred from free energy perturbation approaches.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Structural characterization of PHOX2B and its DNA interaction shed light on the molecular basis of the +7Ala variant pathogenicity in CCHS.Chemical science · 2024Article
- STAG2: Computational Analysis of Missense Variants Involved in Disease.International journal of molecular sciences · 2024Article
- Structural basis of telomeric nucleosome recognition by shelterin factor TRF1.Science advances · 2023Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- The impact of nucleosome structure on CRISPR/Cas9 fidelity.Nucleic acids research · 2023Article
- Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps.Briefings in bioinformatics · 2023Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
- Programmable siRNA pro-drugs that activate RNAi activity in response to specific cellular RNA biomarkers.Molecular therapy. Nucleic acids · 2022Article
- Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.Proteins · 2022Article
- Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNA.Biophysics and physicobiology · 2022Article
- Computational normal mode analysis accurately replicates the activity and specificity profiles of CRISPR-Cas9 and high-fidelity variants.Computational and structural biotechnology journal · 2022Article
- Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.The journal of physical chemistry. B · 2021Article
- Effective Drug Concentration and Selectivity Depends on Fraction of Primitive Cells.International journal of molecular sciences · 2021Article
- Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates.Nature communications · 2021Article
- Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.Biomolecules · 2020Article
- Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids.Nucleic acids research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic acid structure, including the assignment of base pairs and the determination of rigid-body parameters that describe the structure and, in Protocol 3, by a description of the reconstruction of an atomic model of a structure from its rigid-body parameters. The most recent version of 3DNA, version 2.1, has new features for the analysis and manipulation of ensembles of structures, such as those deduced from nuclear magnetic resonance (NMR) measurements and molecular dynamic (MD) simulations; these features are presented in Protocols 4 and 5. In addition to the 3DNA stand-alone software package, the w3DNA web server, located at http://w3dna.rutgers.edu, provides a user-friendly interface to selected features of the software. Protocol 6 demonstrates a novel feature of the site for building models of long DNA molecules decorated with bound proteins at user-specified locations.
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.