ArticleJournal of biomolecular structure & dynamics2008
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.
Article in Journal of biomolecular structure & dynamics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 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
88 citing papers in PubMed, 156 citations in OpenAlex.
- A Study on the Mechanism of Acetyl Tributyl Citrate-Induced Infertility Toxicity and the Protective Action of Icariin Based on Network Toxicology, Network Pharmacology, Molecular-Docking Technology and Molecular Dynamics Simulation.International journal of molecular sciences · 2026Article
- Small-Angle X-ray Scattering (SAXS) Combined with SAXS-Driven Molecular Dynamics for Structural Analysis of Multistranded RNA Assemblies.ACS applied materials & interfaces · 2024Article
- Application and prospects of nucleic acid nanomaterials in tumor therapy.RSC advances · 2023Review
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis.Acta pharmaceutica Sinica. B · 2023Review
- Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures.Small (Weinheim an der Bergstrasse, Germany) · 2022Article
- Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.PloS one · 2022Article
- PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region.RNA biology · 2021Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA.International journal of molecular sciences · 2021Article
- Modeling and Predicting RNA Three-Dimensional Structures.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers.PLoS computational biology · 2021Article
- Improved Nucleic Acid Therapy with Advanced Nanoscale Biotechnology.Molecular therapy. Nucleic acids · 2020Review
- Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA (New York, N.Y.) · 2019Article
- ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow.Journal of computer-aided molecular design · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- RNA structure interactions and ribonucleoprotein processes of the influenza A virus.Briefings in functional genomics · 2018Review
28 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
3 authors at 2 institutions in 1 country.
Funding
Abstract
Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.
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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.