ArticleNucleic acids research2021
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Tools For Building Artificial Biological Nanostructures.ACS nano · 2026Review
- Optimising DNA origami assembly by reducing off-target interactions.Nature communications · 2026Article
- In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing.bioRxiv : the preprint server for biology · 2026Article
- Molecular computation at equilibrium via programmable entropy.Science advances · 2026Article
- Molecular systems engineering of synthetic cells.Nature chemistry · 2026Review
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Acoustically seeded fabrication of a DNA tesseract into a conductive wire.Nucleic acids research · 2025Article
- Nick-and-Digest Strategy for Programmable Circular ssDNA Production and Scalable DNA Origami Assembly.JACS Au · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Switchable RNA motifs for dynamic transcriptional control of RNA condensates.Nucleic acids research · 2025Article
- Realizing mechanical frustration at the nanoscale using DNA origami.Nature communications · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Cancer Spheroid Model.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Melting Profile of DNA in Crowded Solution: Model-Based Study.International journal of molecular sciences · 2025Article
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- Enhancing the speed of DNA walkers through soft confinement.Scientific reports · 2025Article
- Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output.Nature nanotechnology · 2025Article
- Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells.Discover nano · 2025Article
- Crystalline Assemblies of DNA Nanostructures and Their Functional Properties.Angewandte Chemie (International ed. in English) · 2025Review
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5 authors.
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Abstract
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org.
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