ArticleMethods in molecular biology (Clifton, N.J.)2023
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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Who cites it
12 citing papers in PubMed.
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Cancer Spheroid Model.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport.Nature communications · 2024Article
- A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower.Nature nanotechnology · 2024Article
- Prospects and challenges of dynamic DNA nanostructures in biomedical applications.Bone research · 2022Review
- Planar 2D wireframe DNA origami.Science advances · 2022Article
- Unified Nanotechnology Format: One Way to Store Them All.Molecules (Basel, Switzerland) · 2021Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami.Nucleic acids research · 2021Article
- OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures.Nucleic acids research · 2021Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
Indexed as
Identifiers
37166713What 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.