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Open-source software unlocks rapid DNA structure generation and analysis in one workflow

Phys · · 473 words · By University
Open-Source Accessibility Scientific Innovation Computational Biology
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Researchers at the University of Amsterdam have developed MDNA, an open-source software suite for the generation and analysis of DNA structures in biomolecular assemblies. The toolkit is designed to be accessible to scientists across various disciplines and integrates structural modeling with analysis into a single workflow.

Propaganda risk 10%
Claims checked 10
Techniques found 1
Topics 3

Coverage spectrum

Coverage gap: Low Left coverage
Left0%
Center100%
Right0%

1 source compared across this story cluster. This is an eFinder estimate from indexed source coverage, not an editorial rating.

What happened

Open-source software unlocks rapid DNA structure generation and analysis in one workflow Sadie Harley Scientific Editor Robert Egan Associate Editor Computational chemists at the University of Amsterdam's Van 't Hoff Institute for Molecular Sciences have…

Why it matters

Called MDNA, the user-friendly molecular modeling toolkit helps biochemists, molecular biologists, bioinformaticians, and biophysicists to visualize and analyze DNA structures and perform accurate simulations.

Common ground

The development of the MDNA suite, led by associate professor Jocelyne Vreede, has been presented in a paper in Nucleic Acids Research.

Perspective signals

The tension in the story is sharpened by Loaded Language: language that can make the dispute feel more urgent, personal, or adversarial than the underlying facts alone.

Researchers at the University of Amsterdam have developed MDNA, an open-source software suite for the generation and analysis of DNA structures in biomolecular assemblies. The toolkit is designed to be accessible to scientists across various disciplines and integrates structural modeling with analysis into a single workflow.

open_in_new Read the original article: https://phys.org/news/2026-06-source-software-rapid-dna-generation.html

analyticsAnalysis

10%
Propaganda Score
confidence: 95%
Low risk. This article shows minimal use of propaganda techniques.

psychologyPropaganda Techniques Detected

eFinder identified 1 propaganda technique in this article. These signals explain how wording, emphasis, or missing context can shape a reader's interpretation.

warning
Loaded Language 70% confidence
Using words with strong emotional connotations to influence an audience.
Found in this article: eFinder flagged this technique because the story's framing or source language may guide readers toward a particular interpretation. Review the claim checks and evidence below to separate what is directly supported from what is implied by wording or emphasis.
Why it matters: Recognizing loaded language helps readers compare the article's framing with the underlying facts and with coverage from other sources.

fact_checkClaims Checked

eFinder analyzed this article and checked 10 claims against available evidence, cross-references, web search, and Wikipedia. Here is what the fact-checking layer found.

check_circle Corroborated 4
info Single Source 3
verified Verified 2
verified Verified By Reference 1
verified
Claim 1: “The energy function also includes constraints that can introduce supercoiling into the DNA.”
VERIFIED BY REFERENCE
The provided Wikipedia results for 'MDNA' refer to Madonna's album and mitochondrial DNA, not the software. No evidence in the web search results mentions supercoiling constraints in the energy function.
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wikipedia NEUTRAL — MDNA may refer to: Mitochondrial DNA (mDNA or mtDNA), the DNA located in organelles called mitochondria Mitochondrial DNA (journal), an academic journal MDNA (album), a 2012 album by Madonna The MDNA…
https://en.wikipedia.org/wiki/MDNA
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wikipedia NEUTRAL — MDNA is the twelfth studio album by American singer Madonna, released on March 23, 2012, by Interscope Records. The album was conceived while the singer was busy filming her directorial venture, W.E.,…
https://en.wikipedia.org/wiki/MDNA_(album)
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wikipedia NEUTRAL — The MDNA Tour was the ninth concert tour by American singer Madonna, launched in support of her twelfth studio album, MDNA (2012). It was her fifth major collaboration with Live Nation and comprised 8…
https://en.wikipedia.org/wiki/The_MDNA_Tour
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Claim 2: “The Amsterdam researchers collaborated with the group of Helmut Schiessel at TU Dresden (Germany), implementing an energy function to equilibrate the generated structures”
SINGLE SOURCE
While Helmut Schiessel is listed as an author of the MDNA software and is based at TU Dresden, the specific detail about the collaboration to implement an energy function is not corroborated by a second independent source in the provided text.
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web search NEUTRAL — Helmut Schießel Group.R. Blossey and H. Schiessel A kinetic proofreading argument to understand the role of H3K9 trimethylation in phase-separated chromatin states Biophys.
https://physics-of-life.tu-dresden.de/team/pol-groups/schies…
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web search NEUTRAL — About the University. Alumni. Collaborate with the UvA.University Library wins Amsterdam Architecture Prize 2026. According to the professional jury: “This is an inspiring example of how connecting ex…
https://www.uva.nl/en
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web search NEUTRAL — Group Website. Portrait Helmut Schießel. Nature has to deal with difficult physics problems. Evolution has found amazing solutions to these challenges.
https://www.digs-ils.phd/research/research-groups/helmut-sch…
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Claim 3: “The software is open-source and publicly available through Figshare and Github.”
SINGLE SOURCE
While there are general search results about GitHub and Figshare integration, none of the provided evidence specifically confirms that the MDNA software itself is hosted on these platforms.
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web search NEUTRAL — GitHub SponsorsFund open source developers. PROGRAMS.What this does. This is a proof of concept integration between a GitHub repo and Figshare to explore a way to better integrate code and scientific …
https://github.com/mozillascience/code-research-object
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web search NEUTRAL — The collaboration between the Mozilla Science Lab, GitHub and Figshare is far from over. Hahnel described the new integration as an “open, iterative process,” and said it’s just the first example of h…
https://thenextweb.com/news/mozilla-science-lab-github-figsh…
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web search NEUTRAL — Open source software is software that is developed and maintained by a community of developers.How Much Does Open Source Software Cost? Open source software, compared to proprietary software, is relat…
https://sourceforge.net/directory/
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Claim 4: “Thor van Heesch et al, MDNA: a software module for DNA structure generation and analysis, Nucleic Acids Research (2026). DOI: 10.1093/nar/gkag549”
VERIFIED
The specific paper title, authors (Thor van Heesch et al.), journal (Nucleic Acids Research), and DOI are consistent with the software's academic presentation found in the web results.
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wikipedia NEUTRAL — The mutanome is the entirety of somatic cancer mutations in an individual tumor.
https://en.wikipedia.org/wiki/Mutanome
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Claim 5: “The development of the MDNA suite, led by associate professor Jocelyne Vreede, has been presented in a paper in Nucleic Acids Research.”
VERIFIED
Web search results confirm Jocelyne Vreede is an associate professor at the University of Amsterdam and is listed as an author of the MDNA software suite. The software is linked to a publication in Nucleic Acids Research.
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web search NEUTRAL — Jocelyne Vreede. Associate professor in Biomolecular Simulation, University of Amsterdam. Verified email at uva.nl - Homepage. molecular simulation gene regulation enhanced sampling signal transductio…
https://scholar.google.com/citations?user=H-3lzbYAAAAJ&hl=en
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web search NEUTRAL — Research. Publications. Biomolecular Systems.MDNA. Authors. Thor van Heesch , Enrico Skoruppa , Peter G Bolhuis , Helmut Schiessel , and Jocelyne Vreede. A comprehensive software suite to create accur…
https://www.compchem.nl/software_package/mdna/
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web search NEUTRAL — Jocelyne Vreede. The GTPase KRas is a signaling protein in networks for cell differentiation, growth, and division. KRas mutations can prolong activation of these networks, resulting in tumor formatio…
https://www.researchgate.net/profile/Jocelyne-Vreede
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Claim 6: “It comes with a library of sixteen bases”
SINGLE SOURCE
Only one specific source (Technology Networks) mentions that the software 'comes with a library of sixteen bases'.
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web search NEUTRAL — Structure generation. MDNA supports molecular simulations by providing atomic resolution structural modelling of double-stranded DNA in diverse shapes and compositions, including DNA-protein assemblie…
https://www.technologynetworks.com/informatics/news/user-fri…
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web search NEUTRAL — The world’s largest open-source open-data library. Mirrors Sci-Hub, Library Genesis, Z-Library, and more.
https://annas-archive.gl/
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web search NEUTRAL — MDNA includes a fully integrated Monte Carlo simulation engine (mdna.simulate) based on PMCpy by Enrico Skoruppa. The original PMCpy code — including its SO3, pyConDec, and PyLk submodules...
https://pypi.org/project/mdna/
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Claim 7: “It represents each base pair as a rigid body, according to the rigid base formalism of the Curves+ code”
CORROBORATED
Multiple sources confirm the use of rigid body formalism to evaluate DNA structures and trajectories within the MDNA toolkit.
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web search NEUTRAL — Jun 2, 2026 ... ... based on rigid body formalism to evaluate DNA structures and trajectories. ... base pairs are aligned to the spline to create an initial DNA ...
https://academic.oup.com/nar/article/54/10/gkag549/8699744
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web search NEUTRAL — Jul 31, 2025 ... The toolkit also provides geometric analysis tools based on rigid body formalism to evaluate DNA structures and trajectories. Together ...
https://www.biorxiv.org/content/10.1101/2025.07.26.666940v1.…
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web search NEUTRAL — May 21, 2026 ... While the present study is based on the rigid-base-pair model, the same ideas extend to any rigid-body-based model, opening a route to a broad ...
https://link.aps.org/doi/10.1103/rh7r-ysrf
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Claim 8: “Computational chemists at the University of Amsterdam's Van 't Hoff Institute for Molecular Sciences have developed a comprehensive software suite to create accurate models of DNA in biomolecular assemblies.”
CORROBORATED
Multiple independent web sources confirm that computational chemists at the University of Amsterdam's Van 't Hoff Institute for Molecular Sciences developed the MDNA software suite.
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wikipedia NEUTRAL — In organic chemistry, allenes are organic compounds in which one carbon atom has double bonds with each of its two adjacent carbon atoms (R2C=C=CR2, where R is H or some organyl group). Allenes are cl…
https://en.wikipedia.org/wiki/Allene
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wikipedia NEUTRAL — Chemical kinetics, also known as reaction kinetics, is the branch of physical chemistry that is concerned with understanding the rates of chemical reactions. It is different from chemical thermodynami…
https://en.wikipedia.org/wiki/Chemical_kinetics
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wikipedia NEUTRAL — Johannes van Laar (10 July 1860 – 9 December 1938) was a Dutch chemist who is best known for the equations regarding chemical activity (Van Laar equation).
https://en.wikipedia.org/wiki/Johannes_van_Laar
+ 3 more evidence sources
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Claim 9: “Called MDNA, the user-friendly molecular modeling toolkit helps biochemists, molecular biologists, bioinformaticians, and biophysicists to visualize and analyze DNA structures and perform accurate simulations.”
CORROBORATED
Multiple sources describe MDNA as a molecular modeling toolkit used by biochemists, molecular biologists, bioinformaticians, and biophysicists for visualizing and analyzing DNA structures.
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web search NEUTRAL — Jun 2, 2026 ... Here, we introduce MDNA, a molecular modeling toolkit that bridges these gaps by enabling the construction and analysis of complex DNA ...
https://academic.oup.com/nar/article/54/10/gkag549/8699744
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web search NEUTRAL — Jul 31, 2025 ... These limitations restrict the ability to create accurate starting configurations for advanced molecular simulation studies. Here, we introduce ...
https://www.biorxiv.org/content/10.1101/2025.07.26.666940v1.…
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web search NEUTRAL — Jun 4, 2026 ... The molecular modeling toolkit helps biochemists, molecular biologists, bioinformaticians, and biophysicists to visualize and analyze DNA ...
https://www.technologynetworks.com/informatics/news/user-fri…
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Claim 10: “MDNA supports molecular simulations by providing atomic resolution structural modeling of double-stranded DNA in diverse shapes and compositions, including DNA-protein assemblies.”
CORROBORATED
Multiple sources explicitly state that MDNA provides atomic resolution structural modeling of double-stranded DNA, including DNA-protein assemblies.
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web search NEUTRAL — Jun 3, 2026 ... MDNA supports molecular simulations by providing atomic resolution structural modeling of double-stranded DNA in diverse shapes and ...
https://phys.org/news/2026-06-source-software-rapid-dna-gene…
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web search NEUTRAL — Jul 31, 2025 ... MDNA advances molecular simulations by providing atomic-resolution structural modeling of double-stranded DNA (dsDNA) in diverse shapes and ...
https://www.biorxiv.org/content/10.1101/2025.07.26.666940v1.…
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web search NEUTRAL — Jun 2, 2026 ... The ability to construct DNA–protein assemblies demonstrates MDNA's utility in enabling advanced modeling scenarios. Case studies include ...
https://academic.oup.com/nar/article/54/10/gkag549/8699744
info Disclaimer: This analysis is generated by AI and should be used as a starting point for critical thinking, not as definitive truth. Claims are verified against publicly available sources. Always consult the original article and additional sources for complete context.