ArticlePLoS computational biology2025
3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Understanding the three-dimensional (3D) structure and stability of DNA is essential for elucidating its biological functions and advancing structure-based drug design. Here, we present an improved coarse-grained (CG) model for ab initio prediction of DNA folding, integrating a refined electrostatic potential, replica-exchange Monte Carlo simulations, and weighted histogram analysis. The model accurately predicts the 3D structures of DNA with multi-way junctions (e.g., achieving a mean RMSD of ~8.8 Å for top-ranked structures across four DNAs with three- or four-way junctions) from sequence, outperforming existing fragment-assembly and AI-based approaches. The model also reproduces the thermal stability of junctions across diverse sequences and lengths, with predicted melting temperatures deviating by less than 5 °C from experimental values, under both monovalent (Na⁺) and divalent (Mg2⁺) ionic conditions. Furthermore, analysis of the thermal unfolding pathways reveals that the overall stability of multi-way junctions is primarily determined by the relative free energies of key intermediate states. These results provide a robust framework for predicting complex DNA architectures and offer mechanistic insights into DNA folding and function.
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.