ArticleBiophysical journal2017
Martini Coarse-Grained Force Field: Extension to RNA.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 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
62 citing papers in PubMed, 262 citations in OpenAlex.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Enhanced Condensation of RNA Repeats Induced by Terahertz Oscillatory Fields.Molecules (Basel, Switzerland) · 2026Article
- Coarse-Grained Model of the Sodium Dodecyl Sulfate Anionic Surfactant Based on the MDPD-Martini Force Field.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- 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
- Caffeic acid suppresses cyclin D1 expression by directly binding to ribosomal protein S5 in colorectal cancer cells.Scientific reports · 2026Article
- Coarse-grained RNA model for the Martini 3 force field.Biophysical journal · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Structuring of lipid nanoparticle mRNA formulations at acidic and neutral pH: X-ray scattering and molecular dynamics studies.Molecular therapy. Methods & clinical development · 2025Article
- Simulation Insights into the Assembly of Polyplexes for RNA Delivery.Biomacromolecules · 2025Article
- Article
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior.ACS central science · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Chemically Informed Coarse-Graining of Electrostatic Forces in Charge-Rich Biomolecular Condensates.ACS central science · 2025Article
- Martini compatible coarse-grained model of polyethylenimine for pulmonary gene delivery.Scientific reports · 2025Article
- Review
- Ionizable Cationic Lipids and Helper Lipids Synergistically Contribute to RNA Packing and Protection in Lipid-Based Nanomaterials.The journal of physical chemistry. B · 2024Article
- Article
- Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation.The journal of physical chemistry. B · 2024Article
2 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
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA has an important role not only as the messenger of genetic information but also as a regulator of gene expression. Given its central role in cell biology, there is significant interest in studying the structural and dynamic behavior of RNA in relation to other biomolecules. Coarse-grain molecular dynamics simulations are a key tool to that end. Here, we have extended the coarse-grain Martini force field to include RNA after our recent extension to DNA. In the same way DNA was modeled, the tertiary structure of RNA is constrained using an elastic network. This model, therefore, is not designed for applications involving RNA folding but rather offers a stable RNA structure for studying RNA interactions with other (bio)molecules. The RNA model is compatible with all other Martini models and opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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.