ArticleScientific reports2017
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- The Unpaved Road of Non-Coding RNA Structure-Function Relationships: Current Knowledge, Available Methodologies, and Future Trends.Non-coding RNA · 2025Review
- Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy.Frontiers in cellular and infection microbiology · 2024Review
- Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations.International journal of molecular sciences · 2023Article
- Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions.Biophysical journal · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- A Bayes-inspired theory for optimally building an efficient coarse-grained folding force field.Communications in information and systems · 2021Article
- In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- What is the best reference state for building statistical potentials in RNA 3D structure evaluation?RNA (New York, N.Y.) · 2019Article
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Bayesian selection for coarse-grained models of liquid water.Scientific reports · 2019Article
- Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.Journal of chemical theory and computation · 2018Article
- Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.Biophysical journal · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R
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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.