ArticleJournal of chemical theory and computation2018
IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Conjugation of hydrophobic drugs to motile pRNA 4WJ nanoparticles for spontaneous tumor targeting and undetectable toxicity.Nature protocols · 2026Review
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.Current opinion in structural biology · 2025Review
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.PLoS computational biology · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
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Authors and funding
2 authors.
Funding
Abstract
Coarse-grained RNA folding models promise great potential for RNA structure prediction. A key component in a coarse-grained folding model is the force field. One of the challenges in the coarse-grained force field calculation is how to treat the correlation between the different degrees of freedoms. Here, we describe a new approach (IsRNA) to extract the correlated energy functions from the known structures. Through iterative molecular dynamics simulations, we build the correlation effects into the reference states, from which we extract the energy functions. The validity of IsRNA is supported by the close agreement between the simulated Boltzmann-like probability distributions for all the structure parameters and those observed from the experimentally determined structures. The correlated energy functions derived here may provide a new tool for RNA 3D structure prediction.
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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.