ArticlePloS one2014
Vfold: a web server for RNA structure and folding thermodynamics prediction.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.bioRxiv : the preprint server for biology · 2026Article
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- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Generative AI for computational chemistry: A roadmap to predicting emergent phenomena.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- siRNA Interaction and Transfection Properties of Polycationic Phosphorus Dendrimers.Biomacromolecules · 2025Article
- Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.bioRxiv : the preprint server for biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells.ACS nano · 2025Review
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.PLoS computational biology · 2024Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.Biophysical journal · 2024Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
backgroundThe ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies.
resultsThe Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.
conclusionsThe Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".
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