ArticleJournal of structural biology2019
VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.
Article in Journal of structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- 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
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops.Journal of chemical theory and computation · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- RNA 3D Structure Comparison Using RNA-Puzzles Toolkit.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field.ACS nano · 2021Article
- Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.The journal of physical chemistry. B · 2021Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- IsRNA1:Journal of chemical theory and computation · 2021Article
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.Nature communications · 2020Article
- 3dRNA: Building RNA 3D structure with improved template library.Computational and structural biotechnology journal · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA three-dimensional (3D) structures are critical for RNA cellular functions. However, structure prediction for large and complex RNAs remains a challenge, which hampers our understanding of RNA structure-function relationship. We here report a new web server, the VfoldLA server (http://rna.physics.missouri.edu/vfoldLA), for the prediction of RNA 3D structures from nucleotide sequences and base-pair information (2D structure). This server is based on the recently developed VfoldLA, a model that classifies the single-stranded loops (junctions) into four different types and according to the loop-helix connections, assembles RNA 3D structures from the loop/junction templates. The VfoldLA web server provides a user-friendly online interface for a fully automated prediction of putative 3D RNA structures using VfoldLA. With a single-RNA or RNA-RNA complex sequence and 2D structure as input, the server generates structure(s) with the JSmol visualization along with a downloadable PDB file. The output result may serve as useful scaffolds for future structure refinement studies.
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Registered trials
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