ArticleNucleic acids research2024
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.
Article in Nucleic acids research, 2024. 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.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Article
- Single-round evolution of RNA aptamers with GRAPE-LM.Nature biotechnology · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Functions and applications of enzymes in nucleic acid nanotechnology.Journal of nanobiotechnology · 2025Review
- Enhancing Local Functional Structure Features to Improve Drug-Target Interaction Prediction.International journal of molecular sciences · 2025Article
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
- Review
- Article
- AlphaFold3: An Overview of Applications and Performance Insights.International journal of molecular sciences · 2025Review
- Advances and Mechanisms of RNA-Ligand Interaction Predictions.Life (Basel, Switzerland) · 2025Review
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- Assessing interface accuracy in macromolecular complexes.PloS one · 2025Article
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.Computational and structural biotechnology journal · 2025Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods-DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web-based tools due to intellectual property concerns. We focus on reproducing the RNA structure existing in RNA-small molecule complexes, particularly on the ability to model ligand binding sites. Using a comprehensive set of RNA structures from the PDB, which includes diverse structural elements, we found that machine learning (ML)-based methods effectively predict global RNA folds but are less accurate with local interactions. Conversely, non-ML-based methods demonstrate higher precision in modeling intramolecular interactions, particularly with secondary structure restraints. Importantly, ligand-binding site accuracy can remain sufficiently high for practical use, even if the overall model quality is not optimal. With the recent release of AlphaFold 3, we included this advanced method in our tests. Benchmark subsets containing new structures, not used in the training of the tested ML methods, show that AlphaFold 3's performance was comparable to other ML-based methods, albeit with some challenges in accurately modeling ligand binding sites. This study underscores the importance of enhancing binding site prediction accuracy and the challenges in modeling RNA-ligand interactions accurately.
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Registered trials
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