ArticleBioinformatics (Oxford, England)2019
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- DRfold2 is a deep learning-based tool that enables efficient and accurate RNA structure prediction.PLoS biology · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps.Communications biology · 2026Article
- DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure.Briefings in bioinformatics · 2026Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Updates to the CASP Infrastructure in 2024.Proteins · 2026Article
- Template-based RNA structure prediction advanced through a blind code competition.bioRxiv : the preprint server for biology · 2025Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
1 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
motivationComparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search.
resultsWe developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION: https://zhanglab.ccmb.med.umich.edu/RNA-align/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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