ArticleNucleic acids research2017
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- AI foundation models for RNA biology.RNA biology · 2026Review
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.International journal of molecular sciences · 2026Article
- Machine learning for RNA secondary structure prediction: a review of current methods and challenges.RNA (New York, N.Y.) · 2026Review
- Retentive Network promotes efficient RNA language modeling of long sequences.Communications biology · 2026Article
- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.Briefings in bioinformatics · 2026Article
- Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction.Science advances · 2026Article
- NTFold: Structure-Sensing Nucleotide Attention Learning for RNA Secondary Structure Prediction.Sensors (Basel, Switzerland) · 2026Article
- ERNIE-RNA: an RNA language model with structure-enhanced representations.Nature communications · 2025Article
- Improving RNA Secondary Structure Prediction Through Expanded Training Data.bioRxiv : the preprint server for biology · 2025Article
- AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.bioRxiv : the preprint server for biology · 2025Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- Deep generalizable prediction of RNA secondary structure via base pair motif energy.Nature communications · 2025Article
- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- Control ofmBio · 2025Article
- Comprehensive benchmarking of large language models for RNA secondary structure prediction.Briefings in bioinformatics · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- RNA secondary structure prediction by conducting multi-class classifications.Computational and structural biotechnology journal · 2025Article
- A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.PloS one · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
19 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions between all pairs of input sequences are iteratively estimated in TurboFold II by incorporating information from both the sequence identity and secondary structures. A multiple sequence alignment is obtained from these probabilities by using a probabilistic consistency transformation and a hierarchically computed guide tree. To assess TurboFold II, its sequence alignment and structure predictions were compared with leading tools, including methods that focus on alignment alone and methods that provide both alignment and structure prediction. TurboFold II has comparable alignment accuracy with MAFFT and higher accuracy than other tools. TurboFold II also has comparable structure prediction accuracy as the original TurboFold algorithm, which is one of the most accurate methods. TurboFold II is part of the RNAstructure software package, which is freely available for download at http://rna.urmc.rochester.edu under a GPL license.
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