ArticleNucleic acids research2008
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- ERNIE-RNA: an RNA language model with structure-enhanced representations.Nature communications · 2025Article
- Graph neural network and diffusion model for modeling RNA interatomic interactions.Bioinformatics (Oxford, England) · 2025Article
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.bioRxiv : the preprint server for biology · 2025Article
- Deep generalizable prediction of RNA secondary structure via base pair motif energy.Nature communications · 2025Article
- Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.Nucleic acids research · 2024Article
- Evolutionary Structure Conservation and Covariance Scores.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction.Nature communications · 2023Article
- ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring.Bioinformatics (Oxford, England) · 2023Article
- RNA inter-nucleotide 3D closeness prediction by deep residual neural networks.Bioinformatics (Oxford, England) · 2021Article
- RNA 3D structure prediction guided by independent folding of homologous sequences.BMC bioinformatics · 2019Article
- Article
- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
- Translational co-regulation of a ligand and inhibitor by a conserved RNA element.Nucleic acids research · 2018Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single optimization problem. Here, we present a model that formally integrates both the energy-based and evolution-based approaches to predict the folding of multiple aligned RNA sequences. We have implemented an extended version of Pfold that identifies base pairs that have high probabilities of being conserved and of being energetically favorable. The consensus structure is predicted using a maximum expected accuracy scoring scheme to smoothen the effect of incorrectly predicted base pairs. Parameter tuning revealed that the probability of base pairing has a higher impact on the RNA structure prediction than the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested on a set of 46 well-curated Rfam families and its performance compared favorably to that of Pfold and RNAalifold.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.