ArticleAlgorithms for molecular biology : AMB2016
RNA folding with hard and soft constraints.
Article in Algorithms for molecular biology : AMB, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- DeCoRE: A computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA sequencing.Science advances · 2026Article
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- Refined Design and Liquid-Phase Assembly of GalNAc-siRNA Conjugates: Comparative Efficiency Validation in PCSK9 Targeting.Molecules (Basel, Switzerland) · 2026Article
- Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth.Nature communications · 2025Article
- DRP-PSM: Multi-Level Feature Integration Reveals Hierarchical Contributions to Pathogenic Synonymous Mutation Prediction.ACS omega · 2025Article
- Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells.EMBO reports · 2024Article
- Application of plasmid stabilization systems for heterologous protein expression in Escherichia coli.Molecular biology reports · 2024Article
- DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning.Journal of chemical information and modeling · 2024Article
- Accumulation Dynamics of Defective Genomes during Experimental Evolution of Two Betacoronaviruses.Viruses · 2024Article
- SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.Algorithms for molecular biology : AMB · 2024Article
- Multiple sequence alignment-based RNA language model and its application to structural inference.Nucleic acids research · 2024Article
- RNAi-Mediated Silencing in the Insect Cell-Baculovirus Expression System.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Limits of experimental evidence in RNA secondary structure prediction.Frontiers in bioinformatics · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Modified RNAs and predictions with the ViennaRNA Package.Bioinformatics (Oxford, England) · 2023Article
- Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs.Nucleic acids research · 2023Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.Bioinformatics (Oxford, England) · 2023Article
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3 authors.
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Abstract
backgroundA large class of RNA secondary structure prediction programs uses an elaborate energy model grounded in extensive thermodynamic measurements and exact dynamic programming algorithms. External experimental evidence can be in principle be incorporated by means of hard constraints that restrict the search space or by means of soft constraints that distort the energy model. In particular recent advances in coupling chemical and enzymatic probing with sequencing techniques but also comparative approaches provide an increasing amount of experimental data to be combined with secondary structure prediction.
resultsResponding to the increasing needs for a versatile and user-friendly inclusion of external evidence into diverse flavors of RNA secondary structure prediction tools we implemented a generic layer of constraint handling into the ViennaRNA Package. It makes explicit use of the conceptual separation of the "folding grammar" defining the search space and the actual energy evaluation, which allows constraints to be interleaved in a natural way between recursion steps and evaluation of the standard energy function.
conclusionsThe extension of the ViennaRNA Package provides a generic way to include diverse types of constraints into RNA folding algorithms. The computational overhead incurred is negligible in practice. A wide variety of application scenarios can be accommodated by the new framework, including the incorporation of structure probing data, non-standard base pairs and chemical modifications, as well as structure-dependent ligand binding.
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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.