ArticleNucleic acids research2013
RNAlyzer--novel approach for quality analysis of RNA structural models.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures.Biophysical journal · 2024Article
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.International journal of molecular sciences · 2022Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
- RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.BMC bioinformatics · 2018Article
- LCS-TA to identify similar fragments in RNA 3D structures.BMC bioinformatics · 2017Article
- RNAssess--a web server for quality assessment of RNA 3D structures.Nucleic acids research · 2015Article
- The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.Nucleic acids research · 2014Article
- RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.Nucleic acids research · 2014Article
- Genetic and pharmacological strategies to refunctionalize the von Hippel Lindau R167Q mutant protein.Cancer research · 2014Article
- The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures.Nucleic acids research · 2014Article
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Authors and funding
8 authors.
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Abstract
The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development of computational methods supporting exploration of these data. Contemporary functional analysis of RNA molecules, such as ribozymes or riboswitches, covers various issues, among which tertiary structure modeling becomes more and more important. A growing number of tools to model and predict RNA structure calls for an evaluation of these tools and the quality of outcomes their produce. Thus, the development of reliable methods designed to meet this need is relevant in the context of RNA tertiary structure analysis and can highly influence the quality and usefulness of RNA tertiary structure prediction in the nearest future. Here, we present RNAlyzer-a computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models. Our approach is based on the idea of local neighborhood, defined as a set of atoms included in the sphere centered around a user-defined atom. A unique feature of the RNAlyzer is the simultaneous visualization of the model-reference structure distance at different levels of detail, from the individual residues to the entire molecules.
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