ArticleBMC bioinformatics2010
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Dockground: The Resource Expands to Protein-RNA Interactome.Journal of molecular biology · 2025Article
- Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.Nature communications · 2024Article
- ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.Nucleic acids research · 2024Article
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
- Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants.Current genomics · 2023Article
- RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.NAR genomics and bioinformatics · 2023Article
- The difficulty of aligning intrinsically disordered protein sequences as assessed by conservation and phylogeny.PloS one · 2023Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.BMC bioinformatics · 2021Article
- RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing.RNA (New York, N.Y.) · 2020Article
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- Predicting functional long non-coding RNAs validated by low throughput experiments.RNA biology · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Conserved RNA structures in the intergenic regions of ambisense viruses.Scientific reports · 2017Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
- Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.RNA (New York, N.Y.) · 2017Article
- Progress and Current Challenges in Modeling Large RNAs.Journal of molecular biology · 2016Review
- SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.Nucleic acids research · 2014Article
- Solving nucleic acid structures by molecular replacement: examples from group II intron studies.Acta crystallographica. Section D, Biological crystallography · 2013Review
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2 authors.
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Abstract
backgroundIn recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA.
resultsHere we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. DISCUSSION: The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.
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