ArticleNucleic acids research2009
Finding 3D motifs in ribosomal RNA structures.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- GINClus: RNA structural motif clustering using graph isomorphism network.NAR genomics and bioinformatics · 2025Article
- RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.Bioinformatics (Oxford, England) · 2023Article
- On the predictibility of A-minor motifs from their local contexts.RNA biology · 2022Article
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- Polarizable force field for RNA based on the classical drude oscillator.Journal of computational chemistry · 2018Article
- Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.Nucleic acids research · 2018Article
- Composing RNA Nanostructures from a Syntax of RNA Structural Modules.Nano letters · 2017Article
- RNAMotifScanX: a graph alignment approach for RNA structural motif identification.RNA (New York, N.Y.) · 2015Article
- The role of nucleobase interactions in RNA structure and dynamics.Nucleic acids research · 2014Article
- An algebraic view of bacterial genome evolution.Journal of mathematical biology · 2014Article
- RNA structural motif recognition based on least-squares distance.RNA (New York, N.Y.) · 2013Article
- SETTER: web server for RNA structure comparison.Nucleic acids research · 2012Article
- Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.Journal of computational chemistry · 2011Article
- Sequence-based identification of 3D structural modules in RNA with RMDetect.Nature methods · 2011Article
- RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.Nucleic acids research · 2010Article
- FRASS: the web-server for RNA structural comparison.BMC bioinformatics · 2010Article
- Arrangement of 3D structural motifs in ribosomal RNA.Nucleic acids research · 2010Article
- Analysis of interactions between ribosomal proteins and RNA structural motifs.BMC bioinformatics · 2010Article
- Mathematical biology modules based on modern molecular biology and modern discrete mathematics.CBE life sciences education · 2010Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.
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