ArticleNucleic acids research2017
Topology independent comparison of RNA 3D structures using the CLICK algorithm.
Article in Nucleic acids research, 2017. 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.
- Lethal effects of ivermectin structures on malaria vectors and in silico analysis of interactions with their glutamate-gated chloride ion channels.Scientific reports · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks.Non-coding RNA · 2025Article
- ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.Nucleic acids research · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nature methods · 2022Article
- Predicting and designing therapeutics against the Nipah virus.PLoS neglected tropical diseases · 2019Article
- RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.Bioinformatics (Oxford, England) · 2019Article
- AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models.Nucleic acids research · 2019Article
- Article
- Structural and Functional Diversity of Plant Virus 3'-Cap-Independent Translation Enhancers (3'-CITEs).Frontiers in plant science · 2017Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting. In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA-protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html.
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