ArticleNucleic acids research2015
STAR3D: a stack-based RNA 3D structural alignment tool.
Article in Nucleic acids research, 2015. 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.
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.Nucleic acids research · 2024Article
- RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.NAR genomics and bioinformatics · 2023Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nature methods · 2022Article
- Dissecting and predicting different types of binding sites in nucleic acids based on structural information.Briefings in bioinformatics · 2022Article
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.Bioinformatics (Oxford, England) · 2019Article
- RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.BMC genomics · 2019Article
- CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.Nucleic acids research · 2017Article
- WebSTAR3D: a web server for RNA 3D structural alignment.Bioinformatics (Oxford, England) · 2016Article
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2 authors.
Funding
Abstract
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time.
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