ArticleBioinformatics (Oxford, England)2010
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 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
- DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures.Computational and structural biotechnology journal · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs.Nucleic acids research · 2021Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.BMC genomics · 2019Article
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.Nucleic acids research · 2017Article
- CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.Nucleic acids research · 2017Article
- RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.BMC bioinformatics · 2017Article
- Topology independent comparison of RNA 3D structures using the CLICK algorithm.Nucleic acids research · 2017Article
- WebSTAR3D: a web server for RNA 3D structural alignment.Bioinformatics (Oxford, England) · 2016Article
- A deep learning framework for modeling structural features of RNA-binding protein targets.Nucleic acids research · 2016Article
- Article
- DETECTING CONFORMATIONAL DIFFERENCES BETWEEN RNA 3D STRUCTURES.JP journal of biostatistics · 2015Article
- STAR3D: a stack-based RNA 3D structural alignment tool.Nucleic acids research · 2015Article
- MultiSETTER: web server for multiple RNA structure comparison.BMC bioinformatics · 2015Article
- RNAMotifScanX: a graph alignment approach for RNA structural motif identification.RNA (New York, N.Y.) · 2015Article
- Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.BMC bioinformatics · 2015Article
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3 authors.
Funding
Abstract
motivationComparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the 'local alignment' graph.
resultsThe algorithm is implemented in a program suite and web server called 'R3D Align'. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. AVAILABILITY: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location.
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