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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417. Epub 2013 May 28.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

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  • 1Department of Mathematics and Statistics, Ohio Northern University, Ada, OH 45810, USA.


The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at

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