RNA 3D Motif Atlas

is a comprehensive and representative collection of internal and hairpin loop RNA 3D motifs extracted from the Representative Sets of RNA 3D structures.

With release 3.77 we implemented a new clustering strategy. In April 2024, we released J3 motif groups, filling in all the way back to 2018-02-09. See the release notes for each release. Follow us on Twitter.

Hairpin loops Current version: 3.83             Internal loops Current version: 3.83             3-way Junction Current version: 3.83

Latest motif atlas release based on the representative set from: 2024-04-24

RNA 3D motifs are recurrent structural modules that are essential for many biological functions and RNA folding. Usually drawn as unstructured hairpin and internal loops, these motifs are organized by non-canonical basepairs, supplemented by characteristic stacking and base-backbone interactions.

Method. To create the Motif Atlas we extract RNA 3D motif instances from the current representative set using FR3D, a program for symbolic and geometric searching of RNA 3D structures. Next, we use a clustering approach based on maximum cliques to obtain a representative collection of RNA 3D motifs. Unique and stable ids are assigned to all motifs and motif instances.

Citation. The paper describing RNA 3D Motif Atlas has been published in RNA. If you use this resource, please cite:

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Anton I. Petrov, Craig L. Zirbel, and Neocles B. Leontis

RNA October 2013 19: 1327-1340; Published in Advance August 22, 2013, doi:10.1261/rna.039438.113
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