RNAdex: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions.

Authors

Jingyi Li, Jian Wang, Srinivasan Ekambaram, Nikolay V Dokholyan

Published in

Journal of molecular biology. Pages 170047. Sep 30, 2026. Epub Sep 30, 2026.

Abstract

The structures of RNA exhibit recurrent patterns, which are defined as motifs. Motifs are crucial for the biological functions of RNA molecules. A 3D RNA motif library includes 3D RNA structures, providing a resource for motif-based 3D RNA structure prediction and design. Existing motif libraries face challenges in systematically extracting and classifying highly complex topologies with crossing interactions and non-Watson-Crick interactions. To overcome this limitation, we built RNAdex, an RNA motif library that stores 3D atomic coordinates and incorporates non-Watson-Crick interactions and crossing interactions from the Protein Data Bank. Leveraging motifs from RNAdex, we developed a measure of motif-content similarity between RNAs and observed that the pairwise similarity scores resemble a power-law distribution. To explore this macroscopic statistical pattern, we present a physics-inspired, hypothesis-generating framework for RNA structural evolution. RNAdex motif graphs were used to compare motif content and formulate testable hypotheses about RNA structural evolution. RNAdex is available athttps://rnadex.dokhlab.org.

PMID:
42815846
Bibliographic data and abstract were imported from PubMed on 01 Oct 2026.

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