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

Abstract

The structures of RNA exhibit recurrent patterns, which are defined as motifs. Motifs are crucial for the biological functions of RNA molecules. The 3D RNA motif library includes 3D RNA structures, providing a resource for motif-based RNA 3D structure prediction and design. We built the Advanced Template Library for Assembly and Structure (ATLAS) that features graph representations of RNA structures, atomic 3D structures from the Protein Data Bank (PDB), and an isomorphism graph searching algorithm. ATLAS includes nucleotide-level graph representations of RNA motifs and corresponding PDB IDs from the PDB and 3D atomic structures retrieved from the PDB. We provide the web service to search for and download RNA motifs and user-defined structures, supporting non-WC interactions. Graph representations include two types of graphs: motifs with non-Watson-Crick (non-WC) and without non-WC. Compared to existing motif libraries, ATLAS includes graph representations with non-Watson-Crick interactions and pseudoknots and integrates the latest RNA structures from the PDB. We also develop a measure of similarity between RNAs based on shared motifs. We proposed a physics-inspired, time-dependent mechanistic model for RNA evolution, whose steady-state solution fits the global distribution of RNA structural similarity.