RNA ATLAS: 3D RNA Motif Library

Advanced Template Library for Assembly and Structure

ATLAS is a comprehensive 3D RNA motif library that enables researchers to search for RNA structural motifs in the Protein Data Bank. Using graph-based algorithms, ATLAS extracts and catalogs over 433,000 RNA motif structures including hairpins, internal loops, bulges, multiway junctions, and pseudoknots. The database provides atomic-level 3D coordinates for accurate structural analysis and RNA research.

3D RNA Motif Library

We have designed a user-friendly website dedicated to RNA motif search, utilizing a graph-based search algorithm to extract 3D RNA motif structures.

User Guide

Quick Start

ATLAS offers two powerful search methods for RNA structural motifs from the Protein Data Bank.

Type-Based Search

Select motif type: Hairpin, Internal, Bulge, Multiway Junction, or Pseudoknot
Choose motif size (number of unpaired nucleotides)
Download results as CSV (metadata) or ZIP (PDB structures)

Graph-Based Structure Search

Option 1: Draw your custom motif by adding nodes and connecting with edge types (Covalent Bond, Watson-Crick pairs, Non-Watson-Crick pairs)
Option 2: Load an example structure to see how it works
Uses subgraph isomorphism algorithm (may take up to 20 minutes for complex structures)

Database Statistics

Over 433,000 motifs from PDB: 52% Internal loops, 27% Hairpins, 13% Bulges, 6% Junctions, 2% Pseudoknots

View Full User Guide

Type-Based Motif Search

How it Works

Search pre-indexed RNA motifs from ATLAS database by selecting motif type (hairpin, internal loop, bulge, multiway junction, or pseudoknot) and motif size (number of unpaired nucleotides). Results include 3D atomic coordinates and graph representations from the Protein Data Bank (PDB).

Graph-Based Structure Search

How it Works

Draw your own RNA motif structure using an interactive graph-based interface. The search uses subgraph isomorphism algorithm to find matching patterns in RNA structures. Supports non-Watson-Crick interactions for comprehensive structural analysis.