bookmark RAG-3D A dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. The user provides a file in a PDB format or a PDB ID, and receives as output a list of structures or substructures found in our 3D-RAG database with lowest RMSD value with the query structure or substructure. The function of the matching structure is provided and gives a good indicator of the possible function of the query RNA.