title: RAG-3D: a search tool for RNA 3D substructures.
abstract: To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present 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. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.
authors: Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, NY 11201, USA.
authors: Mai
authors: M
authors: Zahran
authors: Department of Chemistry, New York University, New York, NY 10003, USA.
authors: Cigdem
authors: C
authors: Sevim Bayrak
authors: Department of Chemistry, New York University, New York, NY 10003, USA.
authors: Shereef
authors: S
authors: Elmetwaly
authors: Department of Chemistry, New York University, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA schlick@nyu.edu.
authors: Tamar
authors: T
authors: Schlick
mesh_terms: D000465:Algorithms; D030561:Databases, Nucleic Acid; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry; D020733:RNA, Small Cytoplasmic / Q000737:chemistry; D018271:Signal Recognition Particle / Q000737:chemistry; D012984:Software
chemical_list: C115990:7SL RNA; D012338:RNA, Ribosomal, 23S; D020733:RNA, Small Cytoplasmic; D018271:Signal Recognition Particle; D012313:RNA