RAG-3D: A search tool for RNA 3D substructures

Mai Zahran, Cigdem Sevim Bayrak, Shereef Elmetwaly, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

To address many challenges in RNA structure/func tion 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.

Original languageEnglish (US)
Pages (from-to)9474-9488
Number of pages15
JournalNucleic Acids Research
Volume43
Issue number19
DOIs
StatePublished - Oct 30 2015

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RAG-3D : A search tool for RNA 3D substructures. / Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar.

In: Nucleic Acids Research, Vol. 43, No. 19, 30.10.2015, p. 9474-9488.

Research output: Contribution to journalArticle

Zahran, M, Sevim Bayrak, C, Elmetwaly, S & Schlick, T 2015, 'RAG-3D: A search tool for RNA 3D substructures', Nucleic Acids Research, vol. 43, no. 19, pp. 9474-9488. https://doi.org/10.1093/nar/gkv823
Zahran, Mai ; Sevim Bayrak, Cigdem ; Elmetwaly, Shereef ; Schlick, Tamar. / RAG-3D : A search tool for RNA 3D substructures. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 19. pp. 9474-9488.
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