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

Abstract

In this study, 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:
 [1];  [2];  [2];  [2]
  1. New York City College of Technology, City Univ. of New York, Brooklyn, NY (United States)
  2. New York Univ., New York, NY (United States)
Publication Date:
Research Org.:
New York Univ., New York, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1239896
Grant/Contract Number:  
AC02-98CH10886
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 43; Journal Issue: 19; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zahran, Mai, Sevim Bayrak, Cigdem, Elmetwaly, Shereef, and Schlick, Tamar. RAG-3D: A search tool for RNA 3D substructures. United States: N. p., 2015. Web. doi:10.1093/nar/gkv823.
Zahran, Mai, Sevim Bayrak, Cigdem, Elmetwaly, Shereef, & Schlick, Tamar. RAG-3D: A search tool for RNA 3D substructures. United States. doi:10.1093/nar/gkv823.
Zahran, Mai, Sevim Bayrak, Cigdem, Elmetwaly, Shereef, and Schlick, Tamar. Mon . "RAG-3D: A search tool for RNA 3D substructures". United States. doi:10.1093/nar/gkv823. https://www.osti.gov/servlets/purl/1239896.
@article{osti_1239896,
title = {RAG-3D: A search tool for RNA 3D substructures},
author = {Zahran, Mai and Sevim Bayrak, Cigdem and Elmetwaly, Shereef and Schlick, Tamar},
abstractNote = {In this study, 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.},
doi = {10.1093/nar/gkv823},
journal = {Nucleic Acids Research},
number = 19,
volume = 43,
place = {United States},
year = {2015},
month = {8}
}

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