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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. (NYU), 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. https://doi.org/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. https://doi.org/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 = {Mon Aug 24 00:00:00 EDT 2015},
month = {Mon Aug 24 00:00:00 EDT 2015}
}

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Cited by: 23 works
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Non-coding RNAs in human disease
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journal, June 2010


RAG: RNA-As-Graphs database--concepts, analysis, and features
journal, February 2004


ARTS: alignment of RNA tertiary structures
journal, September 2005


INFO-RNA--a fast approach to inverse RNA folding
journal, May 2006


VARNA: Interactive drawing and editing of the RNA secondary structure
journal, April 2009


The Protein Data Bank
journal, January 2000


The tmRNA Website: invasion by an intron
journal, January 2002


Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
journal, June 2003


Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
journal, February 2005


The ARTS web server for aligning RNA tertiary structures
journal, July 2006

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fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
journal, January 2007

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INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints
journal, July 2007

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SARA: a server for function annotation of RNA structures
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WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs
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NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules
journal, May 2012

  • Hamdani, H. Y.; Appasamy, S. D.; Willett, P.
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RNA Bricks—a database of RNA 3D motifs and their interactions
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  • Chojnowski, Grzegorz; Waleń, Tomasz; Bujnicki, Janusz M.
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Ribo-gnome: The Big World of Small RNAs
journal, September 2005


RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
journal, January 2010

  • Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-231

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
journal, August 2013


On the occurrence of the T-loop RNA folding motif in large RNA molecules
journal, June 2003


From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
journal, January 2008


Predicting Helical Topologies in RNA Junctions as Tree Graphs
journal, August 2013


miRBase: tools for microRNA genomics.
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Works referencing / citing this record:

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
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Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
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A pipeline for computational design of novel RNA-like topologies
journal, June 2018

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  • Nucleic Acids Research, Vol. 46, Issue 14
  • DOI: 10.1093/nar/gky524

Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
journal, July 2018