TY - JOUR
T1 - RAG-3D
T2 - A search tool for RNA 3D substructures
AU - Zahran, Mai
AU - Sevim Bayrak, Cigdem
AU - Elmetwaly, Shereef
AU - Schlick, Tamar
N1 - Funding Information:
We thank Namhee Kim for valuable suggestions and comments. We also thank other members of the Biomath group at NYU. New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory are gratefully acknowledged. FUNDING Computing resources of the Computational Center for Nanotechnology Innovations; Empire State Development''s Division of Science, Technology and Innovation [through National Science Foundation (NSF) Group Award TG-MCB080036N]; Department of Energy Grant [DE-AC02-98CH10886 to New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory]; State of New York (to New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory); National Institutes of General Medical Sciences; National Institutes of Health [GM100469; GM081410 to T. S.] Funding for open access charge: NIH. Conflict of interest statement. None declared.
Publisher Copyright:
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2015/10/30
Y1 - 2015/10/30
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkv823
DO - 10.1093/nar/gkv823
M3 - Article
C2 - 26304547
AN - SCOPUS:84959449396
SN - 0305-1048
VL - 43
SP - 9474
EP - 9488
JO - Nucleic acids research
JF - Nucleic acids research
IS - 19
ER -