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COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

Authors
  • Firdaus-Raih, Mohd
  • Hamdani, Hazrina Yusof
  • Nadzirin, Nurul
  • Ramlan, Effirul Ikhwan
  • Willett, Peter
  • Artymiuk, Peter J
Type
Published Article
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Publication Date
Jul 01, 2014
Volume
42
Issue
Web Server issue
Identifiers
DOI: 10.1093/nar/gku438
PMID: 24831543
Source
Medline
License
Unknown

Abstract

Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac.

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