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

Mohd Firdaus Mohd Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, Effirul Ikhwan Ramlan, Peter Willett, Peter J. Artymiuk

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
JournalNucleic Acids Research
Volume42
Issue numberW1
DOIs
Publication statusPublished - 1 Jul 2014

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Nucleic Acids
Hydrogen
RNA
Mutation

ASJC Scopus subject areas

  • Genetics

Cite this

COGNAC : A web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. / Mohd Raih, Mohd Firdaus; Hamdani, Hazrina Yusof; Nadzirin, Nurul; Ramlan, Effirul Ikhwan; Willett, Peter; Artymiuk, Peter J.

In: Nucleic Acids Research, Vol. 42, No. W1, 01.07.2014.

Research output: Contribution to journalArticle

Mohd Raih, Mohd Firdaus ; Hamdani, Hazrina Yusof ; Nadzirin, Nurul ; Ramlan, Effirul Ikhwan ; Willett, Peter ; Artymiuk, Peter J. / COGNAC : A web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures. In: Nucleic Acids Research. 2014 ; Vol. 42, No. W1.
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