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

Mohd Firdaus-Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, E. Ramlan, Peter Willett, Peter J. Artymiuk

Research output: Contribution to journalArticle

6 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.

LanguageEnglish
PagesW382-W388
JournalNucleic Acids Research
Volume42
Issue numberW1
Early online date15 May 2014
DOIs
Publication statusPublished - 1 Jul 2014

Fingerprint

Nucleic Acids
Hydrogen
RNA
Mutation

Cite this

Firdaus-Raih, Mohd ; Hamdani, Hazrina Yusof ; Nadzirin, Nurul ; Ramlan, E. ; 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. pp. W382-W388.
@article{0dfba4d2d1de4cc58b7899d9182d43be,
title = "COGNAC: A web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures",
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.",
author = "Mohd Firdaus-Raih and Hamdani, {Hazrina Yusof} and Nurul Nadzirin and E. Ramlan and Peter Willett and Artymiuk, {Peter J.}",
year = "2014",
month = "7",
day = "1",
doi = "10.1093/nar/gku438",
language = "English",
volume = "42",
pages = "W382--W388",
journal = "Nucleic Acids Research",
issn = "0305-1048",
number = "W1",

}

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

In: Nucleic Acids Research, Vol. 42, No. W1, 01.07.2014, p. W382-W388.

Research output: Contribution to journalArticle

TY - JOUR

T1 - COGNAC

T2 - Nucleic Acids Research

AU - Firdaus-Raih, Mohd

AU - Hamdani, Hazrina Yusof

AU - Nadzirin, Nurul

AU - Ramlan, E.

AU - Willett, Peter

AU - Artymiuk, Peter J.

PY - 2014/7/1

Y1 - 2014/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84904791155&partnerID=8YFLogxK

U2 - 10.1093/nar/gku438

DO - 10.1093/nar/gku438

M3 - Article

VL - 42

SP - W382-W388

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -