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

doi:10.1093/nar/gku438

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 journal › Article › peer-review

16 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 language	English
Pages (from-to)	W382-W388
Journal	Nucleic Acids Research
Volume	42
Issue number	W1
Early online date	15 May 2014
DOIs	https://doi.org/10.1093/nar/gku438
Publication status	Published (in print/issue) - 1 Jul 2014

Funding

Universiti Kebangsaan Malaysia [ICONIC-2013-007]; University Malaya High Impact Research MOE Grant [UM.C/625/1HIR/MoE/FCSIT/002 – Acc. No.: B222001]; Ministry of Education Malaysia [FRGS/1/2013/ST04/UKM/02/2]. Universiti Sains Malaysia postgraduate fellowship (to H.Y.H.); National Science Fellowship, Ministry of Higher Education, Malaysia (to N.N.). Funding for open access charge: University Malaya High Impact Research MOE Grant [UM.C/625/1HIR/MoE/FCSIT/002 – Acc. No.: B222001]. Conflict of interest statement. None declared.

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10.1093/nar/gku438

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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.",

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AU - Firdaus-Raih, Mohd

AU - Hamdani, Hazrina Yusof

AU - Nadzirin, Nurul

AU - Ramlan, E.

AU - Willett, Peter

AU - Artymiuk, Peter J.

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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.

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SN - 0305-1048

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - W1

ER -

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

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