A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

Hazrina Yusof Hamdani, Peter J. Artymiuk, Mohd Firdaus Mohd Raih

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.

Original languageEnglish
Title of host publication2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium
PublisherAmerican Institute of Physics Inc.
Volume1678
ISBN (Electronic)9780735413252
DOIs
Publication statusPublished - 25 Sep 2015
Event2015 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2015 - Selangor, Malaysia
Duration: 15 Apr 201516 Apr 2015

Other

Other2015 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2015
CountryMalaysia
CitySelangor
Period15/4/1516/4/15

Fingerprint

annotations
ribonucleic acids
hydrogen
interactions
nucleic acids
hydrogen bonds
occurrences
platforms

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Hamdani, H. Y., Artymiuk, P. J., & Mohd Raih, M. F. (2015). A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes. In 2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium (Vol. 1678). [030019] American Institute of Physics Inc.. https://doi.org/10.1063/1.4931240

A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes. / Hamdani, Hazrina Yusof; Artymiuk, Peter J.; Mohd Raih, Mohd Firdaus.

2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium. Vol. 1678 American Institute of Physics Inc., 2015. 030019.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hamdani, HY, Artymiuk, PJ & Mohd Raih, MF 2015, A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes. in 2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium. vol. 1678, 030019, American Institute of Physics Inc., 2015 Postgraduate Colloquium of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology, UKM FST 2015, Selangor, Malaysia, 15/4/15. https://doi.org/10.1063/1.4931240
Hamdani HY, Artymiuk PJ, Mohd Raih MF. A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes. In 2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium. Vol. 1678. American Institute of Physics Inc. 2015. 030019 https://doi.org/10.1063/1.4931240
Hamdani, Hazrina Yusof ; Artymiuk, Peter J. ; Mohd Raih, Mohd Firdaus. / A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes. 2015 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2015 Postgraduate Colloquium. Vol. 1678 American Institute of Physics Inc., 2015.
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