Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements

Zatil Hanan Binti Yahaya, Mohd Firdaus Mohd Raih

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

Abstract

The three-dimensional (3D) structures of RNA determine the functionality of the molecules. Knowledge of the functional aspects of RNA molecules from a 3D structure perspective as well as their many vital roles in various biological processes allow for applications of structural analysis such as exploring RNA structures as potential drug targets. The increased availability of experimentally determined RNA 3D structures allow searches for sites in RNA molecules that can specifically bind to small molecules. However, computational searching methods for such structural RNA-ligand interaction analysis have not been deployed on a large scale for such screening exercises. In this paper, we describe classes of interactions of ribonucleotide base residues and small molecules that were sorted according to their functionalities in a structural context. Structural search of RNA-ligand complexes was conducted and classified according to types of ligands involved in an interaction. RNA base residues and drug interaction were obtained together with base residues and metal interactions. For one proof of concept example, superposition of structures that can interact with the drug paromomycin was carried out. The process developed serves as a platform for further high-throughput structural annotation and analysis of RNA structures in the Protein Data Bank to identify sites for drugs as well as for use in drug-repurposing studies.

Original languageEnglish
Title of host publication2018 UKM FST Postgraduate Colloquium
Subtitle of host publicationProceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium
EditorsNoor Hayati Ahmad Rasol, Kamarulzaman Ibrahim, Siti Aishah Hasbullah, Mohammad Hafizuddin Hj. Jumali, Nazlina Ibrahim, Marlia Mohd Hanafiah, Mohd Talib Latif
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735418431
DOIs
Publication statusPublished - 27 Jun 2019
Event2018 UKM FST Postgraduate Colloquium - Selangor, Malaysia
Duration: 4 Apr 20186 Apr 2018

Publication series

NameAIP Conference Proceedings
Volume2111
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

Conference2018 UKM FST Postgraduate Colloquium
CountryMalaysia
CitySelangor
Period4/4/186/4/18

Fingerprint

data mining
ligand
RNA
drugs
ligands
drug
molecules
interactions
annotations
physical exercise
structural analysis
availability
screening
ribonucleotides
platforms
drug interactions
proteins
protein structure
biological processes
metals

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Plant Science
  • Physics and Astronomy(all)
  • Nature and Landscape Conservation

Cite this

Yahaya, Z. H. B., & Mohd Raih, M. F. (2019). Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements. In N. H. A. Rasol, K. Ibrahim, S. A. Hasbullah, M. H. H. Jumali, N. Ibrahim, M. M. Hanafiah, & M. T. Latif (Eds.), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium [040009] (AIP Conference Proceedings; Vol. 2111). American Institute of Physics Inc.. https://doi.org/10.1063/1.5111248

Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements. / Yahaya, Zatil Hanan Binti; Mohd Raih, Mohd Firdaus.

2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. ed. / Noor Hayati Ahmad Rasol; Kamarulzaman Ibrahim; Siti Aishah Hasbullah; Mohammad Hafizuddin Hj. Jumali; Nazlina Ibrahim; Marlia Mohd Hanafiah; Mohd Talib Latif. American Institute of Physics Inc., 2019. 040009 (AIP Conference Proceedings; Vol. 2111).

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

Yahaya, ZHB & Mohd Raih, MF 2019, Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements. in NHA Rasol, K Ibrahim, SA Hasbullah, MHH Jumali, N Ibrahim, MM Hanafiah & MT Latif (eds), 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium., 040009, AIP Conference Proceedings, vol. 2111, American Institute of Physics Inc., 2018 UKM FST Postgraduate Colloquium, Selangor, Malaysia, 4/4/18. https://doi.org/10.1063/1.5111248
Yahaya ZHB, Mohd Raih MF. Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements. In Rasol NHA, Ibrahim K, Hasbullah SA, Jumali MHH, Ibrahim N, Hanafiah MM, Latif MT, editors, 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. American Institute of Physics Inc. 2019. 040009. (AIP Conference Proceedings). https://doi.org/10.1063/1.5111248
Yahaya, Zatil Hanan Binti ; Mohd Raih, Mohd Firdaus. / Predicting and data mining of RNA-ligand pattern interactions against RNA base residue arrangements. 2018 UKM FST Postgraduate Colloquium: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2018 Postgraduate Colloquium. editor / Noor Hayati Ahmad Rasol ; Kamarulzaman Ibrahim ; Siti Aishah Hasbullah ; Mohammad Hafizuddin Hj. Jumali ; Nazlina Ibrahim ; Marlia Mohd Hanafiah ; Mohd Talib Latif. American Institute of Physics Inc., 2019. (AIP Conference Proceedings).
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