Analisis dan Penyaringan Data Lewah Interaksi Kelompok Bes Berikatan Hidrogen dalam Struktur RNA 3-Dimensi

Translated title of the contribution: Analysis and filtering for redundant data of hydrogen-bonded base interaction clusters in RNA 3-dimensional structures

Hazrina Yusof Hamdani, Mohd Firdaus Mohd Raih

Research output: Contribution to journalArticle

Abstract

There is a tendency for 3-dimensional (3D) arrangements to appear differently from different viewing angles. In biological macromolecules, this is a problem that is also encountered by algorithms searching for 3D arrangements. This results in the same output being retrieved repeatedly because they are not considered redundant from different points of the search. This is a problem that is not encountered for sequence level searches. In this study, we developed two approaches to filter such redundant data that are the Prüfer code (based on graph theory) and our own redundant data filtering method. The search results model uses the COnnection tables Graphs for Nucleic ACids (COGNAC) algorithm to search for clusters of bases that are connected by hydrogen bonds. The comparison between the two methods showed that the redundant data filtering method developed in this work was able to identify and filter between 50.5% and 80% of the redundant data from the original COGNAC results compared to the Prüfer code that identified and filtered 50% of the redundant data from the original COGNAC results. This redundant data filtering method was then integrated into the COGNAC computer program. Furthermore, the redundant data filtering method can also be deployed to the results of other sequence independent 3D search algorithms including those for protein 3D structures.

Original languageMalay
Pages (from-to)1731-1739
Number of pages9
JournalSains Malaysiana
Volume47
Issue number8
DOIs
Publication statusPublished - 1 Aug 2018

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Nucleic acids
RNA
Hydrogen
Graph theory
Macromolecules
Computer program listings
Hydrogen bonds
Proteins

ASJC Scopus subject areas

  • General

Cite this

Analisis dan Penyaringan Data Lewah Interaksi Kelompok Bes Berikatan Hidrogen dalam Struktur RNA 3-Dimensi. / Hamdani, Hazrina Yusof; Mohd Raih, Mohd Firdaus.

In: Sains Malaysiana, Vol. 47, No. 8, 01.08.2018, p. 1731-1739.

Research output: Contribution to journalArticle

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