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Automating RNA 3D Motif Comparison and Functional Annotation of Ribosome Structures

Appasamy, Sri Devan
http://orcid.org/0000-0001-6609-3535
http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1715152568956044

Abstract Details

2024, Doctor of Philosophy (Ph.D.), Bowling Green State University, Biological Sciences.
This dissertation addresses the critical need for bioinformatics tools to analyze and annotate the growing number of RNA and ribosome structures available in public databases. RNA molecules, key players in gene regulation, protein synthesis, and catalytic reactions, adopt complex three-dimensional structures that are pivotal for their diverse functions. However, the analysis of these structures is hindered by the redundancy and variability in the datasets, making efficient comparison across different structures a challenging task. To overcome these limitations, this research introduces a novel automated approach for the comparison of RNA motifs 3D structures and the functional annotation of ribosome structures. A new web service, the RNA 3D Motif Correspondence Server (R3DMCS), has been developed to enable the automated comparison and visualization of structural variations within RNA motifs, facilitating a deeper understanding of their functional implications. We illustrate the utility of this web service by examining several RNA 3D motifs in the bacterial small ribosomal subunit. The second part of this dissertation involves automating annotation of ribosome structures based on the occupancy of binding sites for tRNAs, mRNA, protein factors, and ligands. The annotations enhance the identification and comparison of ribosome functional states, which will enable detailed analyses of structural interactions in various states. As the deposition of new RNA structures continues to accelerate, these tools will become increasingly valuable, providing essential capabilities to the scientific community for keeping pace with the expanding frontier of RNA research.
Zhaohui Xu, Ph.D. (Committee Chair)
Anita Simic, Ph.D. (Other)
Julia Halo, Ph.D. (Committee Member)
Scott Rogers, Ph.D. (Committee Member)
Craig Zirbel, Ph.D. (Committee Member)
90 p.
Bioinformatics
RNA; Visualization; Motif finding; Alignment;

Recommended Citations

Citations

  • Appasamy, S. D. (2024). Automating RNA 3D Motif Comparison and Functional Annotation of Ribosome Structures [Doctoral dissertation, Bowling Green State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1715152568956044

    APA Style (7th edition)

  • Appasamy, Sri. Automating RNA 3D Motif Comparison and Functional Annotation of Ribosome Structures. 2024. Bowling Green State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1715152568956044.

    MLA Style (8th edition)

  • Appasamy, Sri. "Automating RNA 3D Motif Comparison and Functional Annotation of Ribosome Structures." Doctoral dissertation, Bowling Green State University, 2024. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1715152568956044

    Chicago Manual of Style (17th edition)

bgsu1715152568956044
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© 2024, all rights reserved.
This open access ETD is published by Bowling Green State University and OhioLINK.