Currently I work in the Dr. Neocles Leontis research group.
Current Research: Development of RNA Internal Loop Library
The continuous growth of atomic resolution RNA structures in the Nucleic Acid Database (NDB) creates a new challenge for biologists and bioinformaticians, which is understanding and analyzing the functions of these molecules. This process is slowed down due to the lack of high-throughput software tools, which could recognize RNA structural motifs and find similar ones. RNA motifs are responsible for different functions that RNA performs in cells, and that accounts for the importance of being able to identify them.
In this research I plan to compose a complete library of one type of RNA 2D motif called internal loops. The internal loops, taken from known ribosomal RNAs (Thermus thermophilus, Escherichia coli and Haloarcula marismortui), will be visualized with Swiss-PDB Viewer and annotated according to the Leontis-Westhof classification. Finally, for each motif a search for motifs with similar geometric structures will be performed using the “Find RNA 3D” (FR3D) program and the results will be manually curated and stored in a specific format. As a result, for each motif, an annotated 2D structure and list of motifs that share the same structural features will be available in an unambiguous and consistent library.
This library can be employed as a training set for self-educating computer programs, which will find patterns from the known structures in the given training set and then will use them for predictions of the internal loops in new RNA structures. This knowledge may be used for functional annotations of RNA molecules.