Talk abstracts

Talk on Saturday 09:45-10:00am submitted by Anton Petrov

RNA 3D Hub - an online resource for RNA structural bioinformatics

Anton I Petrov (Department of Chemistry, Bowling Green State University), Craig L. Zirbel (Department of Mathematics and Statistics, Bowling Green State University), Neocles B. Leontis (Department of Chemistry, Bowling Green State University)

Abstract:
RNA 3D Hub (http://rna.bgsu.edu/rna3dhub) is a new online resource designed to make the RNA 3D structural data deposited in the PDB/NDB more accessible and useful to RNA scientists.

The PDB serves as the international repository of atomic-resolution 3D structures and contains a separate entry for each solved structured deposited by researchers that meets the data quality requirements. Many of these structures are redundant as they represent the same molecule from the same organism.

To address this problem, RNA 3D Hub hosts non-redundant sets of RNA-containing 3D structures and structural annotations of crucial pairwise interactions found in 3D structures, including base-pairing, -stacking, and -backbone interactions. These non-redundant lists of RNA 3D structures are produced by an automated procedure based on sequence similarity, 3D superpositions, and structure quality considerations.

RNA 3D Hub also contains RNA 3D motifs extracted from all atomic-resolution RNA 3D structures deposited in PDB, and the RNA 3D Motif Atlas, a representative collection of RNA 3D motifs.
RNA 3D motifs are recurrent structural modules that are essential for many biological functions and RNA folding. Usually drawn as unstructured hairpin and internal “loops”, these motifs are organized by non-canonical basepairs, supplemented by characteristic stacking and base-backbone interactions.

To create the Motif Atlas we extract RNA 3D motif instances from the current non-redundant list using FR3D, a program for symbolic and geometric searching of RNA 3D structures. Next, we use a clustering approach to obtain a representative collection of RNA 3D motifs. All these data are stored in RNA 3D Hub and can be accessed online. Unique and stable ids are assigned to all motifs, to all motif instances, and to all non-redundant equivalence classes of structure files.

RNA 3D Hub is updated automatically on a regular schedule, and a versioning system is implemented to provide independent access to data snapshots. RNA 3D Hub also provides a rich user interface to allow for efficient data visualization.

Keywords: RNA 3D structure, online database, RNA 3D motifs