Poster abstracts

Poster number 38 submitted by Emil Khisamutdinov

WebFR3D: A web application for finding, annotating, and analyzing new and recurrent RNA 3D motifs

Emil F. Khisamutdinov (Department of Chemistry and Center for Photochemical Science, Bowling Green State University), Anton I. Petrov (Department of Biological Sciences, Bowling Green State University), Craig L. Zirbel (Department of Mathematics and Statistics, Bowling Green State University), Neocles B. Leontis (Department of Chemistry and Center for Photochemical Science, Bowling Green State University)

Abstract:
Many non-coding RNAs, as well as mRNAs, form one or more structured domains, essential for function. The PDB contains atomic-resolution structures for a rapidly increasing number of large and complex RNAs, including RNase P, self-splicing introns, and ribosomal RNAs. Within these structures, a large number of 3D motifs occur, some recurrent and some unique. Modular 3D motifs correspond to hairpin, internal and multi-helix junction loops in secondary structures, and generally comprise characteristic non-Watson-Crick base-pairing, base-phosphate, and stacking interactions. In addition to mediating tertiary interactions, 3D motifs form binding sites for proteins, other nucleic acids, and small molecules and ions, and even catalytic sites of ribozymes. Different sequences can fold to form essentially the same 3D motif; recognizing sequence variants of the same RNA 3D motif is an important sub-goal of research aiming to predict RNA 3D structure starting from sequence, a major challenge of computational biology. We will describe WebFR3D, a web application for searching RNA 3D structures to find similar 3D motifs that is the on-line version of “Find RNA 3D” (FR3D); WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions. In both modes, users can specify sequence, sequence–continuity, base pairing, base-stacking and other constraints on nucleotides and their interactions. WebFR3D can be used to locate potentially new hairpin, internal or junction loop motifs in 3D motifs or to find instances of known recurrent RNA 3D motifs in specific PDB files or across a carefully selected set of non-redundant, representative 3D structure files. The WebFR3D output page provides 3D super-position of the instances and alignments of their sequences, annotated with pairwise interactions. WebFR3D is available at http://rna.bgsu.edu/webfr3d.

Keywords: RNA motif