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ARTS and DARTS: A Method and Database for Exploring RNA Tertiary Structures

Tuesday, October 30, 2007 - 3:05pm - 3:35pm
EE/CS 3-180
Ruth Nussinov (National Cancer Institute)
Joint work with Oranit Dror, Mira Avraham, Haim Wolfson (Tel Aviv University and SAIC, NCI-Frederick).

An increasing number of non-coding RNAs have recently been discovered
as key players in a variety of cellular pathways and pathological
processes. Much like proteins,the function of these active RNAs can be
inferred from their tertiary (3D) structures. However, in contrast to
proteins, the number of tools and databases for 3D structural analysis of
RNA is still limited. With the aim to fill this void, we have developed a
computational method, named ARTS, for aligning RNA tertiary structures.
Given a pair of RNA structures, the method searches for a-priori unknown
common substructures. The search is truly three dimensional and
irrespective of the order of the nucleotide chain. The detected common
substructures are either large global folds or small local tertiary
motifs. The method is highly-efficient and was used in a fully automatic
framework for clustering all the currently available RNA structures. The
result is a database, named DARTS, which reveals the current fold
repertoire of solved RNA structures and provides a hierarchical
classification for them. Both the method and the database should be useful
for structural and functional analysis of RNA. They may shed new light on
the evolutionary relationship between RNAs and reveal possible building
blocks and functional properties.

This publication has been funded in whole or in part with Federal funds
from the National Cancer Institute, National Institutes of Health, under
contract # NO1-CO-12400.