The ARTS web server for aligning RNA tertiary structures

Abstract

RNA molecules with common structural features may share similar functional properties. Structural comparison of RNAs and detection of common substructures is, thus, a highly important task. Nevertheless, the current available tools in the RNA community provide only a partial solution, since they either work at the 2D level or are suitable for detecting predefined or local contiguous tertiary motifs only. Here, we describe a web server built around ARTS, a method for aligning tertiary structures of nucleic acids (both RNA and DNA). ARTS receives a pair of 3D nucleic acid structures and searches for a priori unknown common substructures. The search is truly 3D and irrespective of the order of the nucleotides on the chain. The identified common substructures can be large global folds with hundreds and even thousands of nucleotides as well as small local motifs with at least two successive base pairs. The method is highly efficient and has been used to conduct an all-against-all comparison of all the RNA structures in the Protein Data Bank. The web server together with a software package for download are freely accessible at http://bioinfo3d.cs.tau.ac.il/ARTS.

Figure 1

The ARTS web server. (a) The entrance page of the web server. The user is required to enter an Email address and a pair of nucleic acid structures in PDB format (21). The structures can be either uploaded to the server or retrieved from the PDB. In the second case the user has to enter a four-character PDB code, optionally followed by a colon and a list of chain IDs. (b) A web page with a summary of the 10 top-ranking alignments obtained for ‘1u6b:B’ and ‘1y0q’ PDB codes. (c) The page obtained after clicking on the ‘BP Core Size’ field of the top-ranking alignment in the summary page presented in (b). (d) The superimposition of the input structures displayed by PyMOL (26) after clicking on the ‘PDB Alignment’ field of the top-ranking alignment in the summary page presented in (b). The backbone of the two structures, PDB:1u6bB and PDB:1y0q, is depicted in red and blue, respectively. The matched base pairs are in green and the matched unpaired nucleotides are in yellow.