The ARTS Web Server for Aligning RNA Tertiary Structures

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 18

PMID 16845038

Citations 28

Authors

Oranit Dror

Ruth Nussinov

Haim J Wolfson

Affiliations

Soon will be listed here.

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.

Citing Articles

Two Methods for Superposing the Structures of Like-Molecule Assemblies: Application to Peptide and Protein Oligomers and Aggregates.

Liwo A, Lesniewski M Molecules. 2025; 30(5).

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ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.

Bohdan D, Bujnicki J, Baulin E Nucleic Acids Res. 2024; 52(18):10850-10861.

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A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.

Zhang C, Pyle A iScience. 2022; 25(10):105218.

PMID: 36248743 PMC: 9557024. DOI: 10.1016/j.isci.2022.105218.

US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.

Zhang C, Shine M, Pyle A, Zhang Y Nat Methods. 2022; 19(9):1109-1115.

PMID: 36038728 DOI: 10.1038/s41592-022-01585-1.

RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.

Gong S, Zhang C, Zhang Y Bioinformatics. 2019; 35(21):4459-4461.

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