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

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Abstract

Motivation

Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search.

Results

We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments.

Availability and implementation

https://zhanglab.ccmb.med.umich.edu/RNA-align/.

Supplementary information

Supplementary data are available at Bioinformatics online.

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Most cited references 5

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How significant is a protein structure similarity with TM-score = 0.5?

Jinrui Xu, Yang Zhang (2010)

Protein structure similarity is often measured by root mean squared deviation, global distance test score and template modeling score (TM-score). However, the scores themselves cannot provide information on how significant the structural similarity is. Also, it lacks a quantitative relation between the scores and conventional fold classifications. This article aims to answer two questions: (i) what is the statistical significance of TM-score? (ii) What is the probability of two proteins having the same fold given a specific TM-score? We first made an all-to-all gapless structural match on 6684 non-homologous single-domain proteins in the PDB and found that the TM-scores follow an extreme value distribution. The data allow us to assign each TM-score a P-value that measures the chance of two randomly selected proteins obtaining an equal or higher TM-score. With a TM-score at 0.5, for instance, its P-value is 5.5 x 10(-7), which means we need to consider at least 1.8 million random protein pairs to acquire a TM-score of no less than 0.5. Second, we examine the posterior probability of the same fold proteins from three datasets SCOP, CATH and the consensus of SCOP and CATH. It is found that the posterior probability from different datasets has a similar rapid phase transition around TM-score=0.5. This finding indicates that TM-score can be used as an approximate but quantitative criterion for protein topology classification, i.e. protein pairs with a TM-score >0.5 are mostly in the same fold while those with a TM-score <0.5 are mainly not in the same fold.

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RNA structure alignment by a unit-vector approach.

Marc A. Marti-Renom, Emidio Capriotti (2008)

The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. Supplementary data are available at Bioinformatics online.

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The ARTS web server for aligning RNA tertiary structures

Oranit Dror, Ruth Nussinov, Haim J. Wolfson (2006)

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 .

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Author and article information

Journal

Title: Bioinformatics

Publisher: Oxford University Press (OUP)

ISSN (Print): 1367-4803

ISSN (Electronic): 1460-2059

Publication date Created: November 01 2019

Publication date Created: April 25 2019

Publication date Other: November 01 2019

Publication date (Print): November 01 2019

Publication date (Electronic): April 25 2019

Volume: 35

Issue: 21

Pages: 4459-4461

Affiliations

[1 ]School of Physics and Electronic Information, Huanggang Normal University, Huanggang, China

[2 ]Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA

[3 ]Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA

Article

DOI: 10.1093/bioinformatics/btz282

PubMed ID: 31161212

SO-VID: 5a451d77-2e0c-4bc5-94ee-ffb4ba24cc52

License:

https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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

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Abstract

Motivation

Results

Availability and implementation

Supplementary information

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Most cited references 5

How significant is a protein structure similarity with TM-score = 0.5?

RNA structure alignment by a unit-vector approach.

The ARTS web server for aligning RNA tertiary structures

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