R3D-BLAST: a search tool for similar RNA 3D substructures

Liu, Yun Chen; Yang, Chung Han; Chen, Kun Tze; Wang, Jyun Rong; Cheng, Mei; Chung, Jen Chun; Chiu, Hsien Tai; Lu, Chin Lung

doi:10.1093/nar/gkr379

Cited by 10 publications

(13 citation statements)

References 12 publications

(17 reference statements)

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“…To evaluate RAG-3D's features compared to other tools, we provide motif search results and run time estimates for RAG-3D, R3D-BLAST and ARTS in the Supplementary Data. R3D-BLAST is a BLAST-like search tool that searches the PDB database for structurally similar RNA substructures for a query RNA 3D structure given in a PDB format ( 27 ). R3D-BLAST returns a list of all similar structures with corresponding E -values which measure statistical significance.…”

Section: Resultsmentioning

confidence: 99%

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RAG-3D: a search tool for RNA 3D substructures

et al. 2015

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To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

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Section: Resultsmentioning

confidence: 99%

“…Other search tools comparing RNA 3D folds, include ARTS ( 26 ), R3D-BLAST ( 27 ), WebFR3D ( 28 ), SARA ( 29 ), NASSAM ( 30 ) and RNA-Bricks ( 31 ). Among them, ARTS and R3D-BLAST are somewhat similar to RAG-3D presented here.…”

Section: Introductionmentioning

confidence: 99%

RAG-3D: a search tool for RNA 3D substructures

et al. 2015

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“…To the best of our knowledge among currently available methods only R3D-Blast (47), WebRF3D (19) and FASTR3D (48) fulfill these criteria. WebFR3D and FASTR3D accept as queries only fragments of PDB structures that are stored in a database accompanying these tools.…”

Section: Discussionmentioning

confidence: 99%

RNA Bricks—a database of RNA 3D motifs and their interactions

2013

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The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA–protein complexes. In contrast to other similar tools (RNA 3D Motif Atlas, RNA Frabase, Rloom) RNA motifs, i.e. ‘RNA bricks’ are presented in the molecular environment, in which they were determined, including RNA, protein, metal ions, water molecules and ligands. All nucleotide residues in RNA bricks are annotated with structural quality scores that describe real-space correlation coefficients with the electron density data (if available), backbone geometry and possible steric conflicts, which can be used to identify poorly modeled residues. The database is also equipped with an algorithm for 3D motif search and comparison. The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information. This enables the identification of local structural similarities among evolutionarily related and unrelated RNA molecules. Besides, the search utility enables searching ‘RNA bricks’ according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions.

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“…Therefore, automatic software tools capable of rapidly and accurately searching the PDB database for similar RNA 3D structures or substructures are helpful for the annotation of RNA structures and functions. Since computing similarity between two RNA 3D structures is an intractable task [ 4 ], currently existing tools, including RNA FRABASE [ 5 , 6 ], FASTR3D [ 7 ], R3D-BLAST [ 8 ] and RAG-3D [ 9 ], all employ some heuristic approaches to scan the PDB database for similar RNA 3D structures and/or substructures.…”

Section: Introductionmentioning

confidence: 99%

R3D-BLAST2: an improved search tool for similar RNA 3D substructures

et al. 2017

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BackgroundRNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs.ResultsSince its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structural-alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures into one-dimensional (1D) structural sequences and applies BLAST to the resulting structural sequences for searching similar substructures of RNAs. In this study, we have upgraded R3D-BLAST to develop a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept an RNA structure in the mmCIF format as an input. The results of our experiments on a benchmark dataset have demonstrated that R3D-BLAST2 indeed performs very well in comparison to its earlier version R3D-BLAST and other similar tools RNA FRABASE, FASTR3D and RAG-3D by searching a larger number of RNA 3D substructures resembling those of the input RNA.ConclusionsR3D-BLAST2 is a valuable BLAST-like search tool that can more accurately scan the PDB database for similar RNA 3D substructures. It is publicly available at http://genome.cs.nthu.edu.tw/R3D-BLAST2/.

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R3D-BLAST: a search tool for similar RNA 3D substructures

Cited by 10 publications

References 12 publications

RAG-3D: a search tool for RNA 3D substructures

RAG-3D: a search tool for RNA 3D substructures

RNA Bricks—a database of RNA 3D motifs and their interactions

R3D-BLAST2: an improved search tool for similar RNA 3D substructures

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