InterRNA: a Database of Base Interactions in RNA Structures

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Nov 11

PMID 26553798

Citations 9

Authors

Sri Devan Appasamy

Hazrina Yusof Hamdani

Effirul Ikhwan Ramlan

Mohd Firdaus-Raih

Affiliations

Soon will be listed here.

Abstract

A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database-http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.

Citing Articles

R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.

Appasamy S, Zirbel C Bioinformatics. 2024; 40(11).

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A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.

Tieng F, Abdullah-Zawawi M, Md Shahri N, Mohamed-Hussein Z, Lee L, Mutalib N Brief Bioinform. 2023; 25(1).

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A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.

Bohdan D, Voronina V, Bujnicki J, Baulin E Nucleic Acids Res. 2023; 51(16):8367-8382.

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Developing Community Resources for Nucleic Acid Structures.

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RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.

Hong X, Zheng J, Xie J, Tong X, Liu X, Song Q RNA Biol. 2021; 18(sup2):738-746.

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