CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures

Islam, Shahidul; Ge, Peng; Zhang, Shaojie

doi:10.1093/nar/gkx538

Cited by 5 publications

(5 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Users can provide atomic coordinates in PDB or PDBx/mmCIF format files, or the PDB IDs along with chain IDs and LocalSTAR3D will search and download them from the PDB website automatically. There are several RNA base pair annotation tools, including MC-Annotate ( 23 , 24 ), RNAView ( 25 ), FR3D ( 16 ), DSSR ( 26 ), ClaRNA ( 27 ) and CompAnnotate ( 28 ). LocalSTAR3D uses DSSR to identify the base-pairing interactions as it supports both PDB and PDBx/mmCIF formats.…”

Section: Methodsmentioning

confidence: 99%

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

Chen

Khan

Zhang

2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

show abstract

Section: Methodsmentioning

confidence: 99%

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

Chen

Khan

Zhang

2020

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…RNApdbee 2.0 and El Tetrado enable the analysis of quadruplexes that could be useful for studying telomeric motifs that are often associated with cancer and neurodegenerative diseases [34,36]. Motif analysis on ribosomal structures that are of low resolution could benefit from the method employed by CompAnnotate [32]. For tertiary structure analyses that require a wider range of motif annotations, users can opt for WebFR3D, RNA Frabase 2.0, and NASSAM [9,18,22,26,28,30,35].…”

Section: Comparison Of Computational Approaches In Annotating Rna Base Motifsmentioning

confidence: 99%

Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures

Emrizal

Hamdani

Firdaus-Raih

2021

IJMS

View full text Add to dashboard Cite

The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule’s functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.

show abstract

“…Among the main reasons for the lag in long-range motif exploration are the limitations of existing computational methods designed for the motif search problem, which is formulated as the task of identifying instances of a given 3D motif within a given RNA 3D structure or a set of structures [11,[13][14][15][16][17][18]. The commonly used methods are limited by at least one of three major restraints: RNA sequence (types of bases) [14,15], annotations of interactions (e.g., types of base pairs [19]) [13,15,16,18,20], and backbone topology (types of loops [21,22]) [11,12,14,16,17,[23][24][25]. Sequence restraints may hide rare non-canonical motif variants, such as the U-minor variant of the A-minor interaction motif [26].…”

Section: Introductionmentioning

confidence: 99%

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

Baulin,

Bohdan,

Kowalski

et al. 2024

Preprint

View full text Add to dashboard Cite

The functions of non-coding RNAs are largely defined by their three-dimensional structures. RNA 3D structure is organized hierarchically and consists of recurrent building blocks called tertiary motifs. The computational problem of RNA tertiary motif search remains largely unsolved, as standard approaches are restrained by sequence, interaction network, or backbone topology. We developed the ARTEM superposition algorithm, which is free from these limitations. Here, we present a version of ARTEM that allows automated searches of RNA structure databases to identify 3D structure motifs. We exemplify it by a search of motifs isosteric to the kink-turn motif. This widespread motif plays a role in many aspects of RNA function, and its mutations are known to cause several human syndromes. With ARTEM, we discovered two new kink-turn topologies, multiple no-kink variants of the motif, and showed that a ribosomal junction in bacteria forms either a kink or a no-kink variant depending on the species. Additionally, we identified kink-turns in the catalytic core of group II introns, whose structures have not previously been characterized as containing kink-turns. ARTEM opens a fundamentally new way to study RNA 3D folds and motifs and analyze their correlations and variations.

show abstract

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures

Cited by 5 publications

References 27 publications

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool

Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures

ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs

Contact Info

Product

Resources

About