Vernal: a tool for mining fuzzy network motifs in RNA
Motivation RNA 3D motifs are recurrent substructures, modeled as networks of base pair
interactions, which are crucial for understanding structure–function relationships. The task of …
interactions, which are crucial for understanding structure–function relationships. The task of …
CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching
The functions of non-coding RNAs usually depend on their 3D structures. Therefore,
comparing RNA 3D structures is critical in analyzing their functions. We noticed an …
comparing RNA 3D structures is critical in analyzing their functions. We noticed an …
De novo discovery of structural motifs in RNA 3D structures through clustering
As functional components in three-dimensional (3D) conformation of an RNA, the RNA
structural motifs provide an easy way to associate the molecular architectures with their …
structural motifs provide an easy way to associate the molecular architectures with their …
RNAMotifProfile: a graph-based approach to build RNA structural motif profiles
MM Rahaman, S Zhang - NAR Genomics and Bioinformatics, 2024 - academic.oup.com
RNA structural motifs are the recurrent segments in RNA three-dimensional structures that
play a crucial role in the functional diversity of RNAs. Understanding the similarities and …
play a crucial role in the functional diversity of RNAs. Understanding the similarities and …
RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies
Understanding the 3D structural properties of RNAs will play a critical role in identifying their
functional characteristics and designing new RNAs for RNA-based therapeutics and …
functional characteristics and designing new RNAs for RNA-based therapeutics and …
STAR3D: a stack-based RNA 3D structural alignment tool
P Ge, S Zhang - Nucleic acids research, 2015 - academic.oup.com
The various roles of versatile non-coding RNAs typically require the attainment of complex
high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in …
high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in …
LocalSTAR3D: a local stack-based RNA 3D structural alignment tool
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 …
Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search …
RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families
Motivation The 3D structures of RNA play a critical role in understanding their functionalities.
There exist several computational methods to study RNA 3D structures by identifying …
There exist several computational methods to study RNA 3D structures by identifying …
[HTML][HTML] Graph theoretical methods and workflows for searching and annotation of RNA tertiary base motifs and substructures
R Emrizal, HY Hamdani, M Firdaus-Raih - International Journal of …, 2021 - mdpi.com
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 …
Data Bank (PDB) have led to the need for automated structure annotation methods to …
ARTEM: a method for RNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs
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 …
RNA 3D structure is organized hierarchically and consists of recurrent building blocks called …