ArticleNucleic acids research2014
RNA Bricks--a database of RNA 3D motifs and their interactions.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Tools For Building Artificial Biological Nanostructures.ACS nano · 2026Review
- All-at-once RNA folding with 3D motif prediction framed by evolutionary information.Nature methods · 2025Article
- Dockground: The Resource Expands to Protein-RNA Interactome.Journal of molecular biology · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions.Journal of molecular biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
- R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.Bioinformatics (Oxford, England) · 2024Article
- PERFUMES: pipeline to extract RNA functional motifs and exposed structures.Bioinformatics (Oxford, England) · 2024Article
- Classification and Identification of Non-canonical Base Pairs and Structural Motifs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.Bioinformatics (Oxford, England) · 2023Article
- DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.Nucleic acids research · 2023Article
- Computer-Assisted Design and Characterization of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- Developing Community Resources for Nucleic Acid Structures.Life (Basel, Switzerland) · 2022Review
- On the predictibility of A-minor motifs from their local contexts.RNA biology · 2022Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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