ArticleBMC bioinformatics2010
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed, 156 citations in OpenAlex.
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- Ex.50.T aptamer impairs tumor-stroma cross-talk in breast cancer by targeting gremlin-1.Cell death discovery · 2025Article
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
- Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.PLoS computational biology · 2024Article
- RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction.Journal of molecular biology · 2024Article
- State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction.NAR genomics and bioinformatics · 2024Article
- PERFUMES: pipeline to extract RNA functional motifs and exposed structures.Bioinformatics (Oxford, England) · 2024Article
- AmiR-P3: An AI-based microRNA prediction pipeline in plants.PloS one · 2024Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- Identification and characterization of RNA pentaloop sequence families.NAR genomics and bioinformatics · 2023Article
- Article
- RNAapt3D: RNA aptamer 3D-structural modeling database.Biophysical journal · 2022Article
- Biology and medicine in the landscape of quantum advantages.Journal of the Royal Society, Interface · 2022Review
- rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles.Nucleic acids research · 2022Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- 3dDNA: A Computational Method of Building DNA 3D Structures.Molecules (Basel, Switzerland) · 2022Article
- Cx43-mediated sorting of miRNAs into extracellular vesicles.EMBO reports · 2022Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. DESCRIPTION: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl.
conclusionsRNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.