ArticleNucleic acids research2012
Automated 3D structure composition for large RNAs.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 427 papers.
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Who cites it
427 citing papers in PubMed.
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- A Multi-Engine Consensus Docking Pipeline for RNA Aptamer Screening Against ACC Oxidase (ACO): Statistical Validation, Machine Learning Analysis, and Pilot Cross-Target Evaluation Against ACC Synthase (ACS).International journal of molecular sciences · 2026Article
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- miRNA-Mediated Signaling Networks in Non-Small Cell Lung Cancer: Linking Tumor Progression to Sarcopenia.International journal of molecular sciences · 2026Article
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Structural basis for recognition of diverse localizing mRNAs by Egl-BicD.Nature structural & molecular biology · 2026Article
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- A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution.bioRxiv : the preprint server for biology · 2026Article
- Aptamer discovery via GO-SELEX and GrNP-SELEX for monocrotophos and its comparative analysis.Mikrochimica acta · 2026Article
- Identification and bioinformatic functional analysis of novel and known polymorphisms in the myostatin gene of Ukrainian Carpathian Mountain sheep.Scientific reports · 2026Article
- Artificial intelligence-guided design of LNPs for in vivo targeted mRNA delivery via analysis of the spatial conformation of ionizable lipids.Nature biomedical engineering · 2026Article
- A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions.Nucleic acids research · 2026Article
- FRET-guided selection of RNA 3D structures.Nucleic acids research · 2026Article
367 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues.
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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.