ArticleNucleic acids research2010
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- UFold-X: an enhanced Dual & Dynamic U-Mamba model for long-range RNA secondary structure prediction.Nucleic acids research · 2026Article
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
- Specific suppression of D-RNA G-quadruplex-protein interaction with an L-RNA aptamer.Nucleic acids research · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.Nucleic acids research · 2018Article
- AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.Nucleic acids research · 2018Article
- Structural Basis for NusA Stabilized Transcriptional Pausing.Molecular cell · 2018Article
- Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15.BMC bioinformatics · 2017Article
- Structure Prediction of RNA Loops with a Probabilistic Approach.PLoS computational biology · 2016Article
- JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.Nucleic acids research · 2016Article
- AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.Cell systems · 2016Article
- RNA Bricks--a database of RNA 3D motifs and their interactions.Nucleic acids research · 2014Article
- Solving nucleic acid structures by molecular replacement: examples from group II intron studies.Acta crystallographica. Section D, Biological crystallography · 2013Review
- Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.RNA (New York, N.Y.) · 2013Article
- Article
- Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.Bioinformatics (Oxford, England) · 2012Article
- Sequence-structure relationships in yeast mRNAs.Nucleic acids research · 2012Article
- Coarse-grained prediction of RNA loop structures.PloS one · 2012Article
- An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
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4 authors.
Funding
Abstract
The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.
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