ArticleRNA (New York, N.Y.)2007
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships.
Article in RNA (New York, N.Y.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Small-Molecule Targeting of the Iron-Responsive Element in the APP mRNA 5'-UTR to Control Amyloid Translation in Alzheimer's Disease.International journal of molecular sciences · 2026Review
- Iron-Mediated Overexpression of Amyloid Precursor Protein via Iron Responsive mRNA in Alzheimer's Disease.International journal of molecular sciences · 2025Review
- Identification and characterization of RNA pentaloop sequence families.NAR genomics and bioinformatics · 2023Article
- Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure.Non-coding RNA · 2021Article
- Review
- A functional genetic screen reveals sequence preferences within a key tertiary interaction in cobalamin riboswitches required for ligand selectivity.Nucleic acids research · 2018Article
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- Analysis of stacking overlap in nucleic acid structures: algorithm and application.Journal of computer-aided molecular design · 2014Article
- RNAlyzer--novel approach for quality analysis of RNA structural models.Nucleic acids research · 2013Article
- RNA modularity for synthetic biology.F1000prime reports · 2013Review
- Article
- Improved prediction of RNA tertiary structure with insights into native state dynamics.RNA (New York, N.Y.) · 2012Article
- Structural characterization of naturally occurring RNA single mismatches.Nucleic acids research · 2011Article
- Promoting RNA helical stacking via A-minor junctions.Nucleic acids research · 2011Article
- Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.BMC bioinformatics · 2010Article
- Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.Nucleic acids research · 2010Article
- New metrics for comparing and assessing discrepancies between RNA 3D structures and models.RNA (New York, N.Y.) · 2009Article
- The GA-minor submotif as a case study of RNA modularity, prediction, and design.Wiley interdisciplinary reviews. RNAReview
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2 authors.
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Abstract
Despite an increasing number of experimentally determined RNA structures, the gap between the number of structures and that of RNA families is still growing. To overcome this limitation, efficient and reliable RNA modeling methodologies must be developed. In order to reach this goal, here, we show how triloop sequence-structure relationships have been inferred through a systematic analysis of all triloops found in available high-resolution structures. The structural annotation of all triloops allowed us to define discrete states of the triloop's conformational space, and therefore an explicit sequence-to-structure relation. The sequence-structure relationships inferred from this explicit relation are presented in a convenient modeling table that provides a limited set of possible three-dimensional structures given any triloop sequence. The table is indexed by the two nucleotides that form the triloop's flanking base pair, since they are shown to provide the most information about the triloop three-dimensional structures. We also report the observations in the X-ray crystallographic structures of important conformational variations, which we believe might be the result of RNA dynamic.
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