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2011
The prediction of RNA structure can be a first important step for the functional characterization of novel ncRNAs. Especially for the very meaningful secondary structure, there is a multitude of computational prediction tools. They differ not only in algorithmic details and the underlying models but also in what exactly they are trying to predict. This
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The prediction of RNA structure can be a first important step for the functional characterization of novel ncRNAs. Especially for the very meaningful secondary structure, there is a multitude of computational prediction tools. They differ not only in algorithmic details and the underlying models but also in what exactly they are trying to predict. This
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2010
We give an overview of RNA structure predictions in this chapter. We discuss here the main approaches to RNA structure prediction: combinatorial approaches, comparative approaches, and kinetic approaches. The main algorithms and mathematical concepts such as transformational grammars will be briefly introduced.
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We give an overview of RNA structure predictions in this chapter. We discuss here the main approaches to RNA structure prediction: combinatorial approaches, comparative approaches, and kinetic approaches. The main algorithms and mathematical concepts such as transformational grammars will be briefly introduced.
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RNA helicases: modulators of RNA structure
Trends in Cell Biology, 1994RNA molecules play an essential role in many cellular processes, often as components of ribonucleoprotein complexes. Like proteins, RNA molecules adopt sequence-specific secondary and tertiary structures that are essential for function; alteration of these structures therefore provides a means of regulating RNA function.
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Computational RNA Structure Prediction
Current Bioinformatics, 2008The view of RNA as simple information transfer molecule has been continuously challenged since the discov- ery of ribozymes, a class of RNA molecules with enzyme-like function. Moreover, the recent discovery of tiny RNA molecules such asRNAs and small interfering RNA, is transforming our thinking about how gene expression is regu- lated.
CAPRIOTTI, EMIDIO, Marti Renom, Marc A.
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Mathematical Biosciences, 1991
A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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RNA structure: experimental analysis
Current Opinion in Microbiology, 2007Among all of the biological macromolecules, the functional versatility of RNAs is unique including encoding or transferring genetic information and performing catalysis. These biological functions are highly dependent upon RNA folding and structure.
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Annual Review of Biochemistry, 1999
▪ Abstract An RNA motif is a discrete sequence or combination of base juxtapositions found in naturally occurring RNAs in unexpectedly high abundance. Because all the motifs examined so far have three-dimensional structures independent of the context in which they are embedded, they are important components of the “kit” of structural elements from ...
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▪ Abstract An RNA motif is a discrete sequence or combination of base juxtapositions found in naturally occurring RNAs in unexpectedly high abundance. Because all the motifs examined so far have three-dimensional structures independent of the context in which they are embedded, they are important components of the “kit” of structural elements from ...
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Solution Structure Probing of RNA Structures
2008Single-stranded RNA plant viruses not only code for viral proteins within their RNA genomes, they often maintain elaborate RNA secondary structures. These structures can be integral to a variety of viral processes, such as viral translation, genome replication, subgenomic mRNA transcription, and genome encapsidation.
Marc R, Fabian, K Andrew, White
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RNA Secondary Structure Thermodynamics
2012Several different ways to predict RNA secondary structures have been suggested in the literature. Statistical methods, such as those that utilize stochastic context-free grammars (SCFGs), or approaches based on machine learning aim to predict the best representative structure for the underlying ensemble of possible conformations.
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Structural Probing of RNA Thermosensors
2009Chemical probing of RNA structure has become one of the most popular approaches to map the conformation of RNA molecules of various sizes under well-defined experimental conditions. The method monitors the sensitivity of each nucleotide to various chemicals, which reflects its hydrogen-bonding environment within the RNA molecule.
Chiaruttini, C. +2 more
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