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RNA Structure: Advances and Assessment of 3D Structure Prediction
Annual Review of Biophysics, 2017 Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins.
Zhichao Miao, Eric Westhof
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2021
One of the significant forms of molecules present in living cells is ribonucleic acid (RNA). RNA structural elements moderate various biological process, including epigenetic function, modify mRNA stability, and alternate splicing. The study of the secondary structures of RNA is, therefore, crucial for interpreting the role as well as the regulatory ...
Manoj Kumar Gupta +8 more
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One of the significant forms of molecules present in living cells is ribonucleic acid (RNA). RNA structural elements moderate various biological process, including epigenetic function, modify mRNA stability, and alternate splicing. The study of the secondary structures of RNA is, therefore, crucial for interpreting the role as well as the regulatory ...
Manoj Kumar Gupta +8 more
openaire +1 more source
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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PREDICTION AND VISUALIZATION OF STRUCTURAL SWITCHES IN RNA
Biocomputing '99, 1998There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule, which can be evaluated by RNA folding and structure ...
Giegerich, Robert +2 more
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Advances in RNA 3D Structure Prediction
Journal of Chemical Information and Modeling, 2022RNA molecules carry out various cellular functions, and understanding the mechanisms behind their functions requires the knowledge of their 3D structures. Different types of computational methods have been developed to model RNA 3D structures over the past decade.
Yi Xiao
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Deep Learning for RNA Structure Prediction
Current Opinion in Structural BiologyPredicting RNA structures from sequences with computational approaches is of vital importance in RNA biology considering the high costs of experimental determination. AI methods have revolutionized this field in recent years, enabling RNA structure prediction with increasingly higher accuracy and efficiency.
Liang Hong, Yimin Fan, Jiuming Wang
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In Silico Prediction of RNA Secondary Structure
2017The secondary structure of an RNA molecule represents the base-pairing interactions within the molecule and fundamentally determines its overall structure. In this chapter, we overview the main approaches and existing tools for predicting RNA secondary structures, as well as methods for identifying noncoding RNAs from genomic sequences or RNA ...
Tahi, Fariza +2 more
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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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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
openaire +2 more sources
Predicting RNA Structure: Advances and Limitations
2013RNA secondary structures can be predicted using efficient algorithms. A widely used software package implementing a large number of computational methods is the ViennaRNA Package. This chapter describes how to use programs from the ViennaRNA Package to perform common tasks such as prediction of minimum free-energy structures, suboptimal structures, or ...
Hofacker, Ivo, Lorenz, Ronny
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