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- W2768252242 endingPage "2442" @default.
- W2768252242 startingPage "2442" @default.
- W2768252242 abstract "Riboswitches, which are located within certain noncoding RNA region perform functions as genetic “switches”, regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers. As structural changes in aptamers must be achieved within the certain time window for effective regulation, kinetics is another key point for understanding aptamer function in riboswitch-mediated gene regulation. The coarse-grained self-organized polymer (SOP) model using Langevin dynamics simulation has been successfully developed to investigate folding kinetics of aptamers, while their co-transcriptional folding kinetics can be modeled by the helix-based computational method and BarMap approach. Based on the known aptamers, the web server Riboswitch Calculator and other theoretical methods provide a new tool to design synthetic riboswitches. This review will represent an overview of these computational methods for modeling structure and kinetics of riboswitch aptamers and for designing riboswitches." @default.
- W2768252242 created "2017-12-04" @default.
- W2768252242 creator A5010711856 @default.
- W2768252242 creator A5042304241 @default.
- W2768252242 creator A5059431543 @default.
- W2768252242 creator A5065058975 @default.
- W2768252242 date "2017-11-17" @default.
- W2768252242 modified "2023-10-06" @default.
- W2768252242 title "Computational Methods for Modeling Aptamers and Designing Riboswitches" @default.
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