Titlebook: RNA Structure Prediction; Risa Karakida Kawaguchi,Junichi Iwakiri Book 2023 Springer Science+Business Media, LLC, part of Springer Nature

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Web Services for RNA-RNA Interaction Prediction, action of these RNAs. Therefore, RNA-RNA interaction prediction is an important problem in bioinformatics, and many tools have been developed for the computational prediction of RNA-RNA interactions. In addition to the development of novel algorithms with high accuracy, the development and maintena

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RNA Structure Determination by High-Throughput Structural Analysis,their function. The chemical modification or RNase-mediated digestion of single-stranded RNA has been utilized to experimentally reveal RNA secondary structures. Owing to advances in high-throughput sequencing technology and chemical analysis, RNA structural analyses that enable structural profiling

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Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake, computational tools for targeted tertiary design. As a result, RNA 3D design is traditionally slow, resource-consuming, and dependent on expert modeling. In this chapter, we discuss our recently developed software package: RNAMake, a set of applications capable of designing RNA tertiary structures

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RNA 3D Structure Comparison Using RNA-Puzzles Toolkit,cules with novel functions. An unbiased blind assessment to benchmark the computational modeling is required to understand the achievements and bottlenecks of the prediction, while a standard structure comparison protocol is necessary. RNA-Puzzles is a community-wide effort on the assessment of blin

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RNA Structure Determination by High-Throughput Structural Analysis, at the transcriptomic scale in living cells have been developed. Here, we provide an overview of the high-throughput RNA structural (HTS) analyses and describe the computational processing steps of recent HTS analysis pipelines: PROBer, BUMHMM, and reactIDR.