Titlebook: RNA Folding; Methods and Protocol Ronny Lorenz Book 2024 The Editor(s) (if applicable) and The Author(s), under exclusive license to Spring

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https://doi.org/10.1007/978-1-0716-3519-3Structure Prediction; Pseudoknots; Dynamic Programming; Folding Dynamics; RNApuzzles Experiment

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Estimating RNA Secondary Structure Folding Free Energy Changes with ,.. The . program estimates the folding free energy change and the experimental uncertainty in the folding free energy change. It can be run through the graphical user interface for RNAstructure, from the command line, or a web server. This chapter provides detailed protocols for using efn2.

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Book 2024uctures. This volume discusses the various levels of prediction and algorithmic approaches to RNA folding. The chapters in this book cover topics such as energy parameters of the nearest-neighbor (NN) energy model; classified dynamic programming to address exponential growth of candidate structures

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Estimating RNA Secondary Structure Folding Free Energy Changes with , set of nearest neighbor parameters that models the folding stability of a RNA secondary structure as the sum of folding stabilities of the structural elements that comprise the secondary structure. In the software suite RNAstructure, the free energy change calculation is implemented in the program

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Usage in the Optimization of Nearest-Neighbor Parameters and Prediction of Melting Temperature of ion of melting temperatures but has also found use in RNA secondary structure prediction and theoretical models of hybridization kinetics. One of the key problems is to obtain the NN parameters from melting temperatures, and VarGibbs was designed to obtain those parameters directly from melting temp

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