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RNA Folding

Methods and Protocols

  • Book
  • © 2024

Overview

Editors:
  1. Ronny Lorenz

    1. Institute for Theoretical Chemistry, University of Vienna, Wien, Austria

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2726)

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About this book

To understand and predict the behavior and function of RNAs, sophisticated tools are required to simulate and analyze their potential for forming structures. 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 that an RNA molecule may fold into; sequence evolution and conserved structures among multiple RNA sequences; the latest framework capable of handling both positive and negative RNA sequence design objectives; and kinetic folding approaches that look at the dynamic nature of RNA folding. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, RNA Folding: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this important and developing field.

 



Keywords

Table of contents (15 protocols)

  1. Front Matter

    Pages i-xii
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  2. Estimating RNA Secondary Structure Folding Free Energy Changes with efn2

    • Jeffrey Zuber, David H. Mathews
    Pages 1-13

  3. VarGibbs Usage in the Optimization of Nearest-Neighbor Parameters and Prediction of Melting Temperature of RNA Duplexes

    • Izabela Ferreira, Gerald Weber
    Pages 15-43

  4. RNA Secondary Structure Thermodynamics

    • Ronny Lorenz
    Pages 45-83

  5. RNA Secondary Structure Modeling Following the IPANEMAP Workflow

    • Delphine Allouche, Grégoire De Bisschop, Afaf Saaidi, Pierre Hardouin, Francois-Xavier Lyonnet du Moutier, Yann Ponty et al.
    Pages 85-104

  6. How Parameters Influence Shape-Directed Predictions

    • Torin Greenwood, Christine E. Heitsch
    Pages 105-124

  7. Classified Dynamic Programming in RNA Structure Analysis

    • Björn Voß
    Pages 125-141

  8. Classification and Identification of Non-canonical Base Pairs and Structural Motifs

    • Roman Sarrazin-Gendron, Jérôme Waldispühl, Vladimir Reinharz
    Pages 143-168

  9. Modified Nucleotides and RNA Structure Prediction

    • Yuliia Varenyk, Ronny Lorenz
    Pages 169-207

  10. How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA

    • Martin Raden, Milad Miladi
    Pages 209-234

  11. LocARNA 2.0: Versatile Simultaneous Alignment and Folding of RNAs

    • Sebastian Will
    Pages 235-254

  12. Evolutionary Structure Conservation and Covariance Scores

    • Florian Eggenhofer, Christian Höner zu Siederdissen
    Pages 255-284

  13. Developing Complex RNA Design Applications in the Infrared Framework

    • Hua-Ting Yao, Yann Ponty, Sebastian Will
    Pages 285-313

  14. A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA

    • Stefan Badelt, Ronny Lorenz
    Pages 315-346

  15. Assessing the Quality of Cotranscriptional Folding Simulations

    • Felix Kühnl, Peter F. Stadler, Sven Findeiß
    Pages 347-376

  16. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline

    • Bernhard C. Thiel, Simón Poblete, Ivo L. Hofacker
    Pages 377-399

  17. Back Matter

    Pages 401-402
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Editors and Affiliations

  • Institute for Theoretical Chemistry, University of Vienna, Wien, Austria

    Ronny Lorenz

Bibliographic Information

  • Book Title: RNA Folding

  • Book Subtitle: Methods and Protocols

  • Editors: Ronny Lorenz

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3519-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3518-6Published: 24 May 2024

  • Softcover ISBN: 978-1-0716-3521-6Due: 07 June 2025

  • eBook ISBN: 978-1-0716-3519-3Published: 23 May 2024

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 402

  • Number of Illustrations: 28 b/w illustrations, 70 illustrations in colour

  • Topics: Biochemistry, general

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