RNA Folding: Methods and Protocols

ISBN-13: 9781071635186 / Angielski

Ronny Lorenz

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. Estimating RNA Secondary Structure Folding Free Energy Changes with efn2

Jeffrey Zuber and David H. Mathews

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

Izabela Ferreira and Gerald Weber

3. RNA Secondary Structure Thermodynamics

Ronny Lorenz

4. RNA Secondary Structure Modeling following the IPANEMAP Workflow

Delphine Allouche, Grégoire De Bisschop, Afaf Saaidi, Pierre Hardouin, Francois-Xavier Lyonnet du Moutier, Yann Pontu, and Sargueil Bruno

5. How Parameters Influence SHAPE-Directed Predictions

Torin Greenwood and Christine E. Heitsch

6. Classified Dynamic Programming in RNA Structure Analysis

Björn Voß

7. Classification and Identification of Non-Canonical Base Pairs and Structural Motifs

Roman Sarrazin-Gendron, Jérôme Waldispühl, and Vladimir Reinharz

8. Modified Nucleotides and RNA Structure Prediction

Yuliia Varenyk and Ronny Lorenz

9. How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook using IntaRNA

Martin Raden and Milad Miladi

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

Sebastian Will

11. Evolutionary Structure Conservation and Covariance Scores

Florian Eggenhofer and Christian Höner zu Siederdissen

12. Developing Complex RNA Design Applications in the Infrared Framework

Hua-Ting Yao, Yann Ponty, and Sebastian Will

13. A Guide to Computational Co-Transcriptional Folding featuring the SRP RNA

Stefan Badelt and Ronny Lorenz

14. Assessing the Quality of Co-Transcriptional Folding Simulations

Felix Kühnl, Peter F. Stadler, and Sven Findeiß

15. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline

Bernhard C. Thiel, Simón Poblete, and Ivo L. Hofacker

Subject Index List…

Blurb

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.