RNA Folding

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

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

Chapter 3 RNA Secondary Structure Thermodynamics

Chapter 4 RNA Secondary Structure Modeling Following the IPANEMAP Workflow.

Chapter 5 How Parameters Influence Shape -Directed Predictions

Chapter 6 Classified Dynamic Programming in RNA Structure Analysis.

Chapter 7 Classification and Identification of Non-canonical Base Pairs and Structural Motifs

Chapter 8 Modified Nucleotides and RNA Structure Prediction.

Chapter 9 How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA

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

Chapter 11 Evolutionary Structure Conservation and Covariance Scores

Chapter 12 Developing Complex RNA Design Applications in the Infrared Framework.

Chapter 14 Assessing the Quality of Cotranscriptional Folding Simulations

Chapter 15 The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.