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 11 Evolutionary Structure Conservation and Covariance Scores

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

Chapter 13 A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA

Chapter 14 Assessing the Quality of Cotranscriptional Folding Simulations

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