# Concepts and Algorithms

Our library is grouped into several modules, each addressing different aspects of RNA secondary structure related problems. This is an overview of the concepts and algorithms for which implementations can be found in this library.

Almost all of them rely on the physics based Nearest Neighbor Model for RNA secondary structure prediction.

Modules:

- Free Energy Evaluation
- The RNA Folding Grammar
- The RNA Secondary Structure Landscape
- Minimum Free Energy (MFE) Algorithms
- Partition Function and Equilibrium Properties
- Suboptimals and Representative Structures
- RNA-RNA Interaction
- Classified Dynamic Programming Variants
- Inverse Folding (Design)
- Experimental Structure Probing Data
- Ligands Binding to RNA Structures
- Structure Modules and Pseudoknots
- Post-transcriptional Base Modifications
- Utilities

General Remarks:

- RNAlib API v3.0
- Callback Functions
- Deprecated List