Janssen, Stefan ; Schudoma, Christian; Steger, Gerhard; Giegerich, Robert: Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. In: BMC Bioinformatics. Jg.12 H. 1. 2011
Inhalt
- Goals of the evaluation
- Methods
- The thermodynamic model
- Free energy and partition function
- Abstract shapes
- Implementing the basic energy model - no dangling bases
- Implementing the full energy model - with dangling bases
- Modeling folding spaces with tree grammars
- Tree representation of structures
- From tree grammars to folding algorithms
- Grammars and their relation to established structure prediction programs
- Model NoDangle
- Model OverDangle
- Model MicroState
- Model MacroState
- Results & Discussion
- Data sets
- Evaluation of models for MFE structure prediction
- Evaluating models for partition function and related computations
- Conclusion
- Notes
- Acknowledgements
- Author details
- Authors' contributions
- References