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Bioinformatics. 2019 Mar 28. pii: btz222. doi: 10.1093/bioinformatics/btz222. [Epub ahead of print]

Determining Parameters for Non-Linear Models of Multi-Loop Free Energy Change.

Author information

Computer Science & Software Engineering, The University of Western Australia.
Department of Biochemistry & Biophysics, and Center for RNA Biology, University of Rochester.
The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia.
Department of Biostatistics & Computational Biology, University of Rochester.



Predicting the secondary structure of RNA is a fundamental task in bioinformatics. Algorithms that predict secondary structure given only the primary sequence, and a model to evaluate the quality of a structure, are an integral part of this. These algorithms have been updated as our model of RNA thermodynamics changed and expanded. An exception to this has been the treatment of multi-loops. While more advanced models of multi-loop free energy change have been suggested, a simple, linear model has been used since the 1980s. However, recently, new dynamic programming algorithms for secondary structure prediction that could incorporate these models were presented. Unfortunately, these models appear to have lower accuracy for secondary structure prediction.


We apply linear regression and a new parameter optimization algorithm to find better parameters for the existing linear model and advanced, non-linear multi-loop models. These include the Jacobson-Stockmayer and Aalberts & Nandagopal models. We find that the current linear model parameters may be near optimal for the linear model, and that no advanced model performs better than the existing linear model parameters even after parameter optimization.


Source code and data is available at


Supplementary data are available at Bioinformatics online.

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