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Fitness Functions for RNA Structure Design

View ORCID ProfileMax Ward, Eliot Courtney, View ORCID ProfileElena Rivas
doi: https://doi.org/10.1101/2022.06.16.496369
Max Ward
1Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
2Department of Computer Science & Software Engineering, University of Western Australia, Western Australia, Australia
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  • For correspondence: max.ward@uwa.edu.au
Eliot Courtney
2Department of Computer Science & Software Engineering, University of Western Australia, Western Australia, Australia
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Elena Rivas
1Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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Abstract

An RNA design algorithm takes a target RNA structure and finds a sequence that folds into that structure. This is fundamentally important for engineering therapeutics using RNA. Computational RNA design algorithms are guided by fitness functions, but not much research has been done on the merits of these functions. We survey current RNA design approaches with a particular focus on the fitness functions used. We experimentally compare the most widely used fitness functions in RNA design algorithms on both synthetic and natural sequences. It has been almost 20 years since the last comparison was published, and we find similar results with a major new result: maximizing probability outperforms minimizing ensemble defect. The probability is the likelihood of a structure at equilibrium and the ensemble defect is the weighted average number of incorrect positions in the ensemble. Also, we observe that many recently published approaches minimize structure distance to the minimum free energy prediction, which we find to be a poor fitness function.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 19, 2022.
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Fitness Functions for RNA Structure Design
Max Ward, Eliot Courtney, Elena Rivas
bioRxiv 2022.06.16.496369; doi: https://doi.org/10.1101/2022.06.16.496369
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Fitness Functions for RNA Structure Design
Max Ward, Eliot Courtney, Elena Rivas
bioRxiv 2022.06.16.496369; doi: https://doi.org/10.1101/2022.06.16.496369

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