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. 2017 May;23(5):712–720. doi: 10.1261/rna.060442.116

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© 2017 Mlýnský and Bussi; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 4. — Direct correlation between theory and experiments for nucleotides within two tetraloops. (A) The correlation between calculated ΔG^‡ and barriers derived from experiments for nucleotides within uGAAAg (blue) and cUUCGg (green) tetraloops. Both computed and experimental barriers are displayed as deviations from the corresponding median value. (B) A similar correlation plot obtained using the logarithm of in-line fitness F = −RTln(Fitness) (Soukup and Breaker 1999), instead of the here calculated ΔG^‡. We displayed averaged values of fitness from the set of X-ray structures (considering 41 uGAAAg and 754 cUUCGg tetraloops, respectively) from the PDB database with bars showing their standard deviations. F-values are displayed the same way as ΔG^‡ barriers subtracting medians. Points corresponding to specific residues that are worsening the correlation (outliers) are labeled.