Figure 3

Correlation plots for estimated versus experimental free energies of perfect matches. Each correlation plot consists of 340 data points corresponding to all perfect match duplexes covering all temperatures, sequence and sodium concentrations. The top left plot depicts the correlation between experimental free energies and free energies estimated by MultiRNAFold with SantaLucia parameters. The Pearson correlation equals 0.6917 and the RMSE is 5.35. The bottom left plot depicts the correlation between experimental free energies and free energies estimated by MultiRNAFold with Mathews parameters. The Pearson correlation equals 0.6711 and the RMSE is 5.56. The top middle plot depicts the correlation between experimental free energies and free energies estimated by UNAFold. The Pearson correlation equals 0.6808 and the RMSE is 5.35. The bottom middle plot depicts the correlation between experimental free energies and free energies estimated by Vienna Package. The Pearson correlation equals 0.6785 and the RMSE is 4.31. The top right plot depicts the correlation between experimental free energies and free energies estimated by the TNN-Doublets-PM Model. The Pearson correlation equals 0.8466 and the RMSE is 3.15. The bottom right plot depicts the correlation between experimental free energies and free energies estimated by the TNN-Triplets-PM Model. The Pearson correlation equals 0.9221 and the RMSE is 2.20.