Last modified on 11 October 2011.

Literature Reference:

Gardner D.P., Ren P., Ozer S. & Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2): 473-483.

Manuscript Figures:

Figure 1. Top 20 Comparative / Potential ratio for tetraloops. PDF
Figure 2. Comparison of Statistical Potentials vs 4 other RNA folding programs. PDF
Figure 3. Identification of Comparative and Potential hairpin and internal loops. PDF

Supplemental Information:

Prediction Accuracies for Statistical Potentials and four other RNA folding programs This spreadsheet (Excel 2010) contains the RNA secondary structure prediction accuracies of the new statistical potentials and four other RNA folding programs. The results for the 25 RNA molecular classes used in this studied are found on tab ProgramComp. Additionally, the results for the statistical potentials are broken down further in the following manner:
  • HPILResults contains the results when using hairpin and internal loop molecule-specific statistical potentials seperately.
  • AggHPILResults contains the results when using hairpin and internal loop molecule-independent statistical potentials seperately.
  • ProgramComp8020 contains the validation results when using a 80%/20% split for training and testing.
Supplemental data PDF This PDF contains the following:
  • folding results when using hairpin and internal loop molecule-specific statistical potentials seperately (pages 1-2).
  • folding results when using hairpin and internal loop molecule-independent statistical potentials seperately (pages 3-4).
  • folding results plus standard deviation for molecule-independent statistical potentials and 4 other programs (pages 5-6).
  • folding validation results using a 80%/20% split for training and validation (pages 7-8).
  • folding validation results for 9 new RNA molecular classes not included in the statistical potential generation (pages 9-14).
Hairpin Comparative / Potential ratios for bacterial 16S rRNA This spreadsheet (Excel 2010) contains the Comparative / Potential ratios for all tetraloops (256 in total) when (1) ignoring flanking base pair and (2) allowing only a CG base pair.
Comparison of hairpin loop statistical potentials and experiementally-derived free-energy values This spreadsheet (Excel 2010) contains the absolute difference between our triloop, tetraloop and pentaloop statistical potentials and their corresponding experimentally-derived free-energy values.
Comparison of internal loop statistical potentials and experiementally-derived free-energy values This spreadsheet (Excel 2010) contains the absolute difference between our 1x1 and 2x2 internal loop statistical potentials and their corresponding experimentally-derived free-energy values.