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Table 6 Average, Minimum and Maximum ΔΔG Values for Pairwise Comparisons of Different Suboptimal Folds

From: Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

  Haloferax volcanii Methanosprillum hungatei
Optimal Accuracy1 80% 46%
Total Fold Predictions (Optimal + Suboptimal) 750 750
Total Pairwise Comparisons 280,875 280,875
   Structural variation score of 1 to 50     
Num of Pairwise Comparisons 32,378 12%2 11,016 4%
ΔΔG Min (kcal/mol) 0 0
ΔΔG Max (kcal/mol) 11 8.60
ΔΔG Average (kcal/mol) 2.84 2.19
   Structural variation score of 51 to 100     
Num of Pairwise Comparisons 102,071 36% 32,360 12%
ΔΔG Min (kcal/mol) 0 0
ΔΔG Max (kcal/mol) 11 8.60
ΔΔG Average (kcal/mol) 2.53 2.01
   Structural variation score of 101 to 500     
Num of Pairwise Comparisons 121,805 43% 134,037 48%
ΔΔG Min (kcal/mol) 0 0
ΔΔG Max (kcal/mol) 11 8.6
ΔΔG Average (kcal/mol) 2.24 1.74
   Structural variation score of 501+     
Num of Pairwise Comparisons 24,621 9% 103,462 37%
ΔΔG Min (kcal/mol) 0 0
ΔΔG Max (kcal/mol) 11 8.6
ΔΔG Avg (kcal/mol) 2.24 1.82
  1. Both sequences are 16S rRNAs. For each sequence, Mfold 3.1 predicts one optimal or minimum free energy fold and 749 suboptimal folds (750 total folds). Pairwise comparisons are grouped based on the structural variation between the two folds compared. For details on how structural variation between two folds is calculated see Materials and Methods. The range of ΔΔG values observed is 0–11 kcal/mol for H. volcanii and 0–8.60 kcal/mol for M. hungatei., and all ΔG values are pre-efn2 re-evaluation.
  2. 1 Without efn2 re-evaluation and re-ordering of predicted folds.
  3. 2 Percentage of total pairwise comparisons.