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

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

	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

^†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.
¹ Without efn2 re-evaluation and re-ordering of predicted folds.
² Percentage of total pairwise comparisons.

ISSN: 1471-2105