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Table 2 Summary of results for free energy measurements obtained with EVAL-SS methods.

From: Free energy estimation of short DNA duplex hybridizations

Method Stats MFE_AD [kcal/mol] Pearson coeff. (r)   SSSI Sens. PPV F-measure
MultiRNAFold min 0.000 0.7565 4.35 40.00 0.1667 1 0.2857
(Mathews) q1 0.340    100.00 1.0000 1 1.0000
  median 0.860    100.00 1.0000 1 1.0000
  mean 2.681    95.83 0.9547 1 0.9711
  q3 3.590    100.00 1.0000 1 1.0000
  max 18.400    100.00 1.0000 1 1.0000
  stddev 3.429    10.56 0.1224 0 0.09236
MultiRNAFold min 0.000 0.7663 4.131 40.00 0.1667 1 0.2857
(SantaLucia) q1 0.330    100.00 1.0000 1 1.0000
  median 0.720    100.00 1.0000 1 1.0000
  mean 2.528    96.44 0.9608 1 0.9747
  q3 3.510    100.00 1.0000 1 1.0000
  max 17.200    100.00 1.0000 1 1.0000
  stddev 3.269    10.23 0.1189 0 0.08966
  min 0.000 0.7660 3.992 40.00 0.1667 1 0.2857
  q1 0.256    100.00 1.0000 1 1.0000
  median 0.630    100.00 1.0000 1 1.0000
UNAFold mean 2.374    96.08 0.9571 1 0.9724
  q3 3.016    100.00 1.0000 1 1.0000
  max 11.880    100.00 1.0000 1 1.0000
  stddev 3.212    10.66 0.1231 0 0.09234
Vienna min 0.010 0.7630 3.667 5.882 0.0000 0.0000 0.0000
Package q1 1.700    100.000 1.0000 1.0000 1.0000
  median 2.330    100.000 1.0000 1.0000 1.0000
  mean 3.025    95.210 0.9467 0.9856 0.9616
  q3 3.935    100.000 1.0000 1.0000 1.0000
  max 15.400    100.000 1.0000 1.0000 1.0000
  stddev 2.075    13.74 0.1581 0.1192 0.1387
  1. Summary of results for free energy measurements obtained with EVAL-SS methods. The p-values for the Pearson correlation test were less than 2.2e-16 in all cases.