Before revision:  We also show that on three widely-used folding engines (RNAstructure, Vienna RNAfold, and CONTRAfold), ThreshKnot always outperforms the much more involved MEA algorithm  (1) in structure prediction accuracy, (2) in its capability to predict pseudoknots,  (3) and in its faster running time .
After revision:  We also show that on three widely-used folding engines (RNAstructure, Vienna RNAfold, and CONTRAfold), ThreshKnot always outperforms the much more involved MEA algorithm in (1) in structure prediction accuracy, (2) in its capability to predict pseudoknots, (3) and in its faster running time .