Table 3. RNA fingerprint similarity functions.

X and Y are fingerprints of the two structures being compared.

Similarity Function	Definition
Intersection	SB(X,Y) = |X ∩ Y|
Cosine [50]	${\mathbf{S}}_{\mathbf{C}}(\mathbf{X},\mathbf{Y})=\frac{|\mathbf{X}\cap \mathbf{Y}|}{\sqrt{\left|\mathbf{X}\right|\left|\mathbf{Y}\right|}}$
Dice [51, 52]	${\mathbf{S}}_{\mathbf{D}}(\mathbf{X},\mathbf{Y})=\frac{\mathbf{2}\left|\mathbf{X}\cap \mathbf{Y}\right|}{\left|\mathbf{X}\right|+\left|\mathbf{Y}\right|}$
Hamming [53]	SH(X,Y) = |(X⋂Y) ⋃ (X⋃Y)C|
Jaccard [54]	${\mathbf{S}}_{\mathbf{J}}(\mathbf{X},\mathbf{Y})=\frac{|\mathbf{X}\cap \mathbf{Y}|}{|\mathbf{X}\cup \mathbf{Y}|}$