SimCAL: a flexible tool to compute biochemical reaction similarity

BMC Bioinformatics

Table 2 List of binary similarity measures included in SimCAL

S. No.	Measure	Definition	Range
1.	Tanimoto	\( \frac{a}{\left(a+b\right)+\left(a+c\right)-c} \)	[0-1]
2.	Dice	\( \frac{2a}{2a+b+c} \)	[0-1]
3.	Ochiai	\( \frac{a}{\sqrt{\left(a+b\right)}\left(a+c\right)} \)	[0-1]
4.	Simpson	\( \frac{a}{\min \kern0.5em \left(a+b,a+c\right)} \)	[0-1]
5.	Russell and Rao	\( \frac{a}{a+b+c+d} \)	[0-1]
6.	Sokal and Michener	\( \frac{a+d}{a+b+c+d} \)	[0-1]
7.	Faith	\( \frac{a+0.5d}{a+b+c+d} \)	[0-1]
8.	Gower and Legendre	\( \frac{a+d}{a+0.5\left(b+c\right)+d} \)	[0-1]
9.	Roger and Tanimoto	\( \frac{a+d}{a+2\left(b+c\right)+d} \)	[0-1]

The measures are in correspondence to [45]. a is count of set bits in both fingerprint of both the molecules. b is count of set bits in fingerprint of first molecule and not in second molecule. c is count of set bits in fingerprint of second molecule and not in first molecule. d is count of unset bits in both fingerprint of both the molecules. The size of the fingerprint is given by n = (a + b + c + d)

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