I would like to use a program to automate sorting drug molecules into structurally similar groups. What protocols, or better yet, software, is available to aid this endeavour?

For instance, I know one measure of similarity is the Tanimoto similarity coefficient.

Are there better or even just other methods?


1 Answer 1


According to the highly cited Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

The Tanimoto index, Dice index, Cosine coefficient and Soergel distance were identified to be the best (and in some sense equivalent) metrics for similarity calculations, i.e. these metrics could produce the rankings closest to the composite (average) ranking of the eight metrics. The similarity metrics derived from Euclidean and Manhattan distances are not recommended on their own, although their variability and diversity from other similarity metrics might be advantageous in certain cases (e.g. for data fusion).

rdkit can do the Tanimoto index, Dice index, and Cosine coefficient. It is unclear at the moment if it can do the Soergel distance.

Openbabel can do the Tanimoto index.

ChemDes looks like it makes use of rdkit, openbabel(pybel) and other software, as an umbrella for doing a vast amount of fingerprinting.


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