Dear Phuong,
unfortunately, there is no generic answer to this question since it is
highly dependent on the fingerprint, the type of compounds, your
specific application and also your chemical intuition. I can only
recommend to test a range of different cutoff values and to see how
happy you are with the results.
If you have access to a list of analogs that you definitely want to find
("known actives") and a large set of known irrelevant compounds, you
might be able to use statistical analyses to derive some kind of
"optimal" threshold.
If we are talking about path-oriented fingerprints (like the RDKit
Chemical Fingerprints) and "normal" drug-like molecules, I would
typically go down to 0.70 - 0.75 and then manually weed out false hits.
Hope this helps,
Nils
Am 04.07.2018 um 02:24 schrieb Phuong Chau:
> To whom it may concern,
>
> I was working on finding a group of possible neighbors (similar)
> chemicals based on Tanimoto Similarity. I am not sure what is the
> optimal cutoff for finding similar chemicals. I searched online and they
> said it is 0.85 but there are also many exceptions they mentioned about.
> Do you have any suggestions?
>
> Thank you so much for your help
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
