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Molecular Descriptors Tools (Free for non-commercial use) [message #1743] Fri, 23 September 2022 05:19 Go to next message
aSalem is currently offline  aSalem
Messages: 1
Registered: September 2022
Junior Member
Dear all,

I am looking for a free (non-commercial use) tool for generating molecular descriptors for chemical compounds. I've tried Mordred, but it doesn't provide good coverage for the molecular descriptors.
If someone has any suggestions for some other tools, that would be much appreciated!

Thanks in advance,
Re: Molecular Descriptors Tools (Free for non-commercial use) [message #1744 is a reply to message #1743] Wed, 28 September 2022 20:01 Go to previous message
Paul is currently offline  Paul
Messages: 16
Registered: May 2019
Location: United States
Junior Member
For organic compounds, Mordred is the best overall I have used. It's not been maintained for several years, so some tweaks to the freely available code are necessary (solutions are documented in the Issues tab on the Mordred Descriptor Github page). Mordred is mostly a convenient interface to descriptors calculated by RDKit, so that, too, is obviously an option (Mordred also makes sure implicit H atoms are presented correctly for calculations). Padel Descriptor and CDK Descriptor are free java interfaces to descriptors from CDK libraries. The other free program I've used that calculates a large number of descriptors is MOLDĀ², free from the US FDA.GOV. In any case, users must
supply chemical logic (e.g., say you calculate a descriptor called "average ESP charge on a Q atom." Some programs may return no value for a molecule with no Q atoms, while others may incorrectly return a zero value.) Furthermore, validation is advisable, as descriptor values may vary between the programs, e.g., handling of implicit hydrogen atoms can cause differences. The adage "garbage in, garbage out" applies.

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