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Drug Likeness vs Drug Score [message #1203] Mon, 01 February 2021 17:25 Go to next message
ELFritzen is currently offline  ELFritzen
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Is there a difference between Drug Likeness, calculated from a compound's structure and a Drug Score? The users manual uses both terms, and is not very clear.

Thanks,
Ed


Ed Fritzen
Re: Drug Likeness vs Drug Score [message #1204 is a reply to message #1203] Mon, 01 February 2021 18:37 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
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The manual's page

http://www.openmolecules.org/properties/properties.html

reads like a druglikeness is computed in first place, subsequently used to compute a drug score.

Lipinski's rule of five properties is one, but not the sole approach to define druglikeness. An implementation other than DataWarrior computing the later and others may be SwissADME (https://doi.org/10.1038/srep42717, open access).

[Updated on: Mon, 01 February 2021 18:38]

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Re: Drug Likeness vs Drug Score [message #1206 is a reply to message #1204] Tue, 02 February 2021 16:57 Go to previous messageGo to next message
ELFritzen is currently offline  ELFritzen
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Thanks for the reply. I'm trying to figure out exactly how Datawarrior calculates the Druglikeness and what factors are considered. The calculated value obtained is just a number to me. I'm not sure what the number means and how I might use it to determine the probability of finding a good drug lead. Are bigger numbers better? I can't figure that out. The article you provided is very informative, and it does point to a Web-based calculator which assesses the druglikeness of any molecule submitted, but I can't fine an overall druglikeness number like I see calculated in Datawarrior.

Ed


Ed Fritzen
Re: Drug Likeness vs Drug Score [message #1209 is a reply to message #1206] Tue, 02 February 2021 23:27 Go to previous messageGo to next message
thomas is currently offline  thomas
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The druglikeness is based on a long list of (>5000) substructures of which every one is associated with a numerical value. These substructures basically list all more or less frequent substructures to be found in drug and/or commercially available building blocks. If a fragment is a frequent substructure in building blocks, but rarely found within drugs, then it get a negative value that quantifies this ratio. Fragments that are predominantly found in drug structures have positive values. For calculating the druglikeness, DataWarrior goes through the list of substructures. When a substructure is part of the query molecules, then its value is added to the sum. Finally, the sum is normalized by deviding it by SQRT(fragmentCount).
Building block like molecules get values below zero, while drug like molecules get positive sum. A bar chart in the DataWarrior manual (above link) shows that.

If you are interested to look at the fragments with contributions, you may download the data file from the DataWarrior source code:

https://github.com/Actelion/openchemlib/blob/master/src/main /resources/resources/druglikenessNoIndex.txt

Open it in a text editor, add a first line 'idcode value' (without quotes; make sure that the white space after 'idcode' is a TAB), and save the file. Then you can open it in DataWarrior, where you should see the structures and associated contribution values.

Thomas
Re: Drug Likeness vs Drug Score [message #1218 is a reply to message #1209] Fri, 05 February 2021 16:42 Go to previous messageGo to next message
ELFritzen is currently offline  ELFritzen
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Thanks for the explanation, Thomas. It is very helpful. Do you know why this post never showed up in the Cheminformatics Forum? In order to find my original post and the replies, I needed to show all of my posts.

Thanks,
Ed


Ed Fritzen
Re: Drug Likeness vs Drug Score [message #1220 is a reply to message #1218] Tue, 09 February 2021 16:26 Go to previous message
ELFritzen is currently offline  ELFritzen
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Today the posts showed up.
Thanks,
Ed


Ed Fritzen
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