| Drug Likeness vs Drug Score [message #1203] |
Mon, 01 February 2021 17:25  |
ELFritzen
Messages: 47
Registered: November 2019
Location: North Carolina, US
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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
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| Re: Drug Likeness vs Drug Score [message #1206 is a reply to message #1204] |
Tue, 02 February 2021 16:57  |
ELFritzen
Messages: 47
Registered: November 2019
Location: North Carolina, US
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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
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| Re: Drug Likeness vs Drug Score [message #1209 is a reply to message #1206] |
Tue, 02 February 2021 23:27 |
thomas
Messages: 711
Registered: June 2014
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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
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| Re: Drug Likeness vs Drug Score [message #1218 is a reply to message #1209] |
Fri, 05 February 2021 16:42 |
ELFritzen
Messages: 47
Registered: November 2019
Location: North Carolina, US
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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
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