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Drug score [message #36]

Thu, 15 January 2015 00:14

plonacyrydwan
Messages: 1
Registered: January 2015

Junior Member

How can I calculate overall drug score in DataWarrior? In OSIRIS it is not a problem, but there I can not find anywhere this option.
Best regards

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Re: Drug score [message #41 is a reply to message #36]

Thu, 29 January 2015 21:10

thomas
Messages: 706
Registered: June 2014

Senior Member

DataWarrior does not directly calculate the drugscore as the Property Explorer did.
You can calculate the drugscore with a formula after calculating the properties that
the drugscore is composed of.

I have created a macro file that does everything for you and attached it to this message.
I suggest that you download and save it in your 'Macro' folder of your DataWarrior
installation, which usually would be on Windows here:

c:\Program Files (x86)\DataWarrior\Macro\

If there is no Macro folder, you have to create one. If you work on Linux or the Macintosh,
then it works analogously. Once the dwam file is in the Macro-folder and after starting
DataWarrior you find in its Macro-menu under Run-Macro 'Calculate Properties'.
When you select that, DataWarrior calculates all needed properties and afterwards from
them the DrugScore.

For that to work, you need the current version 4.1.0.

Kind regards,

Thomas

Attachment: Calculate Properties.dwam
(Size: 0.65KB, Downloaded 2575 times)

[Updated on: Thu, 29 January 2015 21:19]

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Re: Drug score [message #182 is a reply to message #41]

Fri, 17 June 2016 02:07

dalafave
Messages: 1
Registered: June 2016
Location: New Jersey

Junior Member

Hi Thomas,

Thank you for creating the macro for DataWarrior, Calculate Properties. It helped me a great deal. I'd like to cite it in my paper. What would the proper citation be? Thanks!

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Re: Drug score [message #183 is a reply to message #182]

Sun, 19 June 2016 21:18

thomas
Messages: 706
Registered: June 2014

Senior Member

since the macro is not described anywhere except on this website I suggest to cite this URL and/or the DataWarrior paper available at http://pubs.acs.org/doi/abs/10.1021/ci500588j. I will soon release a DataWarrior update and the macro will be part of it.

Kind regards, Thomas

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Re: Drug score [message #1103 is a reply to message #183]

Thu, 29 October 2020 14:56

Sifontes
Messages: 1
Registered: October 2020
Location: Cuba

Junior Member

Dear Thomas,
I installed the macro successfully and performed some test calculations. It worked fantasticly. So far, I had run the calculations in a dedicated excel spreadsheet. Thanks for that new contribution!!!
However, I have a doubt. In the formula for the calculation of the drug score, the coefficients for drugability are 1 and 0. That results in and inversely proportional contribution of druglikeness to the drug score, ie. the higher the druglikeness, the lower the drug score. Please, correct me if I´m wrong.
Best wishes,
Sergio

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Re: Drug score [message #1108 is a reply to message #1103]

Thu, 05 November 2020 13:29

thomas
Messages: 706
Registered: June 2014

Senior Member

Dear Sergio,

the contribution factor for the druglikeness part is: *(1-0.5/(1+exp(Druglikeness))).
Thus, if druglikeness increases, then the sum (1+...) grows, 0.5/sum gets smaller and 1-0.5/sum grows towards 1.
Currently, I don't see a problem here. Do you refer to a different formula?

Best wishes, Thomas

[Updated on: Thu, 05 November 2020 13:29]

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