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Where do pKa values in pKaInWater.dwar come from ? [message #269] Wed, 17 May 2017 17:42 Go to next message
DrFunkenstein is currently offline  DrFunkenstein
Messages: 1
Registered: May 2017
Location: Research Triangle Park, N...
Junior Member
Hi,

7913 pKa values are provided in the pKaInWater.dwar file (thank you!!!). I'm wondering where these values came from? Literature? In-house experiments?

Thanks!
DrFunkenstein


Best,

Neal Cariello
neal.cariello@gmail.com
Re: Where do pKa values in pKaInWater.dwar come from ? [message #275 is a reply to message #269] Sun, 28 May 2017 00:30 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 247
Registered: June 2014
Senior Member
this is an old dataset that was originally compiled from the literature and hand-curated such that the structures represent the correct protonation state. Unluckily the original paper reference got lost or was never collected.

Thomas
Re: Where do pKa values in pKaInWater.dwar come from ? [message #502 is a reply to message #275] Tue, 19 March 2019 18:49 Go to previous messageGo to next message
chem95 is currently offline  chem95
Messages: 2
Registered: March 2019
Junior Member
Hi! I was wondering where I can find this pkaInWater dataset? I read about it in a paper but cannot locate it on the website.

Thanks so much Smile
Re: Where do pKa values in pKaInWater.dwar come from ? [message #504 is a reply to message #502] Wed, 20 March 2019 23:14 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 247
Registered: June 2014
Senior Member
it is part of the DataWarrior installation. You find it in the installation folder in the 'reference' folder.
On Linux the instalation folder would be /opt/datawarrior, on Windows it is C:/Program Files/DataWarrior.

Thomas
Re: Where do pKa values in pKaInWater.dwar come from ? [message #507 is a reply to message #504] Thu, 21 March 2019 22:28 Go to previous messageGo to next message
chem95 is currently offline  chem95
Messages: 2
Registered: March 2019
Junior Member
Thank you for such a quick and helpful reply!

Within the dataset I see some identifiers about the molecule such as the "FragFp" and the "Structure". Is there a good way to convert one of these values into a SMILES string so that I can understand the molecules that correspond to these pKa measurements?
Re: Where do pKa values in pKaInWater.dwar come from ? [message #509 is a reply to message #507] Sun, 24 March 2019 22:42 Go to previous message
thomas is currently offline  thomas
Messages: 247
Registered: June 2014
Senior Member
you can open the dataset in DataWarrior and may generate SMILES, export as SD-File or as text file containing the SMILES, if you want.
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