openmolecules.org Forum: Cheminformatics » Where do pKa values in pKaInWater.dwar come from ?

Home » DataWarrior » Cheminformatics » Where do pKa values in pKaInWater.dwar come from ? (pKa Values)

Show: Today's Messages :: Polls :: Message Navigator

Where do pKa values in pKaInWater.dwar come from ? [message #269]

Wed, 17 May 2017 17:42

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

Report message to a moderator

Re: Where do pKa values in pKaInWater.dwar come from ? [message #275 is a reply to message #269]

Sun, 28 May 2017 00:30

thomas
Messages: 731
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

Report message to a moderator

Re: Where do pKa values in pKaInWater.dwar come from ? [message #502 is a reply to message #275]

Tue, 19 March 2019 18:49

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

Report message to a moderator

Re: Where do pKa values in pKaInWater.dwar come from ? [message #504 is a reply to message #502]

Wed, 20 March 2019 23:14

thomas
Messages: 731
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

Report message to a moderator

Re: Where do pKa values in pKaInWater.dwar come from ? [message #507 is a reply to message #504]

Thu, 21 March 2019 22:28

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?

Report message to a moderator

Re: Where do pKa values in pKaInWater.dwar come from ? [message #509 is a reply to message #507]

Sun, 24 March 2019 22:42

thomas
Messages: 731
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.

Report message to a moderator

Previous Topic:	Reading in JSON files....
Next Topic:	issue with permeability

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Wed Jun 04 17:23:12 CEST 2025

Total time taken to generate the page: 0.35077 seconds