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TPSA [message #1025] Mon, 03 August 2020 13:13 Go to next message
sansun is currently offline  sansun
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Registered: April 2019
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I found disagreement between TPSA values calculated from DW and RDKit although both seem to follow same methodology by Peter Ertl et al. in J. Med. Chem. 43, 3714-3717 (2000).

In some case the difference is quite large e.g. 87 vs 252

However, Spearman correlation is > 0.9 for my data set (N > 20000).
Re: TPSA [message #1028 is a reply to message #1025] Tue, 04 August 2020 11:24 Go to previous messageGo to next message
thomas is currently offline  thomas
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Registered: June 2014
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One reason may be that DataWarrior considers the largest fragment only by removing counter ions, water molecules and other small fragments from the main ingredient before the calculation.
Re: TPSA [message #1029 is a reply to message #1028] Tue, 04 August 2020 12:20 Go to previous messageGo to next message
sansun is currently offline  sansun
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Registered: April 2019
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I performed calculations after extracting the largest fragments and used the same file for both programs.
However, I find useful information on the following link which says RDkit doesn't use P and S atoms for TPSA calculation.

Does DW uses these atoms?

https://www.rdkit.org/docs/RDKit_Book.html



Re: TPSA [message #1046 is a reply to message #1029] Mon, 17 August 2020 14:01 Go to previous message
thomas is currently offline  thomas
Messages: 706
Registered: June 2014
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DataWarrior sticks to the original publication, which includes contributions for S and P
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