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items: TPSA
items: Re: TPSA

TPSA
type: item
description: 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).
creator: sansun
date: 2020-08-03T11:13:30-00:00

Re: TPSA
type: item
description: 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.
creator: thomas
date: 2020-08-04T09:24:55-00:00

Re: TPSA
type: item
description: 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
creator: sansun
date: 2020-08-04T10:20:26-00:00

Re: TPSA
type: item
description: DataWarrior sticks to the original publication, which includes contributions for S and P
creator: thomas
date: 2020-08-17T12:01:05-00:00