difference in result of PSA from chemaxon and pubchem

Hi

I am trying to calculate the polar surface area for a series of unrelated compounds. It is my understanding that chemaxon uses the Ertl method for calculation of Polar surface area. Pubchem, a service thats part of Pubmed also calculates the PSA, and uses the same Ertl method. For 5 compounds, the two results are very different. For the remaining 20 compounds we looked at, the results are almost identical. The r2 for all 25 compounds is 0.921, removing the 5 compounds, the r2 jumps to 0.997. If the two, Puchem and chemaxon, use the same formula to calculate the polar surface area why are the results different for some of the compounds?

 

I have attached an excel file with the smiles string, and the results from Puchem and Chemaxon.

 

Thank you

Hi,

 

...why are the results different for some of the 

compounds?

Sulfur atoms are also taken into account by our PSA calculator.  See  incremetns of the sulfur atoms in the attached file. 

We plan to add an option to exclude sulfur atoms from the calculations. This version will be available soon. 

Reference of Ertl's method: J.Med.Chem.2000, 43, 3714-3717

 

 

Jozsi

thanks a lot

when you say soon, you mean in the next few weeks or months?

thank you again

Hi,

...you mean in the next few weeks or months?

 

   I fixed this problem already, however, it will be available  in the upcoming patch release in a   couple week (if I know well).

Jozsi

 

Thanks for posting the sulphur parameters - updated TPSA computation code including these (and yielding the same result for the test set) has been shipped to NCBI.

Hi

How can I find out if the latest Marvin release has fixed the problem of the sulfur atoms in the polar surface area calculation? I was told that this problem has been fixed and is to be included in the next release.

 

Thank you

 

Yash

PSA plugin options panel will contain "Exclude sulfur atoms from calculation" and "Exclude phosphorus atoms from calculation" options. See the attached screenshot. It will be included in next release (Marvin 5.3.3).

Zsolt

Zsolt wrote:

PSA plugin options panel will contain "Exclude sulfur atoms from calculation" and "Exclude phosphorus atoms from calculation" options. See the attached screenshot. It will be included in next release (Marvin 5.3.3). Zsolt

Hi,

Any idea how to perform tha calculation as a chemical terms expression?

My users want to have a PSA db column with both exclude P and exclude S turned OFF.

Łukasz

PS. IJC 5.11.0

Hi Łukasz,

 The relevant Chemical Terms expression to turn off "Exclude sulfur / phosphorus atoms from calculation" options in PSA calculation is the following:

"psa('excludesulfur:false excludephosphorus:false')" 

By default, both options are "true".

Best regards,

Viktoria