TPSA, LogP

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TPSA, LogP

Jean-Marc Nuzillard
Dear Noel,

I recently started to look at descrptor values from various toolkits,
without initially being aware of a two years old blog post of yours:
http://baoilleach.blogspot.com/2008/04/cheminformatics-toolkit-face-off-logp.html

I used paracetamol and another test compound (mol1) in order to make
comparisons.

The result is:

Paracetamol
===========

* Pybel
TPSA: 49.330000
LogP: 1.423600

* RDKit
TPSA: 49.330000
MolLogP: 1.350600

* CDK
TPSA: 49.33
ALOGP: -1.0852000000000002
ALOGP2: 1.1776590400000004
XLOGP: 1.079


Mol1
====

* Pybel
TPSA: 117.560000
LogP: 4.719300

* RDKit
TPSA: 83.880000
MolLogP: 4.629500

* CDK
TPSA: 117.56
ALOGP: 1.4521000000000013
ALOGP2: 2.108594410000004
XLOGP: 0.7899999999999999

Mol1 is described by this smiles chain:
CC(=O)c1ccc(/N=C2\SCCCN2C(=O)c2ccc(CS(C)(=O)=O)cc2)cc1


Even TPSA is not consistent across toolkits.
The diversity of LogP implementations makes difficult
to use published works that rely on LogP values
for the molecule property prediction,
especially when descriptors are calculated
by some not freely available software.
More precisely, I refer to a recently published work
Journal of Molecular Graphics and Modelling 28 (2010) 899?903
that involves LogP(o/w) as calculated by MOE, which is said to be
different from SLogP when calculated by MOE and by RDKit.
What a jungle for a newcomer in the field!

As the author of Cinfony, I would like to have your
opinion about the origin of different values
I obtained for TPSA on compound "mol1".


Best regards,

Jean-Marc Nuzillard



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Re: TPSA, LogP

Noel O'Boyle
Administrator
Cher Jean,

Well, the key point is what is the correct value. If you are able to
work this out from the original papers and identify which projects are
in error, I am sure the individual projects (or cinfony, if it's my
fault) will sort them out.

- Noel

On 21 May 2010 09:45, JEAN MARC NUZILLARD <[hidden email]> wrote:

> Dear Noel,
>
> I recently started to look at descrptor values from various toolkits,
> without initially being aware of a two years old blog post of yours:
> http://baoilleach.blogspot.com/2008/04/cheminformatics-toolkit-face-off-logp.html
>
> I used paracetamol and another test compound (mol1) in order to make
> comparisons.
>
> The result is:
>
> Paracetamol
> ===========
>
> * Pybel
> TPSA: 49.330000
> LogP: 1.423600
>
> * RDKit
> TPSA: 49.330000
> MolLogP: 1.350600
>
> * CDK
> TPSA: 49.33
> ALOGP: -1.0852000000000002
> ALOGP2: 1.1776590400000004
> XLOGP: 1.079
>
>
> Mol1
> ====
>
> * Pybel
> TPSA: 117.560000
> LogP: 4.719300
>
> * RDKit
> TPSA: 83.880000
> MolLogP: 4.629500
>
> * CDK
> TPSA: 117.56
> ALOGP: 1.4521000000000013
> ALOGP2: 2.108594410000004
> XLOGP: 0.7899999999999999
>
> Mol1 is described by this smiles chain:
> CC(=O)c1ccc(/N=C2\SCCCN2C(=O)c2ccc(CS(C)(=O)=O)cc2)cc1
>
>
> Even TPSA is not consistent across toolkits.
> The diversity of LogP implementations makes difficult
> to use published works that rely on LogP values
> for the molecule property prediction,
> especially when descriptors are calculated
> by some not freely available software.
> More precisely, I refer to a recently published work
> Journal of Molecular Graphics and Modelling 28 (2010) 899?903
> that involves LogP(o/w) as calculated by MOE, which is said to be
> different from SLogP when calculated by MOE and by RDKit.
> What a jungle for a newcomer in the field!
>
> As the author of Cinfony, I would like to have your
> opinion about the origin of different values
> I obtained for TPSA on compound "mol1".
>
>
> Best regards,
>
> Jean-Marc Nuzillard
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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