Re: [Rdkit-discuss] Synthetic Accessibility (SA) score

[Axel P. <axe...@gm...>]

Hi Ganesh,

I guess the synthesis of a fragment can be quite different from the
synthesis of a whole molecule containing that fragment, so I don't know
if it is a valid assumtion that the SA scores of the fragments have to
add up to the SA score of the whiole molecule.

Kind regards,
Axel

On 01.04.20 12:34, Ganesh Shahane wrote:
> Hi Axel,
>
> Thank you for your response.
>
> Yes, I tried to implement the aforementioned script. It works very
> well on whole molecules.
>
> However, I am trying to implement the script on fragments.
> For example, if I have fragments: A, B and C that makes up a whole
> molecule "ABC", then the sum of SA scores of the fragments should be
> equal to SA score of the whole molecule.
>
> Right now, the summation doesn't add up.
>
> I was wondering if there is a correction that needs to be made to the
> sum of SA scores such that it is equal to the SA score of the whole
> molecule.
>
> --
> Best,
> Ganesh
>
>
> On Mon, Mar 30, 2020 at 4:30 PM Axel Pahl <axe...@gm...
> <mailto:axe...@gm...>> wrote:
>
>     Hi Ganesh,
>
>     are you aware that the SA Score IS implemented in RDKit:
>
>     https://github.com/rdkit/rdkit/tree/master/Contrib/SA_Score
>
>     Kind regards,
>     Axel
>
>
>
>     On 30.03.20 16:55, Ganesh Shahane wrote:
>>     Dear RDKitters,
>>
>>     I am trying a to find a way to implement the SA score as a sum of
>>     fragments contributions from this paper:
>>
>>     Ertl, Peter, and Ansgar Schuffenhauer. 2009. “Estimation of
>>     Synthetic Accessibility Score of Drug-like Molecules Based on
>>     Molecular Complexity and Fragment Contributions.” /Journal of
>>     Cheminformatics/ 1 (1): 8.
>>
>>     For example, if I have three different fragments: A, B and C and
>>     their respective SA scores, then the SA score of molecule "A+B+C"
>>     should be the sum of all three fragment SA scores.
>>
>>     In practice though, the fragment SA scores do not add up.
>>
>>     I was wondering if anyone across the cheminformatics community
>>     has successfully implemented this or a similar strategy?
>>
>>     --
>>     Best,
>>     Ganesh
>>
>>
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