>
> Message: 1
> Date: Wed, 1 Apr 2020 10:58:56 +
> From: Alan Kerstjens Medina
> To: Ganesh Shahane
> Cc: "rdkit-discuss@lists.sourceforge.net"
>
> Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) scor
t;rdkit-discuss@lists.sourceforge.net"
Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
Message-ID:
Content-Type: text/plain; charset="windows-1252"
Hi Ganesh,
To delve a bit deeper into this, if I recall correctly, SA score is calculated
based
.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
Hi Ganesh,
I would like to challenge your premise. Why do you think that synthetic
accessibility should add up like that?
Theoretically, I would expect that the combinati
20 12:48
> *To: *Ganesh Shahane
> *Cc: *rdkit-discuss@lists.sourceforge.net
> *Subject: *Re: [Rdkit-discuss] Synthetic Accessibility (SA) score
>
>
>
> Hi Ganesh,
>
>
>
> I would like to challenge your premise. Why do you think that synthetic
> accessibility shou
Hi Nils and Axel,
Thank you very much for your response.
I am trying to develop a de-novo drug design framework that uses fragments
as building blocks to assemble a molecule inside a target protein active
site.
The algorithm that I am using assembles fragments into molecules such that
the
Hi Ganesh,
I would like to challenge your premise. Why do you think that synthetic
accessibility should add up like that?
Theoretically, I would expect that the combination of A,B and C to ABC will
require some synthetic effort - so should be SA(A) + SA(B) + SA(C) <
SA(ABC).
Technically, the
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
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
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
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.”
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