Please allow me to do shameless self-promotion. I have developped an
open-source program (using OpenBabel) that aims at creating de novo ligands
by directly growing them in the active site of a target protein. You can
also use it without the protein (I have called it FOG2) : you can define a
core molecule (so-called seed), choose from which atom you will grow new
molecules, and the program will create new molecules by adding fragments to
the seed in a "rational" way. If you want more details, let me know, I can
explain it.
The links: http://pubs.acs.org/doi/10.1021/acs.jmedchem.5b00886,
https://sourceforge.net/projects/opengrowth/
Nicolas
2018-01-30 20:53 GMT+01:00 Chris Swain <sw...@mac.com>:
> Hi,
>
> It depends on the transformations you want to undertake. I did a very
> quick library build about 20 years ago using SMILES strings. Just have
> dummy atoms with unique letters where you want to add functional groups
> then just do a text find and replace with the desired SMILES of the
> building block you want to add (which can of course contain dummy atoms).
> Then run through OpenBabel to generate canonical SMILES. I generated a 10
> million molecule library doing this.
>
> Cheers,
>
> Chris
>
> On 30 Jan 2018, at 19:45, openbabel-discuss-requ...@lists.sourceforge.net
> wrote:
>
> Message: 1
> Date: Tue, 30 Jan 2018 15:25:38 +0000 (UTC)
> From: Siavoush Dastmalchi <siavous...@yahoo.com>
> To: "openbabel-disc...@lists.sf.net" <openbabel-disc...@lists.sf.net>
> Subject: [Open Babel] using Open Babel for virtual library generation
> Message-ID: <1885905137.1937075.1517325938...@mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear List,
> I was wondering if it is possible to use OB for virtual library
> generation. For example adding building blocks in a file to different sites
> of a core structure in a combinatorial manner.
> Many thanks in advance for you help.
> Cheers,Siavoush
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