Hi Brian,
Dave Weininger once showed a fairly simple GA that could generally deduce a
structure from a daylight fingerprint by using SMILES strings as the
chromosomes and tanimoto distance to the target fingerprint as the fitness
function. He may have done a talk about it for MUG or conceivably written
it up. It’d be in JCICS if so, I expect.
You could probably knock up a script to do that in a couple of hours I
would think using a GA library to do the mechanics. If you’re not worried
about high efficiency, you don’t need to do anything fancy with mutation
and crossover of the SMILES strings to ensure you always get a valid
molecule, you can just give a fitness of 0 if the SMILES parser doesn’t
like what you give it.
HTH,
Dave
On Fri, 20 Apr 2018 at 14:45, Nils Weskamp <nils.wesk...@gmail.com> wrote:
> Hi Brian,
>
> in general, it might be difficult to come up with a deterministic
> algorithm that generates exactly one structure for a given fingerprint due
> to many ambiguities in the process. If you are happy with a more "fuzzy"
> (approximate / probabilistic) approach, you might want to take a look at
>
> https://pubs.acs.org/doi/abs/10.1021/ci600383v
> https://link.springer.com/article/10.1007/s10822-005-9020-4
>
> Given this task, I would probably start with a large database of known
> compounds (PubChem, UniChem, GDB17), calculate fingerprints and then do a
> similarity search with my query fingerprint.
>
> Hope this helps,
> Nils
>
>
> On Fri, Apr 20, 2018 at 3:13 PM, Brian Cole <col...@gmail.com> wrote:
>
>> Hi Chem-informaticians:
>>
>> I know it has been talked about in the community that fingerprints are
>> not a way to obfuscate molecules for security, but I don't recall a paper
>> actually demonstrating actual reverse engineering a fingerprint into a
>> chemical structure. Does anyone know if such a paper exists?
>>
>> Code using RDKit to demonstrate the functionality would be an obvious
>> bonus as well. :-)
>>
>> Thanks,
>> Brian
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
