Isn't it the case that more than one molecule can share an identical
fingerprint? (Depending on the specific fingerprint.) Think p-biphenyl,
extended to triphenyl, tetraphenyl, etc. Still, a GA or SA method could
keep going and come up with multiple matches, plus multiple near-misses.
-P.
On Fri, Apr 20, 2018 at 10:58 AM, David Cosgrove <davidacosgrov...@gmail.com
> wrote:
> 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
>>>
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> --
> David Cosgrove
> Freelance computational chemistry and chemoinformatics developer
> http://cozchemix.co.uk
>
>
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