Long ago molecular fingerprints were referred to in the literature as
molecular hash functions. (y'know, those crazy mathematical algorithms
which permitted rapid lookup of some string in a lookup table) As such, we
expected for their to be the associated hash collisions (
https://en.wikipedia.org/wiki/Hash_table#Collision_resolution ). All this
by way of saying that to go from fingerprint to the molecular structure
which produced it is traditionally impossible unless the fingerprint no
longer amounts to a hash(ing) function.
--
j
On Fri, Apr 20, 2018 at 9:56 AM, Peter S. Shenkin <shen...@gmail.com> wrote:
> 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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