Long story short:
PubChem calculates 3D using their brand of MMFF94 for molecules with <= 50
non-hydrogen atoms. There are other molecular constraints:
https://pubchem.ncbi.nlm.nih.gov/release3d.html
Resolver IS CACTUS USING CACTVS (no typo) for identifier interconversion
(Graduate Student Naming Games, evidently involving a real cactus ). For 3D
"calculation" it adds CORINA. CORINA has no atom number limits, but there are
large ring and other issues. My guess is that CORINA coverage of these issues
may not be part of Resolver:
https://www.ics.uci.edu/~dock/manuals/corina_manual.pdf
Otis
Sent from my iPad
> On Mar 22, 2016, at 4:28 PM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> Bob,
>
> If Resolver does not get a connectivity identifier (e.g. taxol), it relies on
> database look up (multi databases, including PubChem). I have no idea what
> the priority is, nor what identifier Resolver seeks if it gets a non IUPAC
> name. But let’s assume it goes to PubChem and seeks the SMILES. PubChem lists
> taxol under paclitaxel, and the paclitaxel listing lists 3D status as,
> "Conformer generation is disallowed since too many atoms.” OK, grab the
> SMILES, go back to Resolver, and give this SMILES to CORINA, Resolver’s
> engine.
>
> A few weeks ago we were talking about Jmolers always using Taxol as a test
> molecule, so I took the PubChem SMILES and hand entered it into Resolver. If
> you give the PubChem taxol SMILES to Resolver, all the king’s horses and all
> the kings men cannot put taxol’s ensembles back together again! So, yes, I
> guess some limit is in place on Resolver also.
>
> I used to think that PubChem used MMFF94. It came out in Bob Bellford's on
> line cheminformatics course that PubChem uses a special version of MMFF94. It
> would be interesting to find out what the atom number limits are on PubChem
> and Resolver. I’ll check both.
>
> Otis
>
> PS
>
> Bob really had a powerhouse faculty of that course - who’s who of
> cheminformatics.
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
>> On Mar 22, 2016, at 2:54 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>>
>>
>>
>> On Tue, Mar 22, 2016 at 11:05 AM, Otis Rothenberger <osrot...@icloud.com>
>> wrote:
>>> Hi Richard,
>>>
>>> That model is coming from Resolver. Resolver does not use MM to compute 3d
>>> models. Basically, the steps are as follows:
>>>
>>> 1) The connection identifier (SMILES, InChI, IUPAC, etc) is broken down
>>> into fragments called ensembles. Fixed geometries for these fragments exist
>>> in memory.
>>> 2) The ensembles are reassembled carrying their fixed geometry into the
>>> final SDF.
>>>
>>
>> I did not know that! Thank you, Otis. So perhaps the problem with taxol is
>> that it doesn't have some sort of fragment it needs?
>>
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