On 09/13/2017 11:46 AM, Markus Sitzmann wrote:
> The case that you have 3D information available for a molecule dataset is 
> rare, if you want it trustworthy it gets even worse than that. And what is 
> the point then to generate the configuration of a molecule first if you can 
> not trust that either?

Veering further off topic, do you even care in the first place? E.g. if
your molecule always exists as a mixture of isomers, except in some
megabuck-per-microgram painstakingly created reference samples, a
3D-based system will represent it as two distinct molecules. Whereas you
want it represented as one.

Last I looked PDB Ligand Expo had two different benzenes. Their software
doesn't (didn't?) do the circle version so they don't have the third one.

Dimitri Maziuk
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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