On 12/11/2021 01:58, Paolo Tosco wrote:
Hi Tim,
Open3DAlign is not shape-based, it is atom-based. The score is
proportional to the # of matched atoms, weighted by similarity. It
will work well for homologous series of compounds with reasonable
scaffold similarity, and will in general perform
Hi Tim,
Open3DAlign is not shape-based, it is atom-based. The score is proportional
to the # of matched atoms, weighted by similarity. It will work well for
homologous series of compounds with reasonable scaffold similarity, and
will in general perform badly with scaffolds that are very
I'm looking into the current status of techniques that use RDKit to perform
3D alignments based on shape (e.g. not using AlignMol()) and struggling to
find what the best tools are and the status of each.
The Open3D align tools are relatively straightforward to use, but in my
hands do not seem to
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