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 badly with scaffolds
that are very dissimilar in size and branching.
Shape-it and Align-it worked reasonably well in the past in my hands.
A Google or Google Scholar search will return many well-established
and more recent methods with different licenses, including but not
limited to:
* ShaEP
* Cresset tools
* ROCS
* LS-Align
* OptiPharm
* WEGA
I came upon this one the other day on github:
Comparison of electrostatic potential and shape
https://github.com/hesther/espsim
I did not try it, but it could be one more candidate.
Regards,
F.
Cheers,
p.
On Thu, Nov 11, 2021 at 4:55 PM Tim Dudgeon <tdudgeon...@gmail.com>
wrote:
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 give good alignments. e.g with this
reference mol:
I get this alignment:
I also stumbled across shape-it e.g.
https://iwatobipen.wordpress.com/2021/03/17/comparison-between-native-implemented-shape-align-method-of-rdkit-and-rdkit-shape-it-chemoinformatics-rdkit-shape-based-align/
But I find this very slow and most alignments seem to fail in my
hands.
Are there any guides to what tools work well here?
Tim
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