Hello Tim, You may take a look at my publication, at https://link.springer.com/article/10.1007/s10822-017-0023-8
There is also a review of existing methods there. Ling Francois Berenger <mli...@ligand.eu> 於 2021年11月11日週四 下午5:34寫道： > 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 > >> > >> _______________________________________________ > >> Rdkit-discuss mailing list > >> Rdkit-discuss@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > _______________________________________________ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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