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
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: > [image: image.png] > I get this alignment: > [image: image.png] > > 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 >
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