This topic (https://sourceforge.net/p/rdkit/mailman/message/35173301/) discussed using conformer generation as input into Open3DAlign.
One thing I noticed is that the conformer generation (using the useExpTorsionAnglePrefs=True and useBasicKnowledge=True options) does not generate conformers that align well for this example. The input is based on the 1DWD_ligand.pdb structure in the RDKit distro. What I find is the the rotation of the benzamidine ring is never in the right place for alignment (the other two ring systems align well). This is when generating up to 10,000 conformers. Does this suggest that the conformer generation does not sample conformational space very effectively? Are there options for improving this? Thanks Tim ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
