Probability or ratio of each variant per ligand

Computer-Aided Drug Design at the Durrant Lab Forums Gypsum-DL Probability or ratio of each variant per ligand

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    • #32345
      Edward Méndez-Otálvaro


      Thank you for Gypsum-DL. It’s a very useful tool for docking and virtual screening studies. I have a question about the probability or ratio of each variant per ligand, since according to the paper there’s a "combinatorial explosion" for each molecule and all of their possible variants (chiral, cis-trans, protonation, etc). I do not know if one can display precisely the ratio or probability of each variant, because sometimes for example, certain isomers are more favorable than others.

      Thank you.

    • #37844
      Jacob Durrant

      Hi Edward. Much thanks for your interest in Gypsum-DL. If I recall correctly, Gypsum prioritize the variants based on their predicted energies, according to RDKit. But there’s also a random component to the variant selection. If you’re not seeing some variants in the generated libraries that you think should be there, you might try allowing a larger number of variants per compound. I hope this helps. Take care.

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