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.
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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