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Reproducibility Docking Scores #1

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Jonas-Verhellen opened this issue Mar 27, 2024 · 0 comments
Open

Reproducibility Docking Scores #1

Jonas-Verhellen opened this issue Mar 27, 2024 · 0 comments

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@Jonas-Verhellen
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Jonas-Verhellen commented Mar 27, 2024

Dear Tianfan Fu ,

I cannot seem to reproduce the docking values for some individual molecules using the oracle from the TDC. For instance these SMILES, from the smiles_lstm_2_5000.txt file, have markedly different reported docking scores than the ones I obtain from the oracle:

O=C(CCOc1ccccc1F)Oc1ccccc1C(=O)CCCCc1ccc(C(F)(F)F)cc1: -15 vs -9.2
O=C(CCOc1ccccc1)Oc1ccccc1C(=O)CCCc1ccccc1F: -15 vs -9.2
O=C(CCOc1ccccc1F)Oc1ccccc1C(=O)CCCOc1ccccc1C(F)(F)F: -15.0 vs -10.3
O=C(Nc1ccccc1F)Oc1ccccc1C(=O)CCc1ccccc1C(F)(F)F: -14.6 vs -9.0
O=C(CCOc1ccccc1F)Oc1ccccc1C(=O)CCCOc1ccccc1Cl: -14.5 vs -9.1
O=C(CCOc1ccccc1F)Oc1ccccc1C(=O)CCCOc1ccccc1F: -14.4 vs -8.9
O=C(CCOc1ccccc1F)Oc1ccccc1C(=O)CCCOCc1ccccc1: -14.4 vs -9.0

Are there some settings that have changed/need to be specified somewhere in the code? Am I missing something? Is there a change in the back-end? Can the results be updated to match the oracle?

Kind regards,
Jonas

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