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Saoge123 / PocketFlow

an autoregressive flow model incorporated with chemical acknowledge for generating drug-like molecules inside protein pockets
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Request for Code for Metrics Calculation #4

Closed HShokaku closed 5 months ago

HShokaku commented 5 months ago

Hi,

Thanks for your impressive work!

I noticed the QED metric of Crossdocked2020 test set as reference in your paper is 0.531 ± 0.210. However, most SBDD papers report results around ~0.48 for this metric.

I could not find the code to calculate metrics (including SAscores etc.) in your repository. Could you please provide it?

@Saoge123

Saoge123 commented 5 months ago

Hi, CrossDocked2020 is based on the data of PDBbind, and produced by the manner of coss-docking. There are a lot of ligands that reappear many times. We remove the repeating molecules when compute metrics (about 11700 different molecules obtained).

HShokaku commented 5 months ago

Hi, CrossDocked2020 is based on the data of PDBbind, and produced by the manner of coss-docking. There are a lot of ligands that reappear many times. We remove the repeating molecules when compute metrics (about 11700 different molecules obtained).

Got it! Thank you!