Install gninatorch

code:https://github.com/RMeli/gnina-torch

manual: https://gnina-torch.readthedocs.io/en/latest/

Run in score_only mode

1. create a index file (score.index) as following:

receptor_1.pdb ligand_1.sdf
receptor_1.pdb ligand_2.sdf
receptor_1.pdb ligand_3.sdf

2.rescore

python -m gninatorch.gnina \
    score.index \
    --batch_size 200 \
    --cnn default

Case study

DUD-E EGFR

Blog: http://blog.molcalx.com.cn/2023/08/31/boosting-virtual-screening-enrichments-with-data-fusion.html

DUDE HIVPR

Blog: http://blog.molcalx.com.cn/2023/09/13/beware-of-the-benchmarking-test.html

Reference

1. Sunseri, J.; Koes, D. R. Virtual Screening with Gnina 1.0. Molecules 2021, 26 (23), 7369. https://doi.org/10.3390/molecules26237369.
2. https://github.com/RMeli/gnina-torch