0xk7w-PosePredictionProtocol.txt

Name

cnn_combined

Software

gnina Nov 21 2016.

System Preparation Parameters

NA

System Preparation Method

remove waters, rdkit for conformer generation

Pose Prediction Parameters

--exhaustiveness 50 --seed 0 --num_modes 20

Pose Prediction Method

Default smina docking. Docked to 7 highest resolution co-crystals + apo.
Rescored all poses with a CNN model trained using pose prediction data from CSAR combined with virtual screening data from DUDE.
gnina -r ../receptors/${i}.pdb -l fxr_docked_${i}.sdf.gz --score_only --cnn_scoring --cnn_model ~/git/models/refmodel3/refmodel3.model --cnn_weights ~/git/models/refmodel3/weights/allfolds_2to1_dude_csar.caffemodel -o fxr_cnn_combined_${i}.sdf.gz --seed 0