How to Score a hitlist from RIDGE using the Physics Based Score?

[Andrew Orry]

Q

I have finished a RIDGE screen and it is scored using the neural network RTCNN score. How to score the hitlist with the Physics Based Score?

A.

You can use the script dockscore.icm which comes with the ICM distribution in $ICMHOME/bin directory. It uses the hitlist sdf file containing 3D coordinates of the docked lignad and your docking project (dockProj)

icm64 dockscore.icm <input_sdf_or_inx_with_docked_poses.sdf> <dockProj>

You can run it in two modes

1. multi-core on a single machine

icm64 dockscore.icm <input_sdf_or_inx_with_docked_poses.sdf> <dockProj> proc=16

2. split into multiple pieces and run with from=<i> to=<i> arguments on multiple nodes
In this case you need to index your SDF and provide index as an input

icm> write index mol "some_large.sdf"   # will create "some_large.inx"

icm64 dockscore.icm some_large.inx mydock.dtb from=1 to=1000
icm64 dockscore.icm some_large.inx mydock.dtb from=1001 to=2000
...

The result will have physics based score (Score) and its components stored in separate columns.