Hello,

I have a protein of interest that I need to perform molecular docking on by multiple ligands (~1000,000).

The protein is in PDB file format, while ligands are in a SDF file format.

Initially, the ligands were divided into multiple SDF files (mini) for hardware sake. 

Then, a python script was developed to handle the docking of each mini SDF file against the protein of interest.

This works nicely, however docking scores (tables) have no ligands IDs associated to distinguish each score.

So, basically I have scoring tables without any key IDs!!

Kindly, I want to know if you have encountered the same problem and what approach you took to solve this.