I drew a ligand in the Maestro workspace, and my colleague did the same. We ran them through LigPrep and Glide docking and got different results! What is happening?

Sampling in Glide is influenced by the input structure conformation. The LigPrep result is also influenced by the input structure conformation. So if you and your colleague drew the ligand slightly differently in the Workspace, it is not surprising that with different binding site sampling you would get different results.

The way to prevent this from happening (if you want to prevent it) is to start with a SMILES or SMARTS string representation of your ligand, instead of a structure with coordinates. If you are doing your docking via Workflows → Virtual Screening Workflow, there is a checkbox "Regularize input geometries" that will do this SMILES conversion automatically if you check it.

Keywords: Glide, SMILES, LigPrep, Maestro

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