Protocol for an automated virtual screening pipeline including library generation and docking evaluation

Here, we present a protocol for an automated virtual screening pipeline. We describe steps for generating compound libraries for computational docking including Food and Drug Administration (FDA)-approved drugs, setting up the receptor and grid box, and docking a library of compounds. We then detail procedures for ranking docking results. This protocol offers scripts for Unix-like systems, lowering the access barrier for researchers interested in structure-based drug discovery and supporting more experienced users by improving the efficiency of their studies.