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. • Steps for setting up a fully local virtual screening pipeline using free software • Instructions for generating compound libraries compatible with AutoDock Vina • Guidance on receptor setup, docking execution, and results ranking using scripts Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.