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Updated: May 13, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Protocol for an automated virtual screening pipeline including library generation and docking evaluation
Pedro José Barbosa Pereira1, Jorge Ripoll-Rozada2, Sandra Macedo-Ribeiro1
1IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
Abstract:
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.
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