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Summary: The search and development of new quorum-sensing (QS) inhibitors are ongoing processes for biofilm control. Here, we present a protocol for in silico characterization of natural-based molecules as QS inhibitors. We describe steps for preparing models of protein receptors for virtual screening. We then detail procedures for construction and virtual screening of phytochemical libraries and hit picking to be experimentally validated by in vitro assays. This protocol allows exploration of a broad range of potential inhibitors for a specific target.For complete details on the use and execution of this protocol, please refer to Fernandes et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.